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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/spaced">Debian Med / spaced</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/e5ed52eb26c7c52e35b7d132214a141f5d0c4337">e5ed52eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T10:38:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add +dfsg suffix since files were removed from upstream tarball
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/3f1306ad27fb01b15f16c1945979230b25c99725">3f1306ad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T10:39:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.0-201605+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/368a377d32a946bee15907cbdd7f3c0fca6082c1">368a377d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T10:39:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.0-201605+dfsg'
Update to upstream version '1.2.0-201605+dfsg'
with Debian dir 52d004bbe69af67d9491d8b3440fb5917fb09b9a</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/9b8c4bb1a62f46121b2015ccd9d7ba51183a023c">9b8c4bb1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T10:42:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide manpage in debian/spaced.1 instead of patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/dca2cda7418644c71aec8ecb2f5570c9cc7b7003">dca2cda7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T10:59:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/cc9aac0f371508a8022c3f560e058a806afb50dc">cc9aac0f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:01:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream source
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/5254e16d4bd7472a6dd98ce64b83cdb58f7d1503">5254e16d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:26:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/519595797d79effb9a0795118cfd30093973fb2b">51959579</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:27:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup behind automake
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/410a008dfc0faf275ebb9c7d7704d5b1a2fa7d48">410a008d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:29:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fake watch file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/08226ad5eac743c25dfdaec868d6999d91123538">08226ad5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:29:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/62e21ee2fa7db94ecd7207d5c9b3efba933a8106">62e21ee2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:30:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/a34e80bf2331d43bdb11658db1525b5d57e8a0ae">a34e80bf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T11:30:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spaced/commit/46b8060cb2374929cf4a11b4feadfb602a9e6841">46b8060c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-09T13:06:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some types
</pre>
</li>
</ul>
<h4>27 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
<span class="new-file">
+
debian/clean
</span>
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#fc932f0eaa389a4e2b93916f3995aae4019ea823">
debian/get-orig-source
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#9e3a6908b4f8b906a04e1798a0bd6dcdecd28495">
<span class="deleted-file">
−
debian/patches/0001-Add-man-page.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#670a3e8adefc1cc1b142378a55874848077f3561">
debian/patches/0002-Fix-FTBFS-without-OpenMP.patch
</a>
</li>
<li class="file-stats">
<a href="#f8328c27c8b0c792a8c8bc001ab0e9996196207d">
debian/patches/0003-Add-autotools-buildsystem.patch
</a>
</li>
<li class="file-stats">
<a href="#7645a3bf7ae86d74208caad4cfb2a709aa5e82a3">
<span class="new-file">
+
debian/patches/0004-signed.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#a6f2034e744c8bb5aebd0f6e23c5e35f03b44f94">
<span class="new-file">
+
debian/spaced.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#3283d870958c09551c30ebbb9d26960e4005457a">
<span class="deleted-file">
−
extkey.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#161f59057218bdf2f270bdb22d6638ef12a19847">
<span class="deleted-file">
−
extkey.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#a69222313c83929659f5fe5e6a6a40b0d20a5fbc">
<span class="deleted-file">
−
patternset.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#da266ff50a98ef860a9b36e2d9ec1648142475d6">
<span class="deleted-file">
−
patternset.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#519597f899fb573748be33af0584bdf3142eacca">
<span class="new-file">
+
src/patternset.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#76d488fea179bfbaad4b3cdb4e31ed97a77d9a18">
<span class="new-file">
+
src/patternset.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#827d9b3126d4d1cea6c5176c34241e1e2cc5a680">
sort.h
→
src/sort.h
</a>
</li>
<li class="file-stats">
<a href="#2947485ced1da9b0e852c6381259845de5d9471d">
spaced.cc
→
src/spaced.cc
</a>
</li>
<li class="file-stats">
<a href="#99dd8f62fef31c460730ff26f487f0b5a7d39de3">
<span class="new-file">
+
src/variance.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#16fcf2292a48cd93a41327a36254348ef5d0b0a4">
<span class="new-file">
+
src/variance.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5469f8ee3db98ebc1fb6aa9dc56b1b5a97554cc">
<span class="deleted-file">
−
variance.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#257fa9bceed7c4724b402cf77b45b9499350579d">
<span class="deleted-file">
−
variance.h
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"></span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> </span>
</pre>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"> g++ <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-<span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">c++11 spaced.cc variance.cpp patternset.cpp extkey.cpp </span><span class="nt" style="color: navy;"><span class="idiff">-o</span></span><span class="idiff"> spaced </span><span class="nt" style="color: navy;"><span class="idiff right">-fopenmp</span></span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"> g++ <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-<span class="idiff left">fopenmp</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">c++11 src/spaced.cc src/variance.cpp src/patternset.cpp </span><span class="nt" style="color: navy;"><span class="idiff">-o</span></span><span class="idiff right"> spaced</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"> </span></pre>
</td>
</tr>
</table>
<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">spaced (1.<span class="idiff left right">0.2+dfsg-2</span>) UNRELEASED; urgency=medium</span>
</pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spaced (1.<span class="idiff left right">2.0-201605+dfsg-1</span>) UNRELEASED; urgency=medium</span>
</pre>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream source</span>
</pre>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Fix get-orig-source script</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Provide manpage in debian/spaced.1 instead of patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Fake watch file</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * debhelper 11</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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5
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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6
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 07 Jul 2018 14:53:39 +0200</span>
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7
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Makefile</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">config.h</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">config.log</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">config.status</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">stamp-h1</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">src/Makefile</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">9</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">11</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: spaced</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Section: science</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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4
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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5
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Fabian Klötzl <kloetzl@evolbio.mpg.de></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">Build-Depends:</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"> debhelper (>= 9),</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"><span class="idiff left right"> dh-autoreconf,</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.7</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/git/debian-med/spaced.git</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/spaced.git</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">Section: science</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">Priority: optional</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">Build-Depends: debhelper (>= 11~)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.1.4</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/spaced</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/spaced.git</span>
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12
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: http://spaced.gobics.de/</span>
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13
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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14
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Package: spaced</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Architecture: any</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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17
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Description: alignment-free sequence comparison using spaced words</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Spaced (Words) is a new approach to alignment-free sequence</span>
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19
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> comparison. While most alignment-free algorithms compare the</span>
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<li id="fc932f0eaa389a4e2b93916f3995aae4019ea823">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#fc932f0eaa389a4e2b93916f3995aae4019ea823"><strong>debian/get-orig-source</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,7 @@ UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d -name "${NAME}*"`</td>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">UPSTREAMTARDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EXCLUDE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># obtain version from file variance.h</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'@version: [0-9][0-9.]\+ [0-9/]\+'</span> <span class="k" style="font-weight: 600;">$(</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> variance.h<span class="k" style="font-weight: 600;">)</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s#.*@version: \([0-9][0-9.]\+\) \([0-9]\+\)/\([0-9]\+\)#\1-\3\2#'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'@version: [0-9][0-9.]\+ [0-9/]\+'</span> <span class="k" style="font-weight: 600;">$(</span>find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> variance.h<span class="k" style="font-weight: 600;">)</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s#.*@version: \([0-9][0-9.]\+\) \([0-9]\+\)/\([0-9]\+\)#\1-\3\2#'</span><span class="sb" style="color: #d14;">`</span><span class="idiff left right">+dfsg</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Fix upstreams non-Gnu naming scheme</span></span>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#9e3a6908b4f8b906a04e1798a0bd6dcdecd28495"><strong>debian/patches/0001-Add-man-page.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian@kloetzl.info></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Date: Wed, 23 Mar 2016 12:00:11 +0100</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Subject: Add man page</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> spaced.1 | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> 1 file changed, 60 insertions(+)</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> create mode 100644 spaced.1</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/spaced.1 b/spaced.1</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">new file mode 100644</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">index 0000000..9878d2b</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/spaced.1</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,60 @@</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TH SPACED "1" "February 2016" "1.0.2" ""</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH NAME</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced \- alignment-free sequence comparison</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH SYNOPSIS</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.B spaced</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+[\fI-r\fR] [\fI-k INT\fR] [\fI-l INT\fR] [\fI-n INT\fR] [\fI-t INT\fR] [\fI-d TYPE\fR] [\fI-f FILE\fR] \fIFILES\fR...</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH DESCRIPTION</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Spaced Words is a new approach to alignment-free sequence comparison. While most alignment-free algorithms compare the word-composition of sequences, Spaced Words uses a pattern of care and don't care positions. The occurrence of a spaced word in a sequence is then defined by the characters at the match positions only, while the characters at the don't care positions are ignored (this was originally inspired by the PatternHunter algorithm for homology search in databases). Instead of comparing the frequencies of contiguous words in the input sequences, our new approach compares the frequencies of the spaced words according to the pre-defined pattern. An information-theoretic distance measure is then used to define pairwise distances on the set of input sequences based on their spaced-word frequencies. The original version of our spaced-words approach was published in Boden et al.(2013). </span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH OUTPUT</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The output is a symmetrical distance matrix similar to \fIPHYLIP\fR format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). </span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH OPTIONS</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-o\fR <file></span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Print the distance matrix to the given \fIfile\fR. Default is \fIDMat\fR.</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-k\fR <int></span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Set the patterns weight. Default: 14.</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-l\fR <int></span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Set \fIdon't care\fR positions for the used patterns. Default: 15.</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-n\fR <int></span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Set the number of patterns. Default: 5.</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-f\fR <file></span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Instead of generating new patterns, use read them from the given file.</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-t\fR <INT></span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The number of threads to be used; by default, 25 threads are used. </span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.br</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Multithreading is only available if \fBspaced\fR was compiled with OpenMP support.</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB-r\fR</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Skip comparison with the reverse complement.</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB-d\fR <type></span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The distances can be compute with different measures. Available options are Euclidean (\fIEU\fR), Jensen-Shannon (\fIJS\fR), and evolutionary distance (\fIEV\fR). Default: EV.</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TP</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\fB\-h\fR</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Prints the synopsis and an explanation of available options.</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH COPYRIGHT</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Copyright \(co 2016 Chris Leimeister <chris.leimeister@stud.uni-goettingen.de></span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+License GPLv3+: GNU GPL version 3 or later.</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.br</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+This is free software: you are free to change and redistribute it.</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+There is NO WARRANTY, to the extent permitted by law.</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The full license text is available at <http://gnu.org/licenses/gpl.html>.</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PP</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH REFERENCES</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+1) C.-A. Leimeister, M. Boden, S. Horwege, S. Lindner, B. Morgenstern (2014). Fast alignment-free sequence comparison using spaced-word frequencies, Bioinformatics <http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu177></span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.br</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+2) S. Horwege, S. Linder, M. Boden, K. Hatje, M. Kollmar, C.-A. Leimeister, B. Morgenstern (2014). Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches, Nucleic Acids Research 42, W7-W11 <http://nar.oxfordjournals.org/content/42/W1/W7.abstract></span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.br</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+3) B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015). Estimating evolutionary distances between genomic sequences from spaced-word matches, Algorithms for Molecular Biology 10,5</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SH BUGS</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SS Reporting Bugs</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Please report bugs to <kloetzl@evolbio.mpg.de> or <chris.leimeister@stud.uni-goettingen.de>.</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.SS</span></span>
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<li id="670a3e8adefc1cc1b142378a55874848077f3561">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#670a3e8adefc1cc1b142378a55874848077f3561"><strong>debian/patches/0002-Fix-FTBFS-without-OpenMP.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,11 +6,9 @@ Subject: Fix FTBFS without OpenMP</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> sort.h | 2 +-</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/sort.h b/sort.h</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index bef900e..4034495 100644</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sort.h</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sort.h</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -153,9 +153,9 @@ void writeDmat(vector<vector<double> > dmat, vector<sequence<uint> >& sequences,</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sort.h</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sort.h</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -153,9 +153,9 @@ void writeDmat(vector<vector<double> > d</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> template<typename uint></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> void spacedDNA(vector<string>& patternSet, unsigned char* seqData, uint n, int distance, int threads, int weight, int dontCare, bool revComp, string output){</span>
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<li id="f8328c27c8b0c792a8c8bc001ab0e9996196207d">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#f8328c27c8b0c792a8c8bc001ab0e9996196207d"><strong>debian/patches/0003-Add-autotools-buildsystem.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,41 +13,19 @@ Subject: Add autotools buildsystem</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> create mode 100644 configure.ac</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> create mode 100644 m4/ax_cxx_compile_stdcxx_11.m4</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/Makefile b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">deleted file mode 100644</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gh" style="color: #999;">index 0515a61..0000000</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +0,0 @@</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: </span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- g++ -O3 -std=c++11 spaced.cc variance.cpp patternset.cpp extkey.cpp -o spaced -fopenmp</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/Makefile.am b/Makefile.am</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff">new file mode 100644</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gh" style="color: #999;">index 0000000..aaee67c</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile.am</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bin_PROGRAMS = spaced</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced_SOURCES = extkey.cpp extkey.h patternset.cpp patternset.h sort.h spaced.cc variance.cpp variance.h</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced_CPPFLAGS = $(OPENMP_CPPFLAGS) -Wall -Wextra -std=c++11 -Wno-char-subscripts</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced_CXXFLAGS = $(OPENMP_CXXFLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+man_MANS = spaced.1</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,3 @@</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SUBDIRS = src</span></span>
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38
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+dist_noinst_DATA = README COPYING</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/configure.ac b/configure.ac</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff">new file mode 100644</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #999;">index 0000000..6808730</span></span>
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43
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.ac</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,2<span class="idiff left right">4</span> @@</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,2<span class="idiff left right">5</span> @@</span></span>
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46
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_PREREQ([2.69])</span></span>
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47
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_INIT([spaced], [1.0.2])</span></span>
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48
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AM_INIT_AUTOMAKE([-Wall foreign])</span></span>
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49
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CONFIG_SRCDIR([extkey.cpp])</span></span>
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51
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CONFIG_HEADERS([config.h])</span></span>
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52
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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53
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_PROG_CXX</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,11 +43,10 @@ index 0000000..6808730</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_FUNCS([pow sqrt])</span></span>
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67
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CONFIG_FILES([Makefile])</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CONFIG_FILES([Makefile</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ src/Makefile])</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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69
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_OUTPUT</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/m4/ax_cxx_compile_stdcxx_11.m4 b/m4/ax_cxx_compile_stdcxx_11.m4</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff">new file mode 100644</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gh" style="color: #999;">index 0000000..f3779d6</span></span>
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73
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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74
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/m4/ax_cxx_compile_stdcxx_11.m4</span></span>
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75
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,162 @@</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -235,3 +212,18 @@ index 0000000..f3779d6</td>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AC_SUBST(HAVE_CXX11)</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fi</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+])</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +0,0 @@</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: </span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- g++ -O3 -fopenmp -std=c++11 src/spaced.cc src/variance.cpp src/patternset.cpp -o spaced</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,5 @@</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bin_PROGRAMS = spaced</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced_SOURCES = patternset.cpp patternset.h sort.h spaced.cc variance.cpp variance.h</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced_CPPFLAGS = $(OPENMP_CPPFLAGS) -Wall -Wextra -std=c++11 -Wno-char-subscripts</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+spaced_CXXFLAGS = $(OPENMP_CXXFLAGS)</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span></pre>
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<li id="7645a3bf7ae86d74208caad4cfb2a709aa5e82a3">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#7645a3bf7ae86d74208caad4cfb2a709aa5e82a3"><strong>debian/patches/0004-signed.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Sat, 07 Jul 2018 14:53:39 +0200</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Fix some types</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sort.h</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sort.h</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -130,7 +130,7 @@ void writeDmat(vector<vector<double> > d</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ofstream outfile;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> outfile.open(filename.c_str());</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> outfile << sequences.size() << endl;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (int i = 0; i < sequences.size(); i++) {</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (unsigned i = 0; i < sequences.size(); i++) {</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> for(uint k=0; k<10;k++){</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> if( k+sequences[i].headerStart <= sequences[i].headerEnd )</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> outfile << seqData[k+sequences[i].headerStart];</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -138,7 +138,7 @@ void writeDmat(vector<vector<double> > d</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> outfile << " ";</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> }</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> outfile << " ";</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (int j = 0; j < sequences.size(); j++) {</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (unsigned j = 0; j < sequences.size(); j++) {</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if (i > j) </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> outfile << setprecision(12) << dmat[i][j] << " ";</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> else if(j>i)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -238,7 +238,7 @@ void spacedDNA(vector<string>& patternSe</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> }</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> }</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> }</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int i=0; i< sequences.size();i++){</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned i=0; i< sequences.size();i++){</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> for(int j=0; j<4;j++){</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> sequences[i].frequencies[j]=sequences[i].frequencies[j]/sequences[i].length;</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> sequences[i].frequenciesRevComp[j]=sequences[i].frequenciesRevComp[j]/sequences[i].length;</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -252,8 +252,8 @@ void spacedDNA(vector<string>& patternSe</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> vector<vector <vector <double> > > dmat(threads, vector< vector<double> >(seqNum, vector<double>(seqNum,0)));</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> vector<vector <double> > dmatFinal(seqNum, vector<double>(seqNum,0));</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> vector<vector<double> > row(threads, vector<double>(seqNum*2));</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int p = 0; p < patternSet.size(); p++ ){</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int k = 0; k < patternSet[p].length(); k++){</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned p = 0; p < patternSet.size(); p++ ){</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned k = 0; k < patternSet[p].length(); k++){</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> if (patternSet[p][k] == '1')</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> matchPos.push_back(k);</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -283,7 +283,7 @@ void spacedDNA(vector<string>& patternSe</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> bits=weight*2-2;</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> unsigned char c;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> bool correctWord=true;</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int o=0; o<matchPos.size();o++){</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned o=0; o<matchPos.size();o++){</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> uint pos=matchPos[o];</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> c= seqData[j+pos];</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> if(c=='N')</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -304,7 +304,7 @@ void spacedDNA(vector<string>& patternSe</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> bits=weight*2-2;</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> unsigned char c;</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> bool correctWord=true;</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int o=0; o<matchPos.size();o++){</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned o=0; o<matchPos.size();o++){</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> uint pos=matchPos[o];</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> c= seqData[j+pos];</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> if(c=='N')</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -551,8 +551,8 @@ void spacedProt(vector<string>& patternS</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> vector<vector <vector <double> > > dmat(threads, vector< vector<double> >(seqNum, vector<double>(seqNum)));</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> vector<vector <double> > dmatFinal(seqNum, vector<double>(seqNum,0));</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> vector<vector<double> > row(threads, vector<double>(seqNum));</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int p = 0; p < patternSet.size(); p++ ){</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int k = 0; k < patternSet[p].length(); k++){</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned p = 0; p < patternSet.size(); p++ ){</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned k = 0; k < patternSet[p].length(); k++){</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> if (patternSet[p][k] == '1')</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> matchPos.push_back(k);</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -576,7 +576,7 @@ void spacedProt(vector<string>& patternS</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> w=0;</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> bits=weight*5-5;</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> unsigned char c;</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for(int o=0; o<matchPos.size();o++){</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for(unsigned o=0; o<matchPos.size();o++){</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> uint pos=matchPos[o];</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> c= seqData[j+pos];</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> w|=(unsigned long long) alphabet[c] << bits;</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0001-Add-man-page.patch</span>
