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| 2783 | </dd> | 2783 | </dd> |
| 2784 | <dt><a·href="jebl/evolution/coalescent/Intervals.html#getSampleCount()"·class="member-name-link">getSampleCount()</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/Intervals.html"·title="class·in·jebl.evolution.coalescent">Intervals</a></dt> | 2784 | <dt><a·href="jebl/evolution/coalescent/Intervals.html#getSampleCount()"·class="member-name-link">getSampleCount()</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/Intervals.html"·title="class·in·jebl.evolution.coalescent">Intervals</a></dt> |
| 2785 | <dd> </dd> | 2785 | <dd> </dd> |
| 2786 | <dt><a·href="jebl/evolution/align/Align.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 2786 | <dt><a·href="jebl/evolution/align/Align.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 2787 | <dd> </dd> | 2787 | <dd> </dd> |
| 2788 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> | 2788 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> |
| 2789 | <dd> </dd> | 2789 | <dd> </dd> |
| 2790 | <dt><a·href="jebl/evolution/align/ | 2790 | <dt><a·href="jebl/evolution/align/SmithWaterman.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWaterman.html"·title="class·in·jebl.evolution.align">SmithWaterman</a></dt> |
| 2791 | <dd> </dd> | 2791 | <dd> </dd> |
| 2792 | <dt><a·href="jebl/evolution/align/BartonSternberg.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/BartonSternberg.html"·title="class·in·jebl.evolution.align">BartonSternberg</a></dt> | 2792 | <dt><a·href="jebl/evolution/align/BartonSternberg.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/BartonSternberg.html"·title="class·in·jebl.evolution.align">BartonSternberg</a></dt> |
| 2793 | <dd> </dd> | 2793 | <dd> </dd> |
| 2794 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolution.align">NeedlemanWunsch</a></dt> | 2794 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolution.align">NeedlemanWunsch</a></dt> |
| 2795 | <dd> </dd> | 2795 | <dd> </dd> |
| 2796 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 2796 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> |
| 2797 | <dd> </dd> | 2797 | <dd> </dd> |
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| 4236 | <dd> </dd> | 4236 | <dd> </dd> |
| 4237 | <dt><a·href="jebl/evolution/io/ImportHelper.html#next()"·class="member-name-link">next()</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> | 4237 | <dt><a·href="jebl/evolution/io/ImportHelper.html#next()"·class="member-name-link">next()</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> |
| 4238 | <dd> </dd> | 4238 | <dd> </dd> |
| 4239 | <dt><a·href="jebl/evolution/align/Align.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 4239 | <dt><a·href="jebl/evolution/align/Align.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 4240 | <dd> | 4240 | <dd> |
| 4241 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4241 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4242 | </dd> | 4242 | </dd> |
| 4243 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">Needle | 4243 | <dt><a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html"·title="class·in·jebl.evolution.align">Need[·...·truncated·by·diffoscope;·len:·22,·SHA:·639928178c9a2ce3cfb55b371ee860ad5f0d11279c70b6a016db6bdcf948fd4a·...·]Affine</a></dt> |
| 4244 | <dd> | 4244 | <dd> |
| 4245 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4245 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4246 | </dd> | 4246 | </dd> |
| 4247 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 4247 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 4248 | <dd> | 4248 | <dd> |
| 4249 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4249 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4250 | </dd> | 4250 | </dd> |
| 4251 | <dt><a·href="jebl/evolution/align/ | 4251 | <dt><a·href="jebl/evolution/align/SmithWaterman.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWaterman.html"·title="class·in·jebl.evolution.align">SmithWaterman</a></dt> |
| 4252 | <dd> | 4252 | <dd> |
| 4253 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4253 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4254 | </dd> | 4254 | </dd> |
