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<h3>
Andreas Tille pushed to branch upstream
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/3f1306ad27fb01b15f16c1945979230b25c99725">3f1306ad</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-07-09T10:39:47+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.0-201605+dfsg</pre>
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<h4>13 changed files:</h4>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#3283d870958c09551c30ebbb9d26960e4005457a">
<span class="deleted-file">
−
extkey.cpp
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<li class="file-stats">
<a href="#161f59057218bdf2f270bdb22d6638ef12a19847">
<span class="deleted-file">
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extkey.h
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<a href="#a69222313c83929659f5fe5e6a6a40b0d20a5fbc">
<span class="deleted-file">
−
patternset.cpp
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patternset.h
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<a href="#519597f899fb573748be33af0584bdf3142eacca">
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src/patternset.cpp
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src/patternset.h
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<li class="file-stats">
<a href="#827d9b3126d4d1cea6c5176c34241e1e2cc5a680">
sort.h
→
src/sort.h
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<li class="file-stats">
<a href="#2947485ced1da9b0e852c6381259845de5d9471d">
spaced.cc
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src/spaced.cc
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<a href="#99dd8f62fef31c460730ff26f487f0b5a7d39de3">
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src/variance.cpp
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src/variance.h
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variance.cpp
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−
variance.h
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</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/spaced/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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>
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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>
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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">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>
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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>
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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>
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<li id="3283d870958c09551c30ebbb9d26960e4005457a">
<a href="https://salsa.debian.org/med-team/spaced/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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<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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<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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<td class="diff-line-num old old_line" data-linenumber="9" 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="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 "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="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="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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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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<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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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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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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<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;"> * 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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<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/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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<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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<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 "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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32
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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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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;"> * @param p The match probability ( = #matches / #l_hom)</span></span>
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87
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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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88
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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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93
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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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95
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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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97
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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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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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<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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<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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<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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110
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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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<td class="diff-line-num old old_line" data-linenumber="114" 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">
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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121
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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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122
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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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124
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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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<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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130
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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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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <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="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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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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<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;">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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<td class="diff-line-num old old_line" data-linenumber="144" 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">
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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<td class="diff-line-num old old_line" data-linenumber="145" 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">
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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<td class="diff-line-num old old_line" data-linenumber="147" 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">
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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<td class="diff-line-num old old_line" data-linenumber="148" 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">
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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<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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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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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"> <span class="p">}</span></span>
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154
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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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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"></span>
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156
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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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166
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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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167
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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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168
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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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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"><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>
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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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<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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<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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<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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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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177
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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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<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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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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<td class="diff-line-num old old_line" data-linenumber="199" 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">
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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<td class="diff-line-num old old_line" data-linenumber="201" 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">
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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<td class="diff-line-num old old_line" data-linenumber="205" 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">
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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<td class="diff-line-num old old_line" data-linenumber="207" 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">
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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<td class="diff-line-num old old_line" data-linenumber="209" 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">
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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<td class="diff-line-num old old_line" data-linenumber="210" 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">
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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<td class="diff-line-num old old_line" data-linenumber="211" 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">
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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<td class="diff-line-num old old_line" data-linenumber="212" 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">
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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<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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220
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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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229
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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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231
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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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<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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<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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<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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259
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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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260
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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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<td class="diff-line-num old old_line" data-linenumber="262" 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">
262
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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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<td class="diff-line-num old old_line" data-linenumber="265" 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">
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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<td class="diff-line-num old old_line" data-linenumber="266" 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">
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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<td class="diff-line-num old old_line" data-linenumber="273" 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">
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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<td class="diff-line-num old old_line" data-linenumber="275" 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">
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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<td class="diff-line-num old old_line" data-linenumber="276" 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">
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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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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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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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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<td class="diff-line-num old old_line" data-linenumber="283" 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">
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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<td class="diff-line-num old old_line" data-linenumber="285" 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">
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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<td class="diff-line-num old old_line" data-linenumber="294" 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">
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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<td class="diff-line-num old old_line" data-linenumber="295" 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">
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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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <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;">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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<td class="diff-line-num old old_line" data-linenumber="304" 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">
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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<td class="diff-line-num old old_line" data-linenumber="305" 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">
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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<td class="diff-line-num old old_line" data-linenumber="307" 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">
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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<td class="diff-line-num old old_line" data-linenumber="313" 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">
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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<td class="diff-line-num old old_line" data-linenumber="314" 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">
314
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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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<td class="diff-line-num old old_line" data-linenumber="315" 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">
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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<td class="diff-line-num old old_line" data-linenumber="316" 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">
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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<td class="diff-line-num old old_line" data-linenumber="317" 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">
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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<td class="diff-line-num old old_line" data-linenumber="319" 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">
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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<td class="diff-line-num old old_line" data-linenumber="320" 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">
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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<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>
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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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<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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327
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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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328
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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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329
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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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334
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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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<td class="diff-line-num old old_line" data-linenumber="339" 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">
339
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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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<td class="diff-line-num old old_line" data-linenumber="340" 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">
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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341
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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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<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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360
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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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<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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<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="LC371" class="line" lang="cpp"></span>
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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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<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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<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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<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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<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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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"></span>
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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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390
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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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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"> <span class="p">}</span></span>
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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="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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394
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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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395
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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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396
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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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399
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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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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="cpp"> <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;">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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406
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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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<td class="diff-line-num old old_line" data-linenumber="408" 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">
408
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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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<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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<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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<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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<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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416
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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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417
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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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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;">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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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <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>
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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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491
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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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<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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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp"> <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="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;">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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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;">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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592
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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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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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<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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600
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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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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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<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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669
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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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<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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<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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793
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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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<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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<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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<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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<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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<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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850
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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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851
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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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852
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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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853
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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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854
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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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855
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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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<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="LC856" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (errmsg == "empty") {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="857" 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">
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>
</pre>
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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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863
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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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<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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<pre style="margin: 0;">-<span id="LC865" 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="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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<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="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>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="869" 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">
869
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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="LC869" 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="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>
</pre>
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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>
</pre>
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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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<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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<pre style="margin: 0;">-<span id="LC874" 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="LC875" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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876