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2
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">0002-Fix-FTBFS-without-OpenMP.patch</span>
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3
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">0003-Add-autotools-buildsystem.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">0004-signed.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with autoreconf</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">get-orig-source:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> . debian/get-orig-source</span></pre>
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<li id="a6f2034e744c8bb5aebd0f6e23c5e35f03b44f94">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#a6f2034e744c8bb5aebd0f6e23c5e35f03b44f94"><strong>debian/spaced.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH SPACED "1" "February 2016" "1.0.2" ""</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spaced \- alignment-free sequence comparison</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.B spaced</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">[\fI-r\fR] [\fI-k INT\fR] [\fI-l INT\fR] [\fI-n INT\fR] [\fI-t INT\fR] [\fI-d TYPE\fR] [\fI-f FILE\fR] \fIFILES\fR...</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Spaced Words is a new approach to alignment-free sequence comparison. While most alignment-free algorithms compare the word-composition of sequences, Spaced Words uses a pattern of care and don't care positions. The occurrence of a spaced word in a sequence is then defined by the characters at the match positions only, while the characters at the don't care positions are ignored (this was originally inspired by the PatternHunter algorithm for homology search in databases). Instead of comparing the frequencies of contiguous words in the input sequences, our new approach compares the frequencies of the spaced words according to the pre-defined pattern. An information-theoretic distance measure is then used to define pairwise distances on the set of input sequences based on their spaced-word frequencies. The original version of our spaced-words approach was published in Boden et al.(2013). </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH OUTPUT</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">The output is a symmetrical distance matrix similar to \fIPHYLIP\fR format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-o\fR <file></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Print the distance matrix to the given \fIfile\fR. Default is \fIDMat\fR.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-k\fR <int></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Set the patterns weight. Default: 14.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-l\fR <int></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Set \fIdon't care\fR positions for the used patterns. Default: 15.</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-n\fR <int></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Set the number of patterns. Default: 5.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-f\fR <file></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Instead of generating new patterns, use read them from the given file.</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-t\fR <INT></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">The number of threads to be used; by default, 25 threads are used. </span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Multithreading is only available if \fBspaced\fR was compiled with OpenMP support.</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB-r\fR</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Skip comparison with the reverse complement.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB-d\fR <type></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">The distances can be compute with different measures. Available options are Euclidean (\fIEU\fR), Jensen-Shannon (\fIJS\fR), and evolutionary distance (\fIEV\fR). Default: EV.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-h\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Prints the synopsis and an explanation of available options.</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.SH COPYRIGHT</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Copyright \(co 2016 Chris Leimeister <chris.leimeister@stud.uni-goettingen.de></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">License GPLv3+: GNU GPL version 3 or later.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">This is free software: you are free to change and redistribute it.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">There is NO WARRANTY, to the extent permitted by law.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">The full license text is available at <http://gnu.org/licenses/gpl.html>.</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.PP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.SH REFERENCES</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">1) C.-A. Leimeister, M. Boden, S. Horwege, S. Lindner, B. Morgenstern (2014). Fast alignment-free sequence comparison using spaced-word frequencies, Bioinformatics <http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu177></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.br</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">2) S. Horwege, S. Linder, M. Boden, K. Hatje, M. Kollmar, C.-A. Leimeister, B. Morgenstern (2014). Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches, Nucleic Acids Research 42, W7-W11 <http://nar.oxfordjournals.org/content/42/W1/W7.abstract></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">3) B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015). Estimating evolutionary distances between genomic sequences from spaced-word matches, Algorithms for Molecular Biology 10,5</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.SH BUGS</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.SS Reporting Bugs</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Please report bugs to <kloetzl@evolbio.mpg.de> or <chris.leimeister@stud.uni-goettingen.de>.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.SS</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Use the d/get-orig-source script until upstream fixes its releases.</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">#version=3</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">#http://spaced.gobics.de/ .*/spaced-(.*)\.tar\.gz</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># if tweaking of source is needed</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># \</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># debian debian/get-orig-source</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># if you need to repack and choose +dfsg prefix</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \</span></pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">opts=dversionmangle=s/.*/0.No-Release/ \</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#3283d870958c09551c30ebbb9d26960e4005457a"><strong>extkey.cpp</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** </span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * extended key object file</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.0.2 11/2015</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "extkey.h"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variables---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*===Main-Part===============================================================*/</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Constructor-& Init------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extkey</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"> <span class="n" style="color: #333;">extkey</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extkey</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Functions---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPos</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetValue</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SetValue</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * extended key object header</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.0.2 11/2015</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef EXTKEY_H_</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define EXTKEY_H_</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">extkey</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"> <span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">extkey</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"> <span class="n" style="color: #333;">extkey</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetPos</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetValue</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetValue</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">extkey</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#a69222313c83929659f5fe5e6a6a40b0d20a5fbc"><strong>patternset.cpp</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * patternset object file</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.0.2 11/2015</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "patternset.h"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variables---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">default_random_engine</span> <span class="n" style="color: #333;">generator</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">random_device</span><span class="p">{}());</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*===Main-Part===============================================================*/</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Constructor-------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default constructor, sets the default vaulues, pattern will be generated automatically.</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * File constructor, sets values only from files; resets automatically if there are problems.</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pattern_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Short constructor, sets some default vaulues, just pattern dimension is set.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The amount of patterns; pattern number.</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param length</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The pattern length for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weigth</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The weight (match positions; '1') for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">)</span> <span class="p">{</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Long constructor, sets the values; resets automatically, if there are problems.</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern_file File, that may contains submitted pattern</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param align_file File, that may contains an alignment file to estimate p, q, l_hom, li and lj</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size The amount of patterns; pattern number.</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param length The pattern length for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weigth The weight (match positions; '1') for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param l_hom In theory, the amount of homologous positions of two sequences in an multiple alignment.</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param l1 In theory, the first(represents each sequence i) sequence length of two observed sequences.</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param l2 In theory, the second(represents each sequence j) sequence length of two observed sequences.</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p The match probability ( = #matches / #l_hom)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param q The background probability for each nucleotide A,C,G,T</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">)</span> <span class="p">{</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pattern_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">randpatleng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInitPattern</span><span class="p">();</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default destructor, deletes all vectors and matrices in the object.</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">patternset</span><span class="p">()</span> <span class="p">{</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Init--------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Creates for the submitted or default values a set of pattern and calculates the first variance.</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * If possible estimates p, q, all sequences lengths and all combinations of homologous sequence positions</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Also reset Pattern if needed, not necessary to create new object</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReInitPattern</span><span class="p">()</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*====Main-TODO=====*/</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgth</span><span class="p">,</span> <span class="n" style="color: #333;">lgt</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">lgth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pattern_file</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">TestPattern</span><span class="p">();</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">VerifyConditions</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">CreateRandomPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ToBit</span><span class="p">(</span><span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">lgt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">lgt</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="p">}</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"> <span class="p">}</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"> <span class="p">}</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">lgth</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lgth</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">size</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"><span class="p">}</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Due to some cases, it is possible necessary to</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * reset some pattern parameters.</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This is not a complete delete, so therefore it</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * it is only a part of the destructor.</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Clear</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Functions---------------------------------------------------------------*/</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * If there is an submitted pattern_file, it will check, if it is containing</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * a possible pattern, and if this pattern is in the correct format.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Pattern can be parsed in a different formats</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TestPattern</span><span class="p">()</span> <span class="p">{</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">patternfile</span><span class="p">;</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">,</span><span class="sc" style="color: #d14;">' '</span><span class="p">,</span><span class="sc" style="color: #d14;">','</span><span class="p">,</span><span class="sc" style="color: #d14;">';'</span> <span class="p">};</span> <span class="cm" style="color: #998; font-style: italic;">/*These tokens are allowed to seperate patterns*/</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">f_size</span><span class="p">;</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">);</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">seekg</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">f_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">tellg</span><span class="p">();</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">patternfile</span><span class="p">)</span> <span class="p">{</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"file"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"> <span class="p">}</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_size</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*[FILE].eof() does not recognize empty files...*/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"empty"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="cpp"> <span class="p">}</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span> <span class="cm" style="color: #998; font-style: italic;">/*..therefore it has also to be closed and opened -.-** */</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reading pattern from submitted patternfile ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <span class="p">}</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">())</span> <span class="p">{</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ValidatePatternsFormat</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*Ignoring each incorrect pattern. It is easier to calculate with all the rests*/</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"> <span class="p">}</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SplitString</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">tokens</span><span class="p">);</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pattern_tmp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span> <span class="cm" style="color: #998; font-style: italic;">/*Each pattern needs to be saved in its own std::string for comparison*/</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="p">}</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cpp"> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="p">}</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*For an empty set we do not habe to validate*/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ValidatePatternConditions</span><span class="p">();</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="p">}</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*Some conditions, like changed weight is too much much amount of work*/</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"pattern"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*Therefore we just use our default values*/</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span> <span class="cm" style="color: #998; font-style: italic;">/*Do not forget to reset, or the pattern set will not replaces, just increased*/</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="p">}</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">)</span><span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PatternLength</span><span class="p">(</span><span class="n" style="color: #333;">string_pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PatternWeight</span><span class="p">(</span><span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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232
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
233
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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235
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">... Done!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">patternfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It will Verify the pattern conditions: is the weight correct,</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * not negative values, weight not above length and so on.. </span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">VerifyConditions</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">leng_new</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">diff</span><span class="p">,</span> <span class="n" style="color: #333;">leng_old</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"size"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="p">}</span> </span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"weight_pat"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="p">}</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">){</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"length"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">diff</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_old</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">63</span><span class="p">){</span> <span class="cm" style="color: #998; font-style: italic;">/*max length of 64-Bit Integer*/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"length"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">63</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">weight</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">63</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="p">}</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">63</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">diff</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">weight</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"length"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">leng_old</span><span class="p">){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_old</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"> <span class="p">}</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">63</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">63</span><span class="p">){</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"nkl"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*...if everything is fucked up and rescue does not work...*/</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">weight</span><span class="p">){</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"max_number_pattern"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="p">}</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">improve</span><span class="p">){</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"noimprove"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="p">}</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"> <span class="n" style="color: #333;">CreateLengths</span><span class="p">();</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">diff</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">)){</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()){</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"max_number_pattern"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_new</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_new</span><span class="p">;</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Functions---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Func-Create-------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Splits a string, read by a pattern file. Mayby each pattern does not get</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * a new line, it has to be parsed, when a pattern starts and ends</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern_split The string containing a few pattern</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param tokens The allowed tokens which can be used to seperate patterns in a line</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SplitString</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern_split</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tokens</span><span class="p">)</span> <span class="p">{</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="p">;</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag_token</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_split</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">);</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pattern_split</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">flag_token</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">flag_token</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*token found, which means in one line more patterns --> start new pattern, save last pattern*/</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">patternset</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp"> <span class="p">}</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pattern_split</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/*concatenating patternparts*/</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">flag_token</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">patternset</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">patternset</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Validates a pattern, if it contains only pattern symbols and seperation tokens</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern_form The pattern which has to be investigate for symbols and tokens</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns true if this one pattern is in right format, false else</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ValidatePatternsFormat</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*allowed tokens in patternformat, also separating tokens*/</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'0'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">';'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"format"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">[</span><span class="n" style="color: #333;">pattern_form</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"startend"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Validates a pattern set, if all patterns have the same length and weight</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns true if this one pattern is in right format, false else</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ValidatePatternConditions</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">com_weight</span><span class="p">,</span> <span class="n" style="color: #333;">com_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">condition</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">com_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">com_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PatternWeight</span><span class="p">(</span><span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span> <span class="cm" style="color: #998; font-style: italic;">/*as fixpoint saving first patternweight*/</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="cpp"> <span class="n" style="color: #333;">condition</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">com_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">PatternWeight</span><span class="p">(</span><span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">com_weight</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"weight"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">condition</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">condition</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimates the weight of a pattern</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern_str The pattern which has to be investigate for the weight</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns true if this one pattern is in right format, false else</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PatternWeight</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern_wght</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">str_weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">str_length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">str_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp"> <span class="n" style="color: #333;">str_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">pattern_wght</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">str_length</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pattern_wght</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">str_weight</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">str_weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimates the weight of a pattern</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern_str The pattern which has to be investigate for the weight</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns true if this one pattern is in right format, false else</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PatternLength</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_length</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pat_length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minp</span><span class="p">,</span> <span class="n" style="color: #333;">maxp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">pat_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="cpp"> <span class="n" style="color: #333;">minp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">pattern_length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="cpp"> <span class="n" style="color: #333;">maxp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">pattern_length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_length</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pattern_length</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">maxp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">pattern_length</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pattern_length</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">minp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">minp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">pattern_length</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">pat_length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">pat_length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pat_length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This function will create for our lenghts intervall</span></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * for each pattern a specific length!.