| 4255 | <dt><a·href="jebl/evolution/align/MaximalSegmentPair.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/MaximalSegmentPair.html"·title="class·in·jebl.evolution.align">MaximalSegmentPair</a></dt> | 4255 | <dt><a·href="jebl/evolution/align/MaximalSegmentPair.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/MaximalSegmentPair.html"·title="class·in·jebl.evolution.align">MaximalSegmentPair</a></dt> |
| 4256 | <dd> </dd> | 4256 | <dd> </dd> |
| 4257 | <dt><a·href="jebl/math/Random.html#nextBoolean()"·class="member-name-link">nextBoolean()</a>·-·Static·method·in·class·jebl.math.<a·href="jebl/math/Random.html"·title="class·in·jebl.math">Random</a></dt> | 4257 | <dt><a·href="jebl/math/Random.html#nextBoolean()"·class="member-name-link">nextBoolean()</a>·-·Static·method·in·class·jebl.math.<a·href="jebl/math/Random.html"·title="class·in·jebl.math">Random</a></dt> |
| 4258 | <dd> | 4258 | <dd> |
| Offset 4685, 47 lines modified | Offset 4685, 47 lines modified | ||
| 4685 | <dd> </dd> | 4685 | <dd> </dd> |
| 4686 | <dt><a·href="jebl/evolution/align/Align.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 4686 | <dt><a·href="jebl/evolution/align/Align.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 4687 | <dd> | 4687 | <dd> |
| 4688 | <div·class="block">Initialises·the·matrices·for·the·alignment.</div> | 4688 | <div·class="block">Initialises·the·matrices·for·the·alignment.</div> |
| 4689 | </dd> | 4689 | </dd> |
| 4690 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> | 4690 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> |
| 4691 | <dd> </dd> | 4691 | <dd> </dd> |
| 4692 | <dt><a·href="jebl/evolution/align/ | 4692 | <dt><a·href="jebl/evolution/align/NeedlemanWunschLinearSpace.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschLinearSpace.html"·title="[·...·truncated·by·diffoscope;·len:·46,·SHA:·50339b6c0ae7c09128e7a2e6fc6ea66e2b4eddc3636a7cb51b230ba0e75954c6·...·]LinearSpace</a></dt> |
| 4693 | <dd> </dd> | 4693 | <dd> </dd> |
| 4694 | <dt><a·href="jebl/evolution/align/ | 4694 | <dt><a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.h[·...·truncated·by·diffoscope;·len:·58,·SHA:·e8bc370fc996737381bc586f8ca4b235dfb6ec9aa3363f1ff53d262501ee4c75·...·]LinearSpaceAffine</a></dt> |
| 4695 | <dd> </dd> | 4695 | <dd> </dd> |
| 4696 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 4696 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 4697 | <dd> </dd> | 4697 | <dd> </dd> |
| 4698 | <dt><a·href="jebl/evolution/align/ | 4698 | <dt><a·href="jebl/evolution/align/SmithWaterman.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWaterman.html"·title="class·in·jebl.evolution.al[·...·truncated·by·diffoscope;·len:·18,·SHA:·de110c75e33a185ce86bd61bad810ee102c278559039263ab19a7eaf4a2f45d1·...·]</a></dt> |
| 4699 | <dd> </dd> | 4699 | <dd> </dd> |
| 4700 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 4700 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> |
| 4701 | <dd> </dd> | 4701 | <dd> </dd> |
| 4702 | <dt><a·href="jebl/evolution/align/ProfileCharacter.html#print()"·class="member-name-link">print()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/ProfileCharacter.html"·title="class·in·jebl.evolution.align">ProfileCharacter</a></dt> | 4702 | <dt><a·href="jebl/evolution/align/ProfileCharacter.html#print()"·class="member-name-link">print()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/ProfileCharacter.html"·title="class·in·jebl.evolution.align">ProfileCharacter</a></dt> |
| 4703 | <dd> </dd> | 4703 | <dd> </dd> |
| 4704 | <dt><a·href="jebl/evolution/align/Output.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Output.html"·title="class·in·jebl.evolution.align">Output</a></dt> | 4704 | <dt><a·href="jebl/evolution/align/Output.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Output.html"·title="class·in·jebl.evolution.align">Output</a></dt> |
| 4705 | <dd> </dd> | 4705 | <dd> </dd> |
| 4706 | <dt><a·href="jebl/evolution/align/SystemOut.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SystemOut.html"·title="class·in·jebl.evolution.align">SystemOut</a></dt> | 4706 | <dt><a·href="jebl/evolution/align/SystemOut.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SystemOut.html"·title="class·in·jebl.evolution.align">SystemOut</a></dt> |
