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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/6797dabf86368630166600b16a2e079241626932">6797dabf</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-12-23T12:12:40+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1169</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
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<li class="file-stats">
<a href="#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">
scripts/last-train
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<li class="file-stats">
<a href="#5f9dbaf068df9da9d036ea6546a588a0c71778be">
src/LastEvaluer.cc
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<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/6797dabf86368630166600b16a2e079241626932#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-12-23 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * scripts/last-train, src/LastEvaluer.cc:</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"> Try to fix floating-point infinite loops</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [829c63f50494] [tip]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">2020-12-15 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * src/Alignment.cc, src/lastal.cc, test/last-test.out, test/last-</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> test.sh:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> New frameshifts: fix print precision of score</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [abed5cbf2f29]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [abed5cbf2f29]</span>
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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">2020-12-11 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<li id="37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/6797dabf86368630166600b16a2e079241626932#37ef3bfb2f847a5a03a3da6d653afee2ea7e05b0"><strong>scripts/last-train</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" 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">@@ -29,24 +29,24 @@ def myOpen(fileName): # faster than fileinput</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rootOfIncreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find x such that func(x, *args) == 0</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lowerBound</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">mid</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="p">(</span><span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">upperBound</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">upperBound</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">0.5</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gap</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</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="LC39" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rootOfDecreasingFunction</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find x such that func(x, *args) == 0</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lowerBound</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">mid</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="p">(</span><span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">upperBound</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">upperBound</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">gap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">0.5</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gap</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</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="LC48" class="line" lang="python"> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</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="LC50" class="line" lang="python"> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">homogeneousLetterFreqs</span><span class="p">(</span><span class="n" style="color: #333;">scale</span><span class="p">,</span> <span class="n" style="color: #333;">matScores</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/6797dabf86368630166600b16a2e079241626932#5f9dbaf068df9da9d036ea6546a588a0c71778be"><strong>src/LastEvaluer.cc</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">@@ -476,14 +476,13 @@ double LastEvaluer::minScore(double queryLettersPerRandomAlignment) const {</td>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sls</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ALP_set_of_parameters</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">parameters</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;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryLettersPerRandomAlignment</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">databaseSeqNum</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;">beg</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="LC479" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">end</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">databaseSeqLen</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;">K</span><span class="p">)</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;">lambda</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;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">len</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">databaseSeqLen</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;">K</span><span class="p">)</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;">lambda</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;">while</span> <span class="p">(</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="LC482" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</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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483
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mid</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evalue</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">huge</span><span class="p">,</span> <span class="n" style="color: #333;">databaseSeqLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">huge</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">x</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;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">len</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="LC483" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mid</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">beg</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mid</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;">evaluer</span><span class="p">.</span><span class="n" style="color: #333;">evalue</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">huge</span><span class="p">,</span> <span class="n" style="color: #333;">databaseSeqLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">huge</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">x</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;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mid</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="cpp"> <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="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"116<span class="idiff left right">8</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"116<span class="idiff left right">9</span>"</span></span></pre>
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