</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CreateLengths</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">step</span><span class="p">,</span> <span class="n" style="color: #333;">leng2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">leng</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cpp"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">weight</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pat_leng</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">one</span><span class="p">,</span> <span class="n" style="color: #333;">leng</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">randpatleng</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pat_leng</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">step</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">leng2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">leng</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="cpp"> <span class="n" style="color: #333;">step</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">one</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">leng</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">leng2</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">step</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">leng2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">one</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span> <span class="cm" style="color: #998; font-style: italic;">/*if one pattern has to be without don't care positions*/</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Creates random a set of pattern. For convention a pattern has to start and end with '1'</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Reason 10010 ~ 1001</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns a randomly created pattern set</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CreateRandomPattern</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">prototype</span><span class="p">,</span> <span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">rbegin</span><span class="p">(),</span><span class="n" style="color: #333;">lengths</span><span class="p">.</span><span class="n" style="color: #333;">rend</span><span class="p">());</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">){</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">prototype</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">prototype</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">prototype</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span><span class="o" style="font-weight: 600;">|</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*Prototype, first and last position is a match!*/</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*better random generater than time, uses likelihood for evenly random distribution*/</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">weight</span><span class="p">)</span> <span class="p">{</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="cpp"> <span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span> <span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">);</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">prototype</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">position</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*have fun and fill with '1' randomly :D */</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="cpp"> <span class="n" style="color: #333;">prototype</span> <span class="o" style="font-weight: 600;">|=</span> <span class="p">(</span><span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">position</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prototype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]){</span></span>
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">flag</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">prototype</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="cpp"> <span class="n" style="color: #333;">string_pat</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BitString</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Scans if there is another pattern in the same format</span></span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns boolean if there is another same pattern</span></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">uniq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">uniq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">uniq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*--Func-Change--------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes two different positions ('1' and '0') in a specific bit-pattern</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Start and end are excluded</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The pattern which has to be modified</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChangeBits</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos1</span><span class="p">,</span> <span class="n" style="color: #333;">pos0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">weight</span><span class="p">){</span> <span class="cm" style="color: #998; font-style: italic;">/*only possible, if lenghts[size-1] == weight*/</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">improve</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">pos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SymbolRandPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;">pos0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SymbolRandPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ChangeBitPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">pos1</span><span class="p">,</span> <span class="n" style="color: #333;">pos0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Exchange of two positions; changing match to don't care and vice versa.</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos The pattern index of the modifying pattern</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos_one Matchposition which has to be a don't care</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos_zero Don'tCare position which has to be a match</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The modified pattern as an 64-Bit integer</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChangeBitPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos_one</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos_zero</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">diff</span><span class="p">,</span> <span class="n" style="color: #333;">one_mask</span><span class="p">,</span> <span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pos_one</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">one_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">one_mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">one_mask</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">one_mask</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="cpp"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">one_mask</span> <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">diff</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mask</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pos_zero</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">diff</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns for a specific symbol ('1', '0') a random chosen position</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The pattern index of the modifying pattern</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param symb The specific symbol, either '1' or '0'</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return A random chosen position in the pattern of the specific symbol</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SymbolRandPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">positions</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="cpp"></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetSymbol</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">symb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distribution</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">positions</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Investigates for a specific symbol all positions of a pattern.</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For a match, the first and last positions are excluded!</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The pattern index of the modifying pattern</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param symb The specific symbol, either '1' or '0'</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return All positions of the pattern of the specific symbol</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSymbol</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">positions</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">lgth</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">symb</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="cpp"> <span class="n" style="color: #333;">chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lgth</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">positions</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---stuff-------------------------------------------------------------------*/</span></span>
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738
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* Method to print the current pattern</span></span>
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Print</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp"> <span class="n" style="color: #333;">ToString</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Saves the current 64-Bit integer in the string pat as printable strings</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ToString</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="cpp"> <span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitString</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Turns a string into a 64-Bit Integer as binary pattern </span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p The number of the pattern in the string pattern set</span></span>
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The binary representation of the input string</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ToBit</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="cpp"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes a pattern in 64-Bit integer format into a printable string</span></span>
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p The pattern in 64-bit integer format</span></span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The printable string of the input pattern</span></span>
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BitString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bit_string</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lgth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">lgth</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lgth</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_string</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_string</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span></span>
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798
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_string</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bit_string</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Determines the maximum number of patterns with weight and length</span></span>
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param weight Complete pattern weight-2, start and end have to be match and do not change</span></span>
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param length Complete pattern lengt-2, start and end have to be match and do not change</span></span>
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@return max number of possible pattern</span></span>
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p_weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p_length</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmpa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faculty</span><span class="p">(</span><span class="n" style="color: #333;">p_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmpb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faculty</span><span class="p">(</span><span class="n" style="color: #333;">p_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p_weight</span><span class="p">);</span></span>
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817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmpc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Faculty</span><span class="p">(</span><span class="n" style="color: #333;">p_weight</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpa</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">tmpb</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpc</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Calculates the faculty</span></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param value Calculating the faculty for value</span></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@return faculty(value) = 'value!'</span></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Faculty</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="p">{</span></span>
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830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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832
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">value</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A Method to collect all errormessages. Just easier for programmer to change</span></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the text or extend.</span></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param errmsg Due to a few possible errormessages, this is the option, which has to be printed.</span></span>
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos The position of the incorrect patterns.</span></span>
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (errmsg == "wrongindex") {</span></span>
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! Pattern " << pos << " does not exist... do nothing\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "file") {</span></span>
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! Pattern file \'" << pattern_file << "\' could not be found!" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to submitted or default values\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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856
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "empty") {</span></span>
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857
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! File \'" << pattern_file << "\' is an empty file!" << std::endl;</span></span>
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858
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to submitted or default values\n" << std::endl;</span></span>
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859
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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860
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
861
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "pattern") {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
862
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! Patternconditions from pattern file were not correct (different weight or length)!" << std::endl;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
863
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to submitted or default values\n" << std::endl;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
864
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
865
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
866
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "nkl") {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
867
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! Wrong values for weight, pattern number or pattern length!" << std::endl;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to default values\n" << std::endl;</span></span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
870
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
871
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "weight_pat") {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
872
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! Weight of a pattern cannot under 2!" << std::endl;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
873
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to submitted or default values\n" << std::endl;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
874
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
875
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
876
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "format") {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
877
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "FORMAT-ERROR: Pattern containes illegal characters!" << std::endl;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
878
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC878" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Allowed characters: '0','1' for pattern; ','|'.'|';'|' ' to seperate patterns" << std::endl;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
879
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC879" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Go on to next pattern.\n" << std::endl;</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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881
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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882
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "max_number_pattern") {</span></span>
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883
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "The number of patterns is too high for your configuration and will be reset!" << std::endl;</span></span>
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884
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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885
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
886
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "size") {</span></span>
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887
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! The number of patterns has to be greater than 0!\n" << std::endl;</span></span>
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888
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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889
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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890
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "weight") {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
891
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! By comparing with the first pattern, the " << pos + 1 << ". pattern has a different weight!\n" << std::endl;</span></span>
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892
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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893
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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894
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if(errmsg == "length"){</span></span>
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<td class="diff-line-num old old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
895
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! The patternlengths has to be greater or equal the weight, greater than 2 and below 63!" << std::endl;</span></span>
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896
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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897
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
898
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "startend") {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
899
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "FORMAT-ERROR: Pattern has to start and end with a match position '1' !\n" << std::endl;</span></span>
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900
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
901
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "noimprove") {</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
903
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Using your pattern conditions it is not sensible to improve your pattern, sorry!" << std::endl;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
904
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Deactivating improve mode\n" << std::endl;</span></span>
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905
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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906
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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907
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "update"){</span></span>
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908
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "\n####IMPROTANT####\nDue to some configuration errors, your submitted parameters have been updated!" << std::endl;</span></span>
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909
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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910
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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911
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="cpp"><span class="p">}</span></span>
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912
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="cpp"></span>
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913
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="cpp"></span>
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914
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Set-&-GetFunc-----------------------------------------------------------*/</span></span>
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915
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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916
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes to silent output, nothing will be printed automatically!</span></span>
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917
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Errors are going to be printed!</span></span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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919
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<pre style="margin: 0;">-<span id="LC919" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Silent</span><span class="p">(){</span></span>
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920
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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921
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="cpp"><span class="p">}</span></span>
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922
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="cpp"></span>
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923
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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924
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes the patternlengths from evenly distributed to random pattern lengths.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
925
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<pre style="margin: 0;">-<span id="LC925" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * One quarter has maximum length, the rest randomly distributed between </span></span>
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<td class="diff-line-num old old_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
926
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * maximum and minimum length.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
927
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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928
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RandPatLength</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">randpatleng</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="cpp"> <span class="n" style="color: #333;">randpatleng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInitPattern</span><span class="p">();</span></span>
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932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="cpp"> <span class="p">}</span></span>
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933
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="cpp"><span class="p">}</span></span>
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934
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="cpp"></span>
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935
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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936
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the weight of each pattern, the match positions</span></span>
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937
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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938
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns weight</span></span>
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939
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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940
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetWeight</span><span class="p">()</span> <span class="p">{</span></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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942
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<pre style="margin: 0;">-<span id="LC942" class="line" lang="cpp"><span class="p">}</span></span>
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943
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="cpp"></span>
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944
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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945
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the amount of patters; number of patterns</span></span>
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946
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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947
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns size</span></span>
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948
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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949
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSize</span><span class="p">()</span> <span class="p">{</span></span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="cpp"><span class="p">}</span></span>
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952
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the length of each pattern</span></span>
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns length</span></span>
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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958
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetLength</span><span class="p">()</span> <span class="p">{</span></span>
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959
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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960
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<pre style="margin: 0;">-<span id="LC960" class="line" lang="cpp"><span class="p">}</span></span>
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961
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="cpp"></span>
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962
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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963
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<pre style="margin: 0;">-<span id="LC963" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the mean of all pattern lengths</span></span>
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964