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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>
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877
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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>
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878
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<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>
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879
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<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>
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880
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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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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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<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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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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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>
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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>
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903
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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>
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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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<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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<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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<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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<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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<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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<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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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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<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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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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929
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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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930
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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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<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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<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="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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<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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977
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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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<td class="diff-line-num old old_line" data-linenumber="978" 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">
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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987
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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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988
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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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989
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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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990
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="cpp"><span class="p">}</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="cpp"></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="cpp"></span>
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993
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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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994
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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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995
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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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997
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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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1002
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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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<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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<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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<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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<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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<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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<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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1048
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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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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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<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/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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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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<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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<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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<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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<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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<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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<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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<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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<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;">ReInitPattern</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;">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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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;">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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79
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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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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;">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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87
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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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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"></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;">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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<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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95
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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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<td class="diff-line-num old old_line" data-linenumber="97" 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">
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;">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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99
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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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100
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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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101
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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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<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/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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24
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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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25
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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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"></span>
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28
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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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29
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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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30
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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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32
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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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33
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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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34
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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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35
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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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<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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41
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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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42
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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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43
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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="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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<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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<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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<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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<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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<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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<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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<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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69
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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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71
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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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72
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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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<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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<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;"> * 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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<td class="diff-line-num new new_line" data-linenumber="94" 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">
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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96
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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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<td class="diff-line-num new new_line" data-linenumber="97" 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">
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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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"></span>
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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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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></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;">/*---Initialization----------------------------------------------------------*/</span></span>
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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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<td class="diff-line-num new new_line" data-linenumber="137" 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">
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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<td class="diff-line-num new new_line" data-linenumber="146" 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">
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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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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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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<td class="diff-line-num new new_line" data-linenumber="153" 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">
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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<td class="diff-line-num new new_line" data-linenumber="155" 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">
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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<td class="diff-line-num new new_line" data-linenumber="156" 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">
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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<td class="diff-line-num new new_line" data-linenumber="157" 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">
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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<td class="diff-line-num new new_line" data-linenumber="158" 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">
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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<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="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> </span>
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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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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"><span class="p">}</span></span>
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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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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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<td class="diff-line-num new new_line" data-linenumber="206" 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">
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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<td class="diff-line-num new new_line" data-linenumber="207" 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">
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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<td class="diff-line-num new new_line" data-linenumber="208" 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">
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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<td class="diff-line-num new new_line" data-linenumber="210" 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">
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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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"></span>
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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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<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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<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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<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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<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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<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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<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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250
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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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251
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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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252
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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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253
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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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<td class="diff-line-num new new_line" data-linenumber="274" 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">
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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<td class="diff-line-num new new_line" data-linenumber="275" 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">
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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<td class="diff-line-num new new_line" data-linenumber="277" 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">
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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<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="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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<td class="diff-line-num new new_line" data-linenumber="282" 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">
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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<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;">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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289
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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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<td class="diff-line-num new new_line" data-linenumber="290" 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">
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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<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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295
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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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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"></span>
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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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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><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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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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<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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<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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314
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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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<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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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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<td class="diff-line-num new new_line" data-linenumber="317" 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">
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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<td class="diff-line-num new new_line" data-linenumber="331" 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">
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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336
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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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338
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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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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="p">}</span></span>
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344
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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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349
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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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353
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<pre style="margin: 0;">+<span id="LC353" 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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">patterns</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"><span class="p">}</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;">/**</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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<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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<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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<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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<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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<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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<td class="diff-line-num new new_line" data-linenumber="377" 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">
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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<td class="diff-line-num new new_line" data-linenumber="378" 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">
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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<td class="diff-line-num new new_line" data-linenumber="379" 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">
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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380
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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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<td class="diff-line-num new new_line" data-linenumber="383" 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">
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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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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<td class="diff-line-num new new_line" data-linenumber="391" 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">
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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<td class="diff-line-num new new_line" data-linenumber="398" 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">
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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<td class="diff-line-num new new_line" data-linenumber="399" 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">
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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<td class="diff-line-num new new_line" data-linenumber="401" 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">
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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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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<td class="diff-line-num new new_line" data-linenumber="412" 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">
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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<td class="diff-line-num new new_line" data-linenumber="413" 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">
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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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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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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423
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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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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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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <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;">return</span> <span class="n" style="color: #333;">read_error</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="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="LC442" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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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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<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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489
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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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492
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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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493
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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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494
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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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495
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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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496
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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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501
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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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505
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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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506
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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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509
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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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510
