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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/king-probe">Debian Med / king-probe</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/457acc77f4f47084c2a741b69ddda0072f4793d7">457acc77</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.16.160404+git20200121.9b198c1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/ca579180dd0044718311706d298b5b1b4dc953aa">ca579180</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/9cf78952a17a4316bf35c2ecf796782e1e04c531">9cf78952</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.16.160404+git20200121.9b198c1'
Update to upstream version '2.16.160404+git20200121.9b198c1'
with Debian dir 05e0a5537a7791043e48f78b7261d59f2ca85ab0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/c299c086e08025ef81d34a2ee4c76b728745f335">c299c086</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/9d777c50574ecef850187d0296c0f2b9873d2851">9d777c50</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/def79bc2a46bc7c964e852aa327c4fd07cb247d6">def79bc2</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/b9d0850000815a0e41a27c266842522d4cbbfca2">b9d08500</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/f2b534f67ecb4e7dc52c6eb8466ae873db0ac7f7">f2b534f6</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:23:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/e45c8834f505cd3bf79348f4402614381d2dcd94">e45c8834</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:24:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/king-probe/-/commit/1c1e8e73a50bc0ab8e80f1724690744c2440abbf">1c1e8e73</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-23T17:24:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<li class="file-stats">
<a href="#ddb51601a1b55dd84e88f3b82e51c0d2d82c0387">
readPDBrecs.c
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">king-probe (2.16.160404+git20200121.9b198c1-1) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debhelper-compat 12 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Secure URI in copyright format (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit.</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sat, 23 May 2020 17:24:01 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">king-probe (2.16.160404+git20180613.a09b012-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Use git mode in watch file</span>
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<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,11 +5,12 @@ Uploaders: Malihe Asemani <ml.asemani@gmail.com>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Michael Prisant <michael.prisant@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>)</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.5</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/king-probe</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/king-probe.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://kinemage.biochem.duke.edu/software/probe.php</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: king-probe</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: probe</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/rlabduke/probe/</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/rlabduke/probe/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/rlabduke/probe/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Reference:</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Author: ></span>
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3
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> J. Michael Word and Simon C. Lovell and Thomas H. LaBean and</span>
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<a href="https://salsa.debian.org/med-team/king-probe/-/compare/44f543a410ef06e2cec818c7356b8d97d28a5324...1c1e8e73a50bc0ab8e80f1724690744c2440abbf#ddb51601a1b55dd84e88f3b82e51c0d2d82c0387"><strong>readPDBrecs.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,6 +44,8 @@ int readRecord(FILE *inf, char buffer[], int maxChars) {</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</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="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">register</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">done</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="LC46" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">makeUpperCase</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="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">setCase</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="LC48" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">linecard</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <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;">inf</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">feof</span><span class="p">(</span><span class="n" style="color: #333;">inf</span><span class="p">))</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;">count</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 class="cm" style="color: #998; font-style: italic;">/* signal end-of-file */</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">@@ -52,15 +54,46 @@ int readRecord(FILE *inf, char buffer[], int maxChars) {</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <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;">done</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getc</span><span class="p">(</span><span class="n" style="color: #333;">inf</span><span class="p">);</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ch</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="LC56" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* special codes turn off forced uppercase */</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* "at sign" used for commands */</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* "hash" used for comments */</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">makeUpperCase</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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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">makeUpperCase</span><span class="p">)</span> <span class="p">{</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// This block added by cjw, 01-21-2020</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forces uppercase on record type, resname, and atomname fields</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Preserves existing case for all other fields, assumes internal file</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// consistency.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</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="LC62" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//set 6-char line identifier (REMARK, ATOM) to uppercase</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//build short record type from first 4 chars</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">linecard</span><span class="p">[</span><span class="n" style="color: #333;">count</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ch</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="p">}</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="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;">count</span> <span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">4</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;">linecard</span><span class="p">[</span><span class="n" style="color: #333;">count</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 class="c1" style="color: #998; font-style: italic;">//finish linecard string</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//setCase if line is applicable record</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">linecard</span><span class="p">,</span> <span class="s" style="color: #d14;">"ATOM"</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">linecard</span><span class="p">,</span> <span class="s" style="color: #d14;">"HETA"</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">linecard</span><span class="p">,</span> <span class="s" style="color: #d14;">"TER"</span><span class="p">,</span> <span class="mi" style="color: #099;">3</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="LC72" class="line" lang="c"> <span class="n" style="color: #333;">setCase</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="LC73" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//0123456789*123456789*123456789*123456789*123456789*123456789*123456789*1234567</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//ATOM 1568 CE2 TYR B 90 0.565 40.044 57.767 1.00 16.94 C</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <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;">setCase</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">16</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fix case for atom (12-15) and resname (17-19)</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;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">ch</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 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>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// This block removed by cjw, 12-09-2019</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// It appears to convert PDB lines to all-uppercase on read-in</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Some large files use lowercase chain IDs, which *must* be preserved</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Be warned that its removal allows past unsupported lower case chars in</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// atomnames, etc</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if ((ch == '@') || (ch == '#')) {</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// /* special codes turn off forced uppercase */</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// /* "at sign" used for commands */</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// /* "hash" used for comments */</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// makeUpperCase = 0;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if (makeUpperCase) {</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// ch = toupper(ch);</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EOF</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="n" style="color: #333;">done</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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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="p">}</span></span>
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