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The mean of all lengths;</span></span>
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966
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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967
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetLengthMean</span><span class="p">(){</span></span>
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968
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<pre style="margin: 0;">-<span id="LC968" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length_mean</span><span class="p">;</span></span>
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969
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="cpp"><span class="p">}</span></span>
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970
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="cpp"></span>
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971
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a boolean, if an improvement is possible</span></span>
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973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Imagine, a improvment for pattern '101' is not possible!</span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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975
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<pre style="margin: 0;">-<span id="LC975" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The boolean, if this improvement is possible</span></span>
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976
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC977" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetImprove</span><span class="p">()</span> <span class="p">{</span></span>
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978
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="cpp"><span class="p">}</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="cpp"></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a boolean, if due to some configuration errors</span></span>
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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * values set by the user had to be updated to better configuration.</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Imagine, the weight was above the pattern length.</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The boolean, if something had been updated.</span></span>
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetUpdate</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">update</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a specific pattern of the pattern set in 64-Bit integer format</span></span>
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return specific string in 64-Bit integer format</span></span>
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"wrongindex"</span><span class="p">,</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="cpp"> <span class="p">}</span></span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="cpp"></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns complete pattern set</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return complete pattern set</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetStringPattern</span><span class="p">()</span> <span class="p">{</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">ToString</span><span class="p">();</span></span>
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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">string_pat</span><span class="p">;</span></span>
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1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="cpp"><span class="p">}</span></span>
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1017
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="cpp"></span>
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1018
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns only one pattern as a string from the current patternset.</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1021
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The index of the chosen pattern</span></span>
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1022
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1023
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The pattern as a printable string</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1025
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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1026
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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1027
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"wrongindex"</span><span class="p">,</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1029
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="cpp"> <span class="p">}</span></span>
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1030
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1031
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">ToString</span><span class="p">();</span></span>
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1032
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">string_pat</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">];</span></span>
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1033
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<pre style="margin: 0;">-<span id="LC1033" class="line" lang="cpp"> <span class="p">}</span></span>
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1034
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<pre style="margin: 0;">-<span id="LC1034" class="line" lang="cpp"><span class="p">}</span></span>
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1035
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<pre style="margin: 0;">-<span id="LC1035" class="line" lang="cpp"></span>
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1036
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<pre style="margin: 0;">-<span id="LC1036" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1037
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<pre style="margin: 0;">-<span id="LC1037" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes a pattern in 64-Bit integer format</span></span>
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1038
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<pre style="margin: 0;">-<span id="LC1038" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The index of the pattern which will be changed</span></span>
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1040
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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1041
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<pre style="margin: 0;">-<span id="LC1041" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param patt The new pattern</span></span>
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1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patt</span><span class="p">){</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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1045
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<pre style="margin: 0;">-<span id="LC1045" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"wrongindex"</span><span class="p">,</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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1046
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<pre style="margin: 0;">-<span id="LC1046" class="line" lang="cpp"> <span class="p">}</span></span>
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1047
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<pre style="margin: 0;">-<span id="LC1047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1048" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patt</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#da266ff50a98ef860a9b36e2d9ec1648142475d6"><strong>patternset.h</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * patternset object header</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.0.2 11/2015</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef PATTERNSET_H_</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PATTERNSET_H_</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <inttypes.h></span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "extkey.h"</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">patternset</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">();</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">);</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">patternset</span><span class="p">();</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReInitPattern</span><span class="p">();</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ChangeBits</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">ChangeBitPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos_one</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos_zero</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetStringPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">GetString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">GetLength</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetLengthMean</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetImprove</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetUpdate</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetValue</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patt</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Silent</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RandPatLength</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TestPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">VerifyConditions</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">SplitString</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tokens</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ValidatePatternsFormat</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern_form</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ValidatePatternConditions</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">PatternWeight</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">pattern_wght</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">PatternLength</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CreateLengths</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CreateRandomPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">IsSetScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pattern</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SymbolRandPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">SymbolCalcPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetSymbol</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ToString</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">ToBit</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">BitString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p_weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Faculty</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">string_pat</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lengths</span><span class="p">;</span> </span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length_mean</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">update</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">randpatleng</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"><span class="p">};</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#519597f899fb573748be33af0584bdf3142eacca"><strong>src/patternset.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * patternset object file</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - L. Hahn, C.-A. Leimeister, B. Morgenstern (2015)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * arXiv:1511.04001[q-bio.GN]</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 12.05.2016, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.2.0 05/2016</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "patternset.h"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variables---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">default_random_engine</span> <span class="n" style="color: #333;">generator</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">//time(0)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*===Main-Part===============================================================*/</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Constructor-------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default constructor, sets the default vaulues.</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">random_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Constructor, sets some default vaulues, just pattern dimension is set.</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size Number of patterns for the patternset.</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weigth Number of match positions ('1') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param min_dontcare Number of minimum don't care positions ('0') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param max_dontcare Number of maximum don't care positions ('0') in each pattern.</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param silent Boolean which (de)activates std::output on commandline (exclusive errors)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">random_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="p">}</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * File constructor, sets values only from files.</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param inFile The file which contains a patternset.</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param silent Boolean which (de)activates std::output on commandline (exclusive errors)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inFile</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inFile</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="p">}</span></span>
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100
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default destructor, deletes all vectors and matrices in the object.</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">patternset</span><span class="p">(){</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_improve</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="p">}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"></span>
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112
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Initialization----------------------------------------------------------*/</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Creates for the submitted or default values a set of pattern; if errors occur, these will be fixed. </span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to get all patterns for a specific combination.</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Size and lenght can be reduced; each pattern is unique.</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param random_length Boolean which (de)activates random generated pattern lengths.</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">random_length</span><span class="p">){</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">read_error</span><span class="p">;</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">random_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">random_length</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isInFile</span><span class="p">){</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReadPattern</span><span class="p">();</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_error</span><span class="p">){</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"nkl"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">CheckParams</span><span class="p">();</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SetImprove</span><span class="p">();</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternToBit</span><span class="p">();</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="p">}</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">read_error</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">CheckParams</span><span class="p">();</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CreateLengths</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CreatePattern</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SetImprove</span><span class="p">();</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternToBit</span><span class="p">();</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="p">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CreatePattern</span><span class="p">();</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_improve</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">improve</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">PatternToBit</span><span class="p">();</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="p">}</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="p">}</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"><span class="p">}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Standard Reinitialization of variance options, creates a new patternset.</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReInit</span><span class="p">(){</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_improve</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="n" style="color: #333;">random_length</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"><span class="p">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Checks the first conditions of the patternset, in special cases resets them.</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Checks, if bitmode is possible.</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CheckParams</span><span class="p">(){</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="p">}</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="p">}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">min_dontcare</span><span class="p">);</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="p">}</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">){</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span><span class="n" style="color: #333;">min_dontcare</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="p">}</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="p">}</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="p">}</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="p">}</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="p">}</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="p">}</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">63</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">63</span><span class="p">){</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="p">}</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"update"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="p">}</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"><span class="p">}</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Functions---------------------------------------------------------------*/</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Func-Create-------------------------------------------------------------*/</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Generates automatically patternlengths; depends on min_dontcare and max_dontcare.</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a vector which contains in descending order the pattern lenghts.</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Two options: 1) nearly linear distributed lenghts </span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * 2) random distributed lenghts</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return All lenghts for the patternset (type: std::vector<uint32_t>)</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CreateLengths</span><span class="p">(){</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">leng_vec</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">steps</span><span class="p">,</span> <span class="n" style="color: #333;">leng</span><span class="p">,</span> <span class="n" style="color: #333;">leng_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">max_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">intervals</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">random_length</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lengths</span><span class="p">(</span><span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="p">}</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">steps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">leng</span><span class="p">);</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">steps</span><span class="p">;</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="p">}</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="p">}</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="p">,</span> <span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">leng_tmp</span><span class="p">){</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">leng_tmp</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_tmp</span><span class="p">;</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_size</span><span class="p">){</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="p">}</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"max_number_pattern"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="p">}</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="p">}</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="p">}</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">leng_tmp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="p">}</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">rbegin</span><span class="p">(),</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">.</span><span class="n" style="color: #333;">rend</span><span class="p">());</span></span>
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296
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">leng_vec</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><span class="p">}</span></span>
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299
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Generates for submitted (and corrected) values a patternset as std::vector< std::vector<char> >.</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Patternset (type: std::vector< std::vector<char> >)</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CreatePattern</span><span class="p">(){</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patterns</span><span class="p">;</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pat</span><span class="p">;</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">tmp_weight</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Generating pattern automatically ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="p">}</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">;</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">;</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">positions</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">tmp_weight</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">positions</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">);</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">){</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_weight</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">;</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="p">}</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="p">}</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="n" style="color: #333;">patterns</span><span class="p">,</span> <span class="n" style="color: #333;">pat</span><span class="p">)){</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">patterns</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="p">}</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="p">}</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="p">}</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'1'</span><span class="p">);</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">patterns</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Done."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="p">}</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">patterns</span><span class="p">;</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"><span class="p">}</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Reads pattern from a submitted file which (may) contains binary strings.</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Each pattern will be verified, if its really a binary pattern with the same weight.</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * If an error occurs (file not found, etc.), it returns false, otherwise true.</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if an error occured or not while pattern processing.</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadPattern</span><span class="p">(){</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">fasta</span><span class="p">;</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">p_size</span><span class="p">;</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="sc" style="color: #d14;">'.'</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="sc" style="color: #d14;">';'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">};</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">token</span><span class="p">,</span> <span class="n" style="color: #333;">read_error</span><span class="p">,</span> <span class="n" style="color: #333;">bad</span><span class="p">;</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">bad</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">inFile</span><span class="p">);</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">fail</span><span class="p">()){</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"file"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">traits_type</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">eof</span><span class="p">()){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"empty"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">()){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="p">}</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">c</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bad</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span> <span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">);</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="p">}</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">bad</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="p">}</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">){</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="p">}</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">bad</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"format"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="p">}</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="p">}</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="p">}</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">fasta</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read_error</span><span class="p">){</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"empty"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="p">}</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="p">}</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">p_size</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="p">}</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">p_size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">){</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"startend"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="p">}</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read_error</span><span class="p">){</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">read_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VerifyPatternCondition</span><span class="p">();</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read_error</span><span class="p">){</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read_error</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"><span class="p">}</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* Checks, if the submitted pattern file is in correct format; if it</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* contains only binary pattern with the same weight.</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">* Sets the wight and max_ and min_dontcare number, if no error occured.</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">VerifyPatternCondition</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">first_weight</span><span class="p">,</span> <span class="n" style="color: #333;">p_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">pattern_error</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="n" style="color: #333;">first_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="n" style="color: #333;">p_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span> <span class="n" style="color: #333;">p_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">first_weight</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])){</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"weight"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">IsBinary</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])){</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"pattern"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_error</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Checks, if there is at least one pattern, which can be improved.</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns true, if there is at least one, otherwise false.</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Checks and saves for each pattern individually, if it can be improved.</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if at least one pattern can be changed.