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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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<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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<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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<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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<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="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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<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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<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="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="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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<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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<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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<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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<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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<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="p">}</span></span>
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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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<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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611
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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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613
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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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614
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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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615
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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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616
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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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617
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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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620
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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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621
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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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<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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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<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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<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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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <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;">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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<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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<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="LC645" 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 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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<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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<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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<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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662
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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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663
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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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678
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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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<td class="diff-line-num new new_line" data-linenumber="703" 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">
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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<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="cm" style="color: #998; font-style: italic;">/**</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;"> * Estimates the number of matches ('1') in a std::vector<char>.</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;"> *</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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738
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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="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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773
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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="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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<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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792
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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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796
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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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805
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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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806
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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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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="cpp"><span class="p">}</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="cpp"></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="cpp"></span>
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810
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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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<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="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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<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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<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="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;">/**</span></span>
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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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<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="LC855" class="line" lang="cpp"></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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860
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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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862
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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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863
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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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874
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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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875
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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="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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<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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<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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923
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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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924
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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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926
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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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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"><span class="p">}</span></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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967
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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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968
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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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969
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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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970
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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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<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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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"></span>
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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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<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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987
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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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988
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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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1016
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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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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;"> *@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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1053
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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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<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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1067
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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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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"></span>
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1071
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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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1073
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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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1074
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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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1076
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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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1077
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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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1080
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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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<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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<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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<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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<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/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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<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 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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<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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<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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<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="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;">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="LC45" class="line" lang="c"></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="LC48" class="line" lang="c"></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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50
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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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51
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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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52
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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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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;">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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<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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<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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<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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<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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71
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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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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;">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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77
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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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86
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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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87
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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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"></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;">private</span><span class="o" style="font-weight: 600;">:</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;">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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<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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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"><span class="p">};</span></span>
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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">@@ -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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<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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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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<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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<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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<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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<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/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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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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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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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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<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 "variance.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 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="LC26" 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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<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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<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="LC44" 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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59
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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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60
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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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61
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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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<td class="diff-line-num new new_line" data-linenumber="63" 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">
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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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"></span>
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68
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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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71
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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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73
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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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74
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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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75
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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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76
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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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78
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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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79
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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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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;"> * @param seq_leng Length of sequences in database, used for variance.</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 p Match probability ( = #matches / #positions), used for sensitivity and variance.</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 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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87
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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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<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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<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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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;"> * @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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105
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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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<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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<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>
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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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<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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<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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<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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147
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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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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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<td class="diff-line-num new new_line" data-linenumber="166" 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">
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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<td class="diff-line-num new new_line" data-linenumber="169" 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">
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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<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">
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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<td class="diff-line-num new new_line" data-linenumber="171" 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">
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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<td class="diff-line-num new new_line" data-linenumber="174" 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">
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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<td class="diff-line-num new new_line" data-linenumber="177" 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">
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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<td class="diff-line-num new new_line" data-linenumber="190" 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">
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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<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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<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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218
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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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228
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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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234
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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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<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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256
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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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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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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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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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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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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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<td class="diff-line-num new new_line" data-linenumber="277" 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">
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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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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<td class="diff-line-num new new_line" data-linenumber="280" 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">
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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<td class="diff-line-num new new_line" data-linenumber="282" 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">
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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<td class="diff-line-num new new_line" data-linenumber="284" 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">
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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<td class="diff-line-num new new_line" data-linenumber="290" 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">
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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<td class="diff-line-num new new_line" data-linenumber="291" 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">
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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<td class="diff-line-num new new_line" data-linenumber="292" 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">
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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<td class="diff-line-num new new_line" data-linenumber="293" 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">
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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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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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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296
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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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298
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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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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"></span>
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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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<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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327
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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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328
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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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329
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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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333
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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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<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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<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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<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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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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360
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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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362
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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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<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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<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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<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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<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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<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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385
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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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386
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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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387
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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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391
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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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<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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405
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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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420