</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SetImprove</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">leng</span><span class="p">,</span> <span class="n" style="color: #333;">p_size</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isImprovable</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_impro</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">isImprovable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">p_size</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="p">}</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)){</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="n" style="color: #333;">isImprovable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_impro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="p">}</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_impro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="p">}</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_improve</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp_impro</span><span class="p">);</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="p">}</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="p">}</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="p">}</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">p_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)){</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333;">isImprovable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_impro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="p">}</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_impro</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="p">}</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_improve</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp_impro</span><span class="p">);</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isImprovable</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*--Func-Change--------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes two different positions ('1' and '0') in a specific bit-pattern</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Start and end are excluded</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The pattern which has to be modified</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChangeBitsRandom</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">zero</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">change</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">change</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">zero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetSymbolRandPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetSymbolRandPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">change</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ChangeBitPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">zero</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Exchange of two positions; changing match to don't care and vice versa.</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos The pattern index of the modifying pattern</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos_one Matchposition which has to be a don't care</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos_zero Don'tCare position which has to be a match</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if two positions could be changed or not.</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChangeBitPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">zero</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">one</span><span class="p">){</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">change</span><span class="p">;</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">change</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_improve</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]){</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bit_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">];</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bit_tmp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">zero</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bit_tmp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">one</span> <span class="p">){</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_tmp</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_tmp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">zero</span><span class="p">);</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">UniqBit</span><span class="p">(</span><span class="n" style="color: #333;">bit_tmp</span><span class="p">)){</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bit_tmp</span><span class="p">;</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="n" style="color: #333;">change</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"> <span class="p">}</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="p">}</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="p">}</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]);</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_tmp</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">zero</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">one</span><span class="p">){</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">pattern_tmp</span><span class="p">[</span><span class="n" style="color: #333;">zero</span><span class="p">],</span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">[</span><span class="n" style="color: #333;">one</span><span class="p">]);</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">,</span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">)){</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">],</span> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">);</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">change</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_tmp</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="p">}</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="p">}</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="p">}</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="p">}</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">change</span><span class="p">;</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Investigates for a specific symbol all positions of a pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For a match, the first and last positions are excluded!</span></span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Chooses a position randomly and returns the position</span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The pattern index of the modifying pattern</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param symb The specific symbol, either '1' or '0'</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return A random chosen position of all positions matching the symbol.</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSymbolRandPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">positions</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_improve</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]){</span></span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tmp_pat</span><span class="p">,</span> <span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp_pat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">symb</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">){</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="p">}</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp_pat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">symb</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">){</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="p">}</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="p">}</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">symb</span><span class="p">){</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="p">}</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <span class="p">}</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uniform_int_distribution</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">posits</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">posits</span><span class="p">(</span><span class="n" style="color: #333;">generator</span><span class="p">);</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">positions</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="n" style="color: #333;">positions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---stuff-------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A Method to collect all errormessages. Just easier for programmer to change</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the text or extend.</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param errmsg Due to a few possible errormessages, this is the option, which has to be printed.</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos The position of the incorrect patterns.</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">){</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"file"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mERROR! "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Pattern file </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">inFile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> could not be found!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Return to submitted or default values"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="p">}</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"empty"</span><span class="p">)</span> <span class="p">{</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mERROR! "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"File </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">inFile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> is an empty file!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Return to submitted or default values"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="p">}</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pattern"</span><span class="p">)</span> <span class="p">{</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mERROR! "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Patternconditions from pattern "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file were not correct (different weight, etc.)!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Go on to next pattern."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"> <span class="p">}</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"startend"</span><span class="p">)</span> <span class="p">{</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mFORMAT-ERROR: "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Pattern "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" has to start and end with a match position '1' !"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="p">}</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"format"</span><span class="p">)</span> <span class="p">{</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mFORMAT-ERROR: "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Pattern containes illegal characters!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Allowed characters: '0','1' for pattern; ','|'.'|';'|' ' to seperate patterns"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Go on to next pattern."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="p">}</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if(!silent){</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"nkl"</span><span class="p">)</span> <span class="p">{</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mERROR! "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Wrong values for weight, pattern number or pattern length!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Return to default values"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="p">}</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"max_number_pattern"</span><span class="p">)</span> <span class="p">{</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;33m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"The number of patterns is too high for your configuration and will be reset!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp"> <span class="p">}</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"weight"</span><span class="p">)</span> <span class="p">{</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mERROR! "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"By comparing with the first pattern, the "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">". pattern has a different weight!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="p">}</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"update"</span><span class="p">){</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31m</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">####IMPROTANT####</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Due to some configuration errors, your submitted parameters have been updated!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="p">}</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"><span class="p">}</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimates the number of matches ('1') in a std::vector<char>.</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern Pattern as std::vector<char></span></span>
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Number of matches ('1').</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetWeight</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">){</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">weight_p</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">weight_p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimates if a std::vector<char> pattern is in binary format ('1' or '0').</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern Pattern as std::vector<char></span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if the submitted std::vector<char> pattern is binary.</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IsBinary</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">binary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'0'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"> <span class="n" style="color: #333;">binary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">binary</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Creates a bitpattern (64-Bit Integer) from a char vector pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param pattern Pattern as std::vector<char></span></span>
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@return Pattern as uint64_t (64-Bit Integer)</span></span>
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StringToBit</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bitpat</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">bitpat</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"> <span class="n" style="color: #333;">bitpat</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">tmp_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bitpat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Creates a char vector pattern. from a bitpattern (64-Bit Integer).</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param pattern Pattern as uint64_t (64-Bit Integer)</span></span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@return Pattern as std::vector<char></span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BitToString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bitpat</span><span class="p">){</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">one</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="n" style="color: #333;">one</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">bitpat</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bitpat</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'1'</span><span class="p">);</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"> <span class="n" style="color: #333;">bitpat</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="n" style="color: #333;">one</span><span class="p">;</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes the current patternset into a bitpattern set.</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PatternToBit</span><span class="p">(){</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringToBit</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"> <span class="p">}</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes the current bitpattern set into a patternset (vector of char vectors).</span></span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BitToPattern</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitToString</span><span class="p">(</span><span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---------------------------------------------------------------------------*/</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Determines the maximum number of patterns with weight and length</span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param weight Complete pattern weight-2, start and end have to be match and do not change</span></span>
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@param length Complete pattern lengt-2, start and end have to be match and do not change</span></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@return max number of possible pattern</span></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">l</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">max_number</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">max_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">k</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="cpp"> <span class="n" style="color: #333;">max_number</span> <span class="o" style="font-weight: 600;">*=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">max_number</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Scans if there is another pattern in the same format in a patternset</span></span>
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pats The patternset, in which we are looking for a similar pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pat The pattern, the query, we are looking for to be unique.</span></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns a boolean, if the submitted pattern is not existing in the patternset.</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pats</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pat</span><span class="p">){</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">uniq</span><span class="p">,</span> <span class="n" style="color: #333;">no_common</span><span class="p">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"> <span class="n" style="color: #333;">uniq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="cpp"></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pats</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pats</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()){</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">no_common</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pats</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pat</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]){</span></span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"> <span class="n" style="color: #333;">no_common</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> <span class="p">}</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">no_common</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"> <span class="n" style="color: #333;">uniq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">uniq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Scans if there is another bitpattern in the same format in a bitpattern set</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pats The bitpattern set, in which we are looking for a similar bitpattern.</span></span>
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pat The bitpattern, the query, we are looking for to be unique.</span></span>
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Returns a boolean, if the submitted bitpattern is not existing in the bitpattern set.</span></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UniqBit</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bit_pat</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">bit_pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">bit_pat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> </span>
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Prints the current patternset to the commandline.</span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Print</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="cpp"> <span class="n" style="color: #333;">BitToPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"> <span class="p">}</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---------------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the patternset as std::vector< std::vector<char> ></span></span>
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the current patternset vector (type: std::vector< std::vector<char> >)</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">BitToPattern</span><span class="p">();</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="p">}</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"><span class="p">}</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the patternset as bitpattern as std::vector<uint64_t></span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the current bit-patternset vector (type: std::vector<uint64_t>)</span></span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(){</span></span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">;</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="p">}</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="p">}</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"><span class="p">}</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a pattern of the patternset as std::vector<char></span></span>
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the 'number'th pattern of the current patternset vector (type: std::vector<char>)</span></span>
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BitToString</span><span class="p">(</span><span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a pattern of the patternset as uint64_t.</span></span>
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the 'number'th pattern of the current patternset vector (type: uint64_t)</span></span>
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="cpp"> <span class="p">}</span></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">];</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"><span class="p">}</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp"></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a vector in which (in pattern order) for each pattern there is a boolean, if the pattern</span></span>
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * can be changed or not.</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Vector<bool> which contains for each pattern the boolean of improvement.</span></span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetDontCareVec</span><span class="p">(){</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a boolean, if the 'number'th patterncan be improved/changed, or not.</span></span>
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if the 'number'th patterncan be improved/changed.</span></span>
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetImprove</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_improve</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a boolean, if there is at least one pattern, which can be improved/changed, or not.</span></span>
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if at least one pattern can be changed.</span></span>
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetImprove</span><span class="p">(){</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"><span class="p">}</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="cpp"></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current patternset weight.</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern weight.</span></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSize</span><span class="p">(){</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"><span class="p">}</span></span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"></span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current patternset weight.</span></span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern weight.</span></span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetWeight</span><span class="p">(){</span></span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cpp"><span class="p">}</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"></span>
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1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="cpp"></span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current lenght of the 'number'th pattern.</span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Weight + don't care positions</span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *@return Current lenght of the 'number'th pattern.</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cpp"> <span class="n" style="color: #333;">leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <span class="p">}</span></span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">leng</span><span class="p">;</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"><span class="p">}</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns boolean if the current patternset modus is bitmode oder not.</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current bitmode boolean (true, if bitmode).</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetBitMode</span><span class="p">(){</span></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bitmode</span><span class="p">;</span></span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"><span class="p">}</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="cpp"></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns boolean if the current patternset modus has been updated</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current patternmode has been updated.</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetUpdate</span><span class="p">(){</span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">update</span><span class="p">;</span></span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Sets a bitpattern at the 'number'th positions of the bitpattern set.</span></span>
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The position where the bitpattern should be saved.</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pat The bitpattern, that should be saved.</span></span>
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">pat</span><span class="p">){</span></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">])){</span></span>
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp"><span class="p">}</span></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp"></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Sets a pattern at the 'number'th positions of the patternset.</span></span>
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number The position where the pattern should be saved.</span></span>
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pat The pattern, that should be saved.</span></span>
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pat</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)){</span></span>
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringToBit</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"> <span class="p">}</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()){</span></span>
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#76d488fea179bfbaad4b3cdb4e31ed97a77d9a18"><strong>src/patternset.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * patternset object header</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * - L. Hahn, C.-A. Leimeister, B. Morgenstern (2015)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * arXiv:1511.04001[q-bio.GN]</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * - B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 12.05.2016, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.2.0 05/2016</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef PATTERNSET_H_</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PATTERNSET_H_</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdint></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">patternset</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">patternfile</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">patternset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">random_length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReInit</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ChangeBitsRandom</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ChangeBitPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">zero</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">one</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">StringToBit</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">BitToString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bitpat</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*-----------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetBitPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetDontCareVec</span><span class="p">();</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetImprove</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetImprove</span><span class="p">();</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetBitMode</span><span class="p">();</span> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetUpdate</span><span class="p">();</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CheckParams</span><span class="p">();</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">CreateLengths</span><span class="p">();</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">CreatePattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ReadPattern</span><span class="p">();</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">VerifyPatternCondition</span><span class="p">();</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">SetImprove</span><span class="p">();</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PatternToBit</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BitToPattern</span><span class="p">();</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">GetSymbolRandPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">symb</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pats</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">UniqBit</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">bit_pat</span><span class="p">);</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">);</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">IsBinary</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern</span><span class="p">);</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">MaxNumberPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">l</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Faculty</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bit_pattern_set</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_dontcare</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_improve</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_uniq</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inFile</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">bitmode</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">random_length</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isInFile</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">update</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">initialized</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"><span class="p">};</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "variance.h"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">revComp</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="n" style="color: #333;">distanceType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">EV</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="n" style="color: #333;">distanceType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">JS</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">patternFile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"DMat"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printHelp</span><span class="p">(){</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,20 +31,11 @@ void printHelp(){</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;"> -f <file>: use patterns in <file> instead of random patterns"</span> </span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;"> -t <integer>: numer of threads (default: 25 threads)"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;"> -r: don't consider the reverse complement"</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;"> -d EU | JS | EV: change distance type to Euclidean, Jensen-Shannon, evolutionary distance (default: <span class="idiff left right">EV</span>)"</span> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;"> -d EU | JS | EV: change distance type to Euclidean, Jensen-Shannon, evolutionary distance (default: <span class="idiff left right">JS</span>)"</span> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">parsePattern</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">filePath</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">patternSet</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">file</span><span class="p">(</span><span class="n" style="color: #333;">filePath</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">str</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">str</span><span class="p">)){</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">patternSet</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">file</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">parseParameters</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">argv</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// too few?</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,18 +157,28 @@ int main(int argc, char *argv[]){</td>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readData</span><span class="p">(</span><span class="n" style="color: #333;">inputFile</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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167
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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168
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"></span>
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169
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patternSet</span><span class="p">;</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp_pat_set</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">variance</span> <span class="n" style="color: #333;">variance_obj</span><span class="p">;</span></span>
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170
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">patternFile</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variance_obj</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">laenge</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">laenge</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">laenge</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dontcare</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span><span class="n" style="color: #333;">laenge</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Silent</span><span class="p">();</span> </span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="mi" style="color: #099;">500</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//5000 mal versuchen ein Pattern zu verbessern</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">patternSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_obj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">();</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="p">,</span><span class="n" style="color: #333;">dontcare</span><span class="p">,</span><span class="n" style="color: #333;">dontcare</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="mi" style="color: #099;">5000</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//5000 mal versuchen ein Pattern zu verbessern </span></span>
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178
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">parsePattern</span><span class="p">(</span><span class="n" style="color: #333;">patternFile</span><span class="p">,</span> <span class="n" style="color: #333;">patternSet</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">patternFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="mf" style="color: #099;">0.75</span><span class="p">,</span><span class="mf" style="color: #099;">0.25</span><span class="p">,</span><span class="mi" style="color: #099;">16000</span><span class="p">);</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="p">}</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">GetMinDontcare</span><span class="p">();</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_pat_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_obj</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">();</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tmp_pat_set</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">patternSet</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">tmp_pat_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">tmp_pat_set</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">()));</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="p">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_pat_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"></span>
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181
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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182
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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183
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dna</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#99dd8f62fef31c460730ff26f487f0b5a7d39de3"><strong>src/variance.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * variance object file</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - L. Hahn, C.-A. Leimeister, B. Morgenstern (2015)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * arXiv:1511.04001[q-bio.GN]</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 12.05.2016, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.2.0 05/2016</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "variance.h"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variables---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*===Main-Part===============================================================*/</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Constructor-------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default constructor, sets the default vaulues, pattern will be generated automatically.</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16000</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.75</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.25</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Short constructor, sets some default vaulues, just pattern dimension is set.</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size Number of patterns for the patternset.</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weigth Number of match positions ('1') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param min_dontcare Number of minimum don't care positions ('0') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param max_dontcare Number of maximum don't care positions ('0') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16000</span><span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.75</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.25</span><span class="p">;</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Long constructor, sets the values; resets automatically, if there are problems.</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size Number of patterns for the patternset.</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weight Number of match positions ('1') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param min_dontcare Number of minimum don't care positions ('0') in each pattern.</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param max_dontcare Number of maximum don't care positions ('0') in each pattern.</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param seq_leng Length of sequences in database, used for variance.</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p Match probability ( = #matches / #positions), used for sensitivity and variance.</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param q Background probability, used for variance.</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * File constructor, sets values only from files; resets automatically if there are problems.</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param inFile The file which contains a patternset.</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inFile</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inFile</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">isInFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"><span class="p">}</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default destructor, deletes all vectors and matrices in the object.</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">variance</span><span class="p">(){</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="p">}</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Initialization----------------------------------------------------------*/</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Standard Initialization of variance options.</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Init</span><span class="p">(){</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"outfile.pat"</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">oc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">isOutFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">random_leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="n" style="color: #333;">oc</span><span class="p">,</span> <span class="n" style="color: #333;">improve</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">silent</span><span class="p">,</span> <span class="n" style="color: #333;">random_leng</span><span class="p">,</span> <span class="n" style="color: #333;">outFile</span><span class="p">);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="p">}</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"><span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Initialization of variance options with specific parameter.</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param oc Boolean which (de)activates the overlap complexity/variance calculation</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param improve Boolean which (de)activates the improvement of the patternset.</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param quiet Boolean which (de)activates just a short output of the improvement</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param silent Boolean which (de)activates std::output on commandline (exclusive errors)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param randpatleng Boolean which (de)activates random generated pattern lengths</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param outFile Char array which contains name and path to outputfile (commandline parameter)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">oc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">improve</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">random_leng</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outFile</span><span class="p">){</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">oc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oc</span><span class="p">;</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quiet</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outFile</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">random_leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">random_leng</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">best_silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">impro_silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">loops</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">outFile</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outFile</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">){</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">isOutFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="p">}</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">isOutFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="p">}</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"overlap-complexity</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">= "</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"variance</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">= "</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="p">}</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="p">}</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInit</span><span class="p">();</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="p">}</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"><span class="p">}</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Standard Reinitialization of variance options, with a new patternset.</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReInit</span><span class="p">(){</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isInFile</span><span class="p">){</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="n" style="color: #333;">inFile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="p">}</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> </span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="p">}</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="n" style="color: #333;">random_leng</span><span class="p">);</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInit</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">);</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"><span class="p">}</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Standard Reinitialization of variance options, with a given patternset.</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReInit</span><span class="p">(</span><span class="n" style="color: #333;">patternset</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pat</span><span class="p">){</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="p">}</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pat</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> </span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">max_dontcare</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">bitmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitMode</span><span class="p">();</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">improve</span><span class="p">){</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetImprove</span><span class="p">();</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">improve</span><span class="p">){</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"noimprove"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="p">}</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="p">}</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">norm_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">);</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.75</span><span class="p">;</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.25</span><span class="p">;</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"pq"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * First Initializing of the variance/oc where each value of the matrix has </span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * to be created, instead of updated variance, where it is not necessary to</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * recalculate each value/entry.</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InitVariance</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp_pair</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var_hom</span><span class="p">,</span> <span class="n" style="color: #333;">var_bac</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">oc_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">lower_length</span><span class="p">,</span> <span class="n" style="color: #333;">upper_length</span><span class="p">,</span> <span class="n" style="color: #333;">length_mean</span><span class="p">;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_current_contribute</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_last_contribute</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">lower_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> </span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="p">}</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lower_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">upper_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">)</span> <span class="p">{</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="p">}</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> </span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">));</span> </span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="p">}</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">lower_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">upper_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> </span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="p">(</span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_bac</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="p">}</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> </span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="p">}</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="p">}</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetImprove</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)){</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">tmp_pair</span><span class="p">);</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="p">}</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="p">}</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"><span class="p">}</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of the destructor; could be used in other cases for </span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * reinitializing the variance/oc new.</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Clear</span><span class="p">(){</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"><span class="p">}</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variance-----------------------------------------------------------------*/</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Instead of recalculating each value, only the matrix entries which</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * belong to the modified pattern have to be recalculated. </span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param number Patternindex of the modified pattern </span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var_hom</span><span class="p">,</span> <span class="n" style="color: #333;">var_bac</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">oc_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">lower_length</span><span class="p">,</span> <span class="n" style="color: #333;">upper_length</span><span class="p">,</span> <span class="n" style="color: #333;">length_mean</span><span class="p">;</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">lower_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lower_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">upper_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">)</span> <span class="p">{</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> </span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">));</span> </span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="p">}</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">lower_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">upper_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="p">(</span><span class="n" style="color: #333;">seq_leng</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span><span class="p">);</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_bac</span><span class="p">;</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="p">}</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> </span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="p">}</span> </span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Shifts pattern and counts the number of common match positions.</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p1 Position of the first used pattern of the pattern set.</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p2 Position of the second used pattern of the pattern set.</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * NOTE: possible is p1 = p2</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param s The shift of the second pattern, s < 0 := shift left </span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * pattern 2, s > := shift right pattern 2.</span></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Calculates and returns current variance.</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span><span class="p">){</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stra</span><span class="p">,</span> <span class="n" style="color: #333;">strb</span><span class="p">;</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">pata</span><span class="p">,</span> <span class="n" style="color: #333;">patb</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">maxi</span><span class="p">,</span> <span class="n" style="color: #333;">maxa</span><span class="p">,</span> <span class="n" style="color: #333;">maxb</span><span class="p">;</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">patb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="n" style="color: #333;">number2</span><span class="p">);</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="p">}</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">patb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patb</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="p">}</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">maxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pata</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">maxb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">patb</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">maxi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">maxa</span><span class="p">,</span><span class="n" style="color: #333;">maxb</span><span class="p">);</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">patb</span><span class="p">;</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxi</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="p">}</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="p">}</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="p">}</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="p">}</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">stra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">strb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">number2</span><span class="p">);</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">maxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">maxb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetLength</span><span class="p">(</span><span class="n" style="color: #333;">number2</span><span class="p">);</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">);</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">maxa</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">maxb</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">shift</span><span class="p">;</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">stra</span><span class="p">,</span><span class="n" style="color: #333;">strb</span><span class="p">);</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">maxi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">maxa</span><span class="p">,</span><span class="n" style="color: #333;">maxb</span><span class="p">);</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxi</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">stra</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strb</span><span class="p">[</span><span class="n" style="color: #333;">strb</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">maxi</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * If the random swap leads to a worse oc/variance, the old values have</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * to be restored.</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ResetContribute</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">number</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Improvment--------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The improvement method.</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param limits The number of patterns which have to be selected and mayby modified.</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">limits</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">var_iterator</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">last_pat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp_pair</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">last_bit_pat</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">best_variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">worst_pat</span><span class="p">,</span> <span class="n" style="color: #333;">better_pattern</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">improve</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">best_variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="n" style="color: #333;">var_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">var_iterator</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="n" style="color: #333;">last_bit_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="p">}</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">limits</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">worst_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_iterator</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">last_bit_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="p">}</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">last_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="p">}</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">ChangeBitsRandom</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">best_variance_val</span><span class="p">){</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">best_variance_val</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">variance_val</span><span class="p">){</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">var_iterator</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()){</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="n" style="color: #333;">var_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="p">}</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="p">}</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">best_variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">var_iterator</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">pattern_variance</span><span class="p">[</span><span class="n" style="color: #333;">worst_pat</span><span class="p">],</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">tmp_pair</span><span class="p">);</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="n" style="color: #333;">var_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">better_pattern</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> </span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">loops</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">impro_silent</span><span class="p">)){</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span><span class="p">){</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"*** BETTER PATTERN "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" *** </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">(random permutation)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Step "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" / "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">limits</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Patternset: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="p">}</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">*** BETTER PATTERN "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" *** </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">(random permutation)"</span><span class="p">;</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="p">}</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="p">}</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">last_pat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp"> <span class="p">}</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="p">}</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">var_iterator</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()){</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="n" style="color: #333;">var_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_set</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="p">}</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bitmode</span><span class="p">){</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">,</span> <span class="n" style="color: #333;">last_bit_pat</span><span class="p">);</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"> <span class="p">}</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">,</span> <span class="n" style="color: #333;">last_pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="p">}</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">ResetContribute</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">var_iterator</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="p">}</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">quiet</span><span class="p">){</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="p">}</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"noimprove"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Improvement with reinitialization. Improves a patternset, resets it 'loops' times and</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * and sets the best patternset with the best detected oc/variance.