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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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<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;">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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425
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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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<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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<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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442
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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="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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484
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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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489
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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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<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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512
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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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<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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528
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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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531
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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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543
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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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544
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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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547
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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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<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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<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="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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<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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<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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<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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<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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<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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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="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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<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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<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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655
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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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656
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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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657
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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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669
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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="LC672" class="line" lang="cpp"></span>
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673
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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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<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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<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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<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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<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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<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="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="LC749" class="line" lang="cpp"><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="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="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="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="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="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;"> * 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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<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="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="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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<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="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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<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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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"><span class="p">}</span></span>
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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/commit/3f1306ad27fb01b15f16c1945979230b25c99725#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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<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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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"></span>
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57
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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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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;">GetWeight</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;">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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<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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<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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<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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<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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<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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<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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<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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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>
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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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<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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<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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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="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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105
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<pre style="margin: 0;">+<span id="LC105" 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;">outFile</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>
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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;">isInFile</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;">isOutFile</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;">bitmode</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="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">random_leng</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="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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113
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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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114
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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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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">best_silent</span><span class="p">;</span></span>
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116
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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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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"><span class="p">};</span></span>
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119
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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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<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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<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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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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<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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<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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94
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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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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"><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>
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97
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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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98
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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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99
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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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100
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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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103
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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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<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="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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<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="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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<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="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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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"></span>
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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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<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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<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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<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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<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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<td class="diff-line-num old old_line" data-linenumber="128" 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">
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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<td class="diff-line-num old old_line" data-linenumber="129" 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">
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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<td class="diff-line-num old old_line" data-linenumber="130" 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">
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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<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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<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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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp"></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;">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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138
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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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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>
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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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<td class="diff-line-num old old_line" data-linenumber="154" 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">
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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<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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160
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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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<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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<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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<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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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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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;"> * 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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<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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<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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206
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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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209
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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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210
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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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211
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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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214
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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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215
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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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218
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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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<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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296
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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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310
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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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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"></span>
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313
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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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314
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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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315
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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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324
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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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325
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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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326
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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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<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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<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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<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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<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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379
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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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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="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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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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394
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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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<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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<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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<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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402
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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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404
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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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411
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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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412
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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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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;">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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416
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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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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<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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<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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517
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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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520
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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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<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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<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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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="cpp"><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="cm" style="color: #998; font-style: italic;">/**</span></span>
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575
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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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576
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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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577
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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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<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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<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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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="cpp"></span>
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584
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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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585
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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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586
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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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587
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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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588
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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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590
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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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591
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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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<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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617
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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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618
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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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620
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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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621
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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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622
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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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625
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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="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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<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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<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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<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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<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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743
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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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<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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<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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<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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<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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<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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<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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<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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<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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<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;"> * 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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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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25
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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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<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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35
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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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37
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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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<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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<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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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"></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;">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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<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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<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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<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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<td class="diff-line-num old old_line" data-linenumber="63" 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="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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<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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<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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<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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<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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<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;">Gauss</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;">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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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"></span>
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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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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="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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90
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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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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="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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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="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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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;">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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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;">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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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;">int</span> <span class="n" style="color: #333;">l_hom</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;">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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104
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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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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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<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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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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