</span></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param limits The number of patterns which have to be selected and mayby modified.</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param loops The number of reinitializations to find better oc/variance patternsets.</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">limits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loops</span><span class="p">){</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">initialized</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">improve</span><span class="p">){</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">patternset</span> <span class="n" style="color: #333;">best_pattern_set</span><span class="p">;</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">pattern_out</span><span class="p">;</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_str</span><span class="p">;</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">best_variance_val</span><span class="p">;</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">better_pattern</span><span class="p">;</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loops</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loops</span><span class="p">;</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">best_silent</span><span class="p">){</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">===== First patternset ====="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="p">}</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">best_variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="n" style="color: #333;">best_pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">loops</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="n" style="color: #333;">limits</span><span class="p">);</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">best_variance_val</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance_val</span><span class="p">){</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">better_pattern</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">loops</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">impro_silent</span><span class="p">)){</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span><span class="p">){</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">*** BETTER PATTERN "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" *** </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">(oc/variance optimization)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Step "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" / "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">loops</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Patternset: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="p">}</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">*** BETTER PATTERN "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" *** </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">(oc/variance optimization)"</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="p">}</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> <span class="p">}</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"> <span class="n" style="color: #333;">best_variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"> <span class="n" style="color: #333;">best_pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span> </span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"> <span class="p">}</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInit</span><span class="p">();</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="p">}</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">best_silent</span><span class="p">){</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="p">}</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">best_pattern_set</span><span class="p">;</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInit</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">);</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">best_silent</span><span class="p">){</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">===== Best patternset ======"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="p">}</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isOutFile</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">best_silent</span><span class="p">){</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_out</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">outFile</span><span class="p">);</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">out_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">out_str</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="p">}</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetFormat</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetFormat</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="p">}</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"noimprove"</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---stuff-------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Prints the current patternset to the commandline.</span></span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PrintPatternSet</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A Method to collect all errormessages. Just easier for programmer to change</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the text or extend.</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param errmsg Due to a few possible errormessages, this is the option, which has to be printed.</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos The position of the incorrect patterns.</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"noimprove"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;33m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Using your pattern conditions it is not sensible to improve your pattern, sorry!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Deactivating improve mode</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="p">}</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errmsg</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pq"</span><span class="p">)</span> <span class="p">{</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;32m</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">--> IMPORTANT <--</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[1;31mError "</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%c[0m"</span><span class="p">,</span> <span class="mi" style="color: #099;">27</span><span class="p">);</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"while parsing your p and/or q value: </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0 < q <= p <= 1!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Return to default values:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">p = 0.75 </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">q=0.25</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Set&Get-----------------------------------------------------------------*/</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the patternset object</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the current patternset object (type: patternset)</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"><span class="n" style="color: #333;">patternset</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPatternSet</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the patternset as std::vector< std::vector<char> ></span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the current patternset vector (type: std::vector< std::vector<char> >)</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a pattern of the patternset as std::vector<char></span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the 'number'th pattern of the current patternset vector (type: std::vector<char>)</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the patternset as bitpattern as std::vector<uint64_t></span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the current bit-patternset vector (type: std::vector<uint64_t>)</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a pattern of the patternset as uint64_t.</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Copy of the 'number'th pattern of the current patternset vector (type: uint64_t)</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current variance/oc value.</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern variance/oc.</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetVariance</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current norm variance/oc value.</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern norm variance/oc.</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetNormVariance</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variance_val</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">norm_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current patternset size.</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern size.</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSize</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current patternset weight.</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern weight.</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetWeight</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current patternset minimum don't care number.</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern minimum don't care number.</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetMaxDontcare</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current patternset maximum don't care number.</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current pattern maximum don't care number.</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetMinDontcare</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current dataset sequence length for variance calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current dataset sequence length for variance calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSequenceLength</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current match probability for variance calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current match probability for variance calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetP</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current background probability for variance calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current background probability for variance calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetQ</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns boolean if the current patternset modus is bitmode oder not.</span></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current bitmode boolean (true, if bitmode).</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetBitMode</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetBitMode</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns boolean if the current patternset modus has been updated</span></span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Current patternmode has been updated.</span></span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetUpdate</span><span class="p">(){</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">GetUpdate</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A special option, if silent == true but, first and best pattern should be printed.</span></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param sil Boolean, if output first and best pattern, although silent == true.</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BestSilent</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">sil</span><span class="p">){</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">best_silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sil</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A special option, if silent == true but the number of improved pattern should be printed.</span></span>
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param sil Boolean, if print number of improvements, although silent == true.</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ImproSilent</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">sil</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="cpp"> <span class="n" style="color: #333;">impro_silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sil</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a string containing a speacial output format, if its overlap complexity or not.</span></span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return String which contains current pattern mode overlap complexity or variance calculation. </span></span>
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetFormat</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">outvar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns a boolean, if there is at least one pattern, which can be improved/changed, or not.</span></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Boolean, if at least one pattern can be changed.</span></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetImprove</span><span class="p">(){</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"><span class="p">}</span></span>
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868
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869
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Prints the current patternset to the commandline.</span></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Print</span><span class="p">(){</span></span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="p">.</span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#16fcf2292a48cd93a41327a36254348ef5d0b0a4"><strong>src/variance.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * variance object header</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * - L. Hahn, C.-A. Leimeister, B. Morgenstern (2015)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * arXiv:1511.04001[q-bio.GN]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * - B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 12.05.2016, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.2.0 05/2016</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef VARIANCE_H_</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VARIANCE_H_</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdint></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <set></span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <utility></span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "patternset.h"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">variance</span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inFile</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">variance</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Init</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Init</span><span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">oc</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">improve</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">random_leng</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outFile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReInit</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">limits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">limits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loops</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PrintPatternSet</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*-----------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span> <span class="n" style="color: #333;">GetPatternSet</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetBitPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">GetBitPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetMaxDontcare</span><span class="p">();</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetMinDontcare</span><span class="p">();</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">GetSequenceLength</span><span class="p">();</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetP</span><span class="p">();</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetQ</span><span class="p">();</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetBitMode</span><span class="p">();</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetUpdate</span><span class="p">();</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BestSilent</span><span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sil</span><span class="p">);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ImproSilent</span><span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sil</span><span class="p">);</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">GetFormat</span><span class="p">();</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">GetImprove</span><span class="p">();</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReInit</span><span class="p">(</span><span class="n" style="color: #333;">patternset</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVariance</span><span class="p">();</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span><span class="p">);</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ResetContribute</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance_mat</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance_set</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_variance</span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_current_contribute</span><span class="p">;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_last_contribute</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">outvar</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_dontcare</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max_dontcare</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seq_leng</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">norm_size</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">loops</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isInFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">initialized</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">random_leng</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">quiet</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">impro_silent</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">oc</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#a5469f8ee3db98ebc1fb6aa9dc56b1b5a97554cc"><strong>variance.cpp</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * variance object file</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.0.2 11/2015</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "variance.h"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variables---------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*===Main-Part===============================================================*/</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Constructor-------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default constructor, sets the default vaulues, pattern will be generated automatically.</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">Ctor</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mf" style="color: #099;">0.75</span><span class="p">,</span> <span class="mf" style="color: #099;">0.25</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * File constructor, sets values only from files; resets automatically if there are problems.</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">14</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">Ctor</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mf" style="color: #099;">0.75</span><span class="p">,</span> <span class="mf" style="color: #099;">0.25</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Short constructor, sets some default vaulues, just pattern dimension is set.</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size The amount of patterns; pattern number.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param length The pattern length for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weigth The weight (match positions; '1') for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">)</span> <span class="p">{</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">Ctor</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mf" style="color: #099;">0.75</span><span class="p">,</span> <span class="mf" style="color: #099;">0.25</span><span class="p">,</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Long constructor, sets the values; resets automatically, if there are problems.</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pattern_file File, that may contains submitted pattern</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param align_file File, that may contains an alignment file to estimate p, q, l_hom, li and lj</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param size The amount of patterns; pattern number.</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param length The pattern length for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param weigth The weight (match positions; '1') for each pattern of the pattern set.</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param l_hom In theory, the amount of homologous positions of two sequences in an multiple alignment.</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param l1 In theory, the first(represents each sequence i) sequence length of two observed sequences.</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param l2 In theory, the second(represents each sequence j) sequence length of two observed sequences.</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p The match probability ( = #matches / #l_hom)</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param q The background probability for each nucleotide A,C,G,T</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_hom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">H</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">Ctor</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">l_hom</span><span class="p">,</span> <span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">H</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default destructor, deletes all vectors and matrices in the object.</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">variance</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Ctor</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_hom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">H</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l2</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">H</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">H</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">oc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"variance: "</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVariance</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"><span class="p">}</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Init--------------------------------------------------------------------*/</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Complete Initializing of the Variance, which also creates the patternsets</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * calculates the first variance/oc and checks if each parameter is in its </span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * own correct size and dimension.</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InitVariance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">){</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">patternset</span><span class="p">(</span><span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetLength</span><span class="p">();</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetLengthMean</span><span class="p">();</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">improve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetImprove</span><span class="p">();</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetUpdate</span><span class="p">();</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*Incorrect values for variance have to be corrected*/</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"pq"</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.9</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.25</span><span class="p">;</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l_hom</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l2</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"length"</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">l_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">l2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"> <span class="p">}</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVarMatrix</span><span class="p">();</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVar</span><span class="p">();</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">update</span><span class="p">){</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">Quiet</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part Initialzinig of the Variance, it will not reset complete.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Only for ReInitializin a new pattternset with most values in</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * common.</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Public Access, so other programs can 'reload' it</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReInitVariance</span><span class="p">(){</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ReInitPattern</span><span class="p">();</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetLengthMean</span><span class="p">();</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVarMatrix</span><span class="p">();</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVar</span><span class="p">();</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="cpp"><span class="p">}</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of the destructor; could be used in other cases for </span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * reinitializing the variance/oc new.</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Clear</span><span class="p">(){</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="p">}</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"><span class="p">}</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Up to different patternsizes a specific matrix will be created.</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Necessary for reinitliazing.</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InitVarMatrix</span><span class="p">()</span> <span class="p">{</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cpp"> <span class="p">}</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cpp"><span class="p">}</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="cpp"></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * First Initializing of the variance/oc where each value of the matrix has </span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * to be created, instead of updated variance, where it is not necessary to</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * recalculate each value/entry. Only of those, which alter due to pattern</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * modification.</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InitVar</span><span class="p">()</span> <span class="p">{</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var_hom</span><span class="p">,</span> <span class="n" style="color: #333;">var_bac</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">// ,hom_val, back_val;</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span><span class="p">,</span> <span class="n" style="color: #333;">lower_length</span><span class="p">,</span> <span class="n" style="color: #333;">upper_length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">oc_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//hom_val = 0;</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//back_val = 0;</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="cpp"></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*i and j represents Pi and Pj of the set of pattern*/</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">lower_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lower_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upper_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*As in the formula, the shift goes from max shift left to max shift right*/</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*At least one position has to overlap*/</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/*summation of the homologue first part*/</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> </span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">));</span> </span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">l_hom</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="p">(</span><span class="n" style="color: #333;">l2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_bac</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// hom_val += hom;</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// back_val += back;</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">back</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*For each pair Pi and Pj this is the direct contribute to the complete variance*/</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span> </span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Variance</span><span class="p">();</span> </span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/*Sets the contribute of each pattern in the beginning*/</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">ResetPatternOrder</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "homologue contribute: " << hom_val/variance_val << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "background contribute: " << back_val/variance_val << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Variance-----------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * IF neccessary, it calculates the current variance/oc from the matrix.</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns current variance/oc</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Variance</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">var</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Instead of recalculating each value, only the matrix entries which</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * belong to the modified pattern have to be recalculated. </span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pat Patternindex of the modified pattern </span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pat</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var_hom</span><span class="p">,</span> <span class="n" style="color: #333;">var_bac</span><span class="p">,</span> <span class="n" style="color: #333;">hom</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">shift</span><span class="p">,</span> <span class="n" style="color: #333;">lower_length</span><span class="p">,</span> <span class="n" style="color: #333;">upper_length</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">oc_hom</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp"></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">lower_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">));</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> </span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">upper_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lower_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upper_length</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*As in the formula, the shift goes from max shift left to max shift right*/</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*At least one position has to overlap*/</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">)</span> <span class="p">{</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/*summation of the homologue first part*/</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">var_bac</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">shift</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">weight</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">var_hom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">oc_hom</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">shift</span><span class="p">));</span> </span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp"> </span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">l_hom</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="p">(</span><span class="n" style="color: #333;">l2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">length_mean</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">var_bac</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hom</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">back</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*For each pair Pi and Pj this is the direct share of the complete variance...*/</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">pat</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">var_sum</span><span class="p">[</span><span class="n" style="color: #333;">pat</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Shifts pattern and counts the number of common match positions</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p1 Position of the first used pattern of the pattern set</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param p2 Position of the second used pattern of the pattern set</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * NOTE: possible is p1 = p2</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param s The shift of the second pattern, s < 0 := shift left pattern 2, s > := shift right pattern 2</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return Calculates and returns current variance</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span><span class="p">,</span> <span class="n" style="color: #333;">maxi</span><span class="p">,</span> <span class="n" style="color: #333;">maxa</span><span class="p">,</span> <span class="n" style="color: #333;">maxb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">pata</span><span class="p">,</span> <span class="n" style="color: #333;">patb</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">patb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">number2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*LookUp Counter*/</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*Negative shift means, the upper pattern is shifted right*/</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/*otherweise the lower pattern is shifted right*/</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">patb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">patb</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">maxa</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">pata</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">maxb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">log2</span><span class="p">(</span><span class="n" style="color: #333;">patb</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">maxi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">maxa</span><span class="p">,</span><span class="n" style="color: #333;">maxb</span><span class="p">);</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxi</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(((</span><span class="n" style="color: #333;">pata</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">patb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">oc</span><span class="p">){</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*Allows us to calculate th n(p,p',s) value in a way...*/</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/*...with not so much space. We do not need to look for...*/</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/*...each position containing at least one match*/</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the position of the worst pattern, estimated by the maximum variancepart</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * for each pattern pair</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param n The pattern index of the chosen pattern.</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns position worst matrix by max_value</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">WorstPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_order_sort</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPos</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ResetPatternOrder</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pattern_order_sort</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order_sort</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">weight</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">extkey</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">pattern_order</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span> <span class="cm" style="color: #998; font-style: italic;">/*Using an extended key to store each contribute and the ...*/</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_order_sort</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/*pattern number.*/</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">pattern_order_sort</span><span class="p">.</span><span class="n" style="color: #333;">rbegin</span><span class="p">(),</span> <span class="n" style="color: #333;">pattern_order_sort</span><span class="p">.</span><span class="n" style="color: #333;">rend</span><span class="p">());</span> </span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The improvement method</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param limit The number of patterns which have to be selected and mayby modified.</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">vec</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">pat_save</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var_save</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_var</span><span class="p">,</span> <span class="n" style="color: #333;">best_by</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">worst_pat</span><span class="p">,</span> <span class="n" style="color: #333;">better_pattern</span><span class="p">,</span> <span class="n" style="color: #333;">counter</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::string str_out = "Output_variance";</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::ofstream fout;</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fout.open(str_out);</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="cpp"> <span class="n" style="color: #333;">best_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"First "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"First norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fout << 0 << "\t" << GetNormVariance() << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">loop_opt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Silent</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">loop_opt</span><span class="p">;</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp"> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">worst_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">=================</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">And do it again!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">ReInitVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">improve</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">limit</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">var_save</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">worst_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetWorstPat</span><span class="p">(</span><span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">%</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">pattern_order_sort</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()));</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << counter << "\t" << worst_pat << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="cpp"> <span class="n" style="color: #333;">pat_save</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ChangeBits</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="cpp"> <span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span> </span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_var</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmp_var</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">var_save</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">UniqPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"> <span class="n" style="color: #333;">better_pattern</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">var_save</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">*** BETTER PATTERN "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ***"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"*** BETTER PATTERN "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">better_pattern</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ***"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Step "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" / "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">limit</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Patternset: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"norm_"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Do-Nothing</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">ResetPatternOrder</span><span class="p">();</span></span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fout << i << "\t" << GetNormVariance() << std::endl;</span></span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cpp"> <span class="p">}</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span> </span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">,</span> <span class="n" style="color: #333;">pat_save</span><span class="p">);</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="n" style="color: #333;">worst_pat</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">best_by</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">loop_opt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">best_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cpp"> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">loop_opt</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Best pattern:</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Best "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Best norm_"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp"> <span class="p">}</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fout << limit << "\t" << GetNormVariance() << std::endl;</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cpp"> <span class="p">}</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if(update){</span></span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//SecureMessage("update");</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">loop_opt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetPattern</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">vec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="cpp"> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">best_by</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">silent</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Best pattern:</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Best "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Best norm_"</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">vec</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//fout.close();</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Turns the current calculation from variance to overlap complexity.</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The matrix has to be recalculated complete.</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ImproveOC</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">oc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">outvar</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"oc: "</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVar</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---stuff-------------------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Method calculate the number of all pattern combinations</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Actually the gauss summation (n*(n+1)/2)</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return the number of maximum pattern combinations</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gauss</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes to quiet output, only the number of better patterns will be printed </span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * automatically, and the best patternset by the variance/oc minimization.</span></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Errors arr going to be printed!</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Quiet</span><span class="p">()</span> <span class="p">{</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Changes to silent output, nothing will be printed automatically!</span></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Errors are going to be printed!</span></span>
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Silent</span><span class="p">()</span> <span class="p">{</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quiet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Silent</span><span class="p">();</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Resets the pattern lengths from evenly distributed lengths between maximum</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * and minimum to random created pattern lengths.</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * One quarter of the set will have maximum length, the rest will have the</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * length between maximum and minimum randomly distributed.</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RandPatLength</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">RandPatLength</span><span class="p">();</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">InitVar</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Sets the number of times the improvement method should be executed again.</span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * It will save the best variance/oc and its patternset.</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param n The number of iterations for the improvement method</span></span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LoopOpt</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="cpp"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="cpp"> <span class="n" style="color: #333;">loop_opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Prints complete the current patternset</span></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PrintPattern</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Print</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A Method to collect all errormessages. Just easier for programmer to change</span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the text or extend.</span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param errmsg</span></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Due to a few possible errormessages, this is the option, which has to be printed.</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param pos</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The position of the incorrect patterns.</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*if (errmsg == "noimprove") {</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Using your pattern conditions it is not sensible to improve your pattern, sorry!" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Deactivating improve mode\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "update"){</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "\n\n--> IMPORTANT <--\nDue to some configuration errors, your submitted parameters have been updated!\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "pq") {</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Error while parsing your p and/or q value: \t0 < q <= p <= 1!" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to default values:\tp = 0.9 \tq=0.25\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "length") {</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Error while parsing your sequence length S: \t 0 < S!" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "Return to default value: \tS = 10000\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "wrongindex") {</span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "ERROR! Pattern does not exist... do nothing\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "speed"){</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cerr << "\n\n\nUPDATE! SpEED lenghts optimization is used, creating a new patternset!!!\n\n\n\n" << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return;</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*---Set-&-GetFunc-----------------------------------------------------------*/</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(){</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetStringPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetString</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current variance</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns variance</span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetVariance</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current variance, normalized</span></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns norm_variance</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetNormVariance</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variance_val</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Gauss</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the position of the worst pattern, estimated by the maximum variancepart</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * for each pattern pair</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns position worst matrix by max_value</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetWorstPat</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">size</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">WorstPattern</span><span class="p">(</span><span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the weight of each pattern, the match positions</span></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns weight</span></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetWeight</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the amount of patters; number of patterns</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns size</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetSize</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the length of each pattern</span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns length</span></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetLength</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_set</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetLength</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the match probability</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns p value</span></span>
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731
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetP</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the background probabillity, summation over all nucleotids</span></span>
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738
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns q value</span></span>
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetQ</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the length of the homologous sequence pair</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns homologous positions</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetLHom</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">l_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the length of the first observed sequence</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns length sequence 1</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetL1</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">l1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the length of the second observed sequence</span></span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return returns length sequence 2</span></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetL2</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">l2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the current format, variance or overlap complexity</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return the format string, either 'variance' or 'oc' </span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetFormat</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">outvar</span><span class="p">;</span></span>
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779
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="cpp"></span>
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781
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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782
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Returns the length of a random homolgue region on a dataset</span></span>
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783
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @return The length of random homolgue region</span></span>
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785
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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786
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetH</span><span class="p">(){</span></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">H</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/spaced/compare/9538252c4c10beb02948b546844f5eaa4ba17e31...46b8060cb2374929cf4a11b4feadfb602a9e6841#257fa9bceed7c4724b402cf77b45b9499350579d"><strong>variance.h</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This programm calculates the variance/OC and/or the sensitivity of a set of pattern with the same weight.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * It is possible to improve your patternset and read patterns from a file.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * variance object header</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * For theory please have a look at:</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Estimating evolutionary distances between genomic sequences from spaced-word matches</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Algorithms for Molecular Biology 10, 5. (http://www.almob.org/content/10/1/5/abstract)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @author: Lars Hahn - 26.10.2015, Georg-August-Universitaet Goettingen</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @version: 1.0.2 11/2015</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef VARIANCE_H_</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VARIANCE_H_</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <inttypes.h></span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "patternset.h"</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "extkey.h"</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">variance</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">);</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_hom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">H</span><span class="p">);</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">variance</span><span class="p">();</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReInitVariance</span><span class="p">();</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">RandPatLength</span><span class="p">();</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Improve</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ImproveOC</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">GetPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">GetPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetWorstPat</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetWeight</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetSize</span><span class="p">();</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">GetLength</span><span class="p">();</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PrintPattern</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">GetFormat</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetNormVariance</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetP</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">GetQ</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetLHom</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetL1</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetL2</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">GetH</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LoopOpt</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Quiet</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Silent</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Ctor</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_hom</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">H</span><span class="p">);</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVariance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">);</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVarMatrix</span><span class="p">();</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">InitVar</span><span class="p">();</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SetPatOrder</span><span class="p">();</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variance</span><span class="p">();</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">UpdateVariance</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ShiftPos</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">WorstPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number</span><span class="p">);</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ResetPatternOrder</span><span class="p">();</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Gauss</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SecureMessage</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">errmsg</span><span class="p">);</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">var_sum</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">patternset</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pattern_set</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pattern_order</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">extkey</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">pattern_order_sort</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">outvar</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">variance_val</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length_mean</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_hom</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l1</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">H</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">loop_opt</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">oc</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">improve</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">quiet</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">silent</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">update</span><span class="p">;</span> </span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"><span class="p">};</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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