| 4707 | <dd> </dd> | 4707 | <dd> </dd> |
| 4708 | <dt><a·href="jebl/evolution/align/Align.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 4708 | <dt><a·href="jebl/evolution/align/Align.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 4709 | <dd> | 4709 | <dd> |
| 4710 | <div·class="block">Print·the·matrix·(matrices)·used·to·compute·the·alignment</div> | 4710 | <div·class="block">Print·the·matrix·(matrices)·used·to·compute·the·alignment</div> |
| 4711 | </dd> | 4711 | </dd> |
| 4712 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 4712 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> |
| 4713 | <dd> | 4713 | <dd> |
| 4714 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4714 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4715 | </dd> | 4715 | </dd> |
| 4716 | <dt><a·href="jebl/evolution/align/ | 4716 | <dt><a·href="jebl/evolution/align/NeedlemanWunschLinearSpace.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschLinearSpace.html"·title="class·in·jebl.evolution.align">Nee[·...·truncated·by·diffoscope;·len:·12,·SHA:·8ca2d23b5f6cec2df64763fa034216a01b0c34909a1dcbda3fbbd447b8a68e54·...·]LinearSpace</a></dt> |
| 4717 | <dd> | 4717 | <dd> |
| 4718 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4718 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4719 | </dd> | 4719 | </dd> |
| 4720 | <dt><a·href="jebl/evolution/align/ | 4720 | <dt><a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html"·title="class·in·jebl.evolutio[·...·truncated·by·diffoscope;·len:·24,·SHA:·27521478537c1d29e09a2c0bed98a973c44646c90e8158def70ca9ff12656dff·...·]LinearSpaceAffine</a></dt> |
| 4721 | <dd> | 4721 | <dd> |
| 4722 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4722 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4723 | </dd> | 4723 | </dd> |
| 4724 | <dt><a·href="jebl/evolution/align/ | 4724 | <dt><a·href="jebl/evolution/align/SmithWaterman.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWaterman.html"·title="class·in·jebl.evolution.align">SmithWaterman</a></dt> |
| 4725 | <dd> | 4725 | <dd> |
| 4726 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4726 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4727 | </dd> | 4727 | </dd> |
| 4728 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 4728 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 4729 | <dd> | 4729 | <dd> |
| 4730 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4730 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4731 | </dd> | 4731 | </dd> |
| Offset 5263, 15 lines modified | Offset 5263, 15 lines modified | ||
| 5263 | </dd> | 5263 | </dd> |
| 5264 | <dt><a·href="jebl/evolution/trees/SimpleTree.html#setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)"·class="member-name-link">setEdgeLength(Node,·Node,·double)</a>·-·Method·in·class·jebl.evolution.trees.<a·href="jebl/evolution/trees/SimpleTree.html"·title="class·in·jebl.evolution.trees">SimpleTree</a></dt> | 5264 | <dt><a·href="jebl/evolution/trees/SimpleTree.html#setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)"·class="member-name-link">setEdgeLength(Node,·Node,·double)</a>·-·Method·in·class·jebl.evolution.trees.<a·href="jebl/evolution/trees/SimpleTree.html"·title="class·in·jebl.evolution.trees">SimpleTree</a></dt> |
| 5265 | <dd> | 5265 | <dd> |
| 5266 | <div·class="block">Set·edge·distance·between·two·adjacent·nodes.</div> | 5266 | <div·class="block">Set·edge·distance·between·two·adjacent·nodes.</div> |
| 5267 | </dd> | 5267 | </dd> |
| 5268 | <dt><a·href="jebl/evolution/io/ImportHelper.html#setExpectedInputLength(long)"·class="member-name-link">setExpectedInputLength(long)</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> | 5268 | <dt><a·href="jebl/evolution/io/ImportHelper.html#setExpectedInputLength(long)"·class="member-name-link">setExpectedInputLength(long)</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> |
| 5269 | <dd> </dd> | 5269 | <dd> </dd> |
| 5270 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 5270 | <dt><a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschLinearSpaceAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschLi[·...·truncated·by·diffoscope;·len:·9,·SHA:·c60f71378350abca0af679825242be0bbadddc299e3becdadf451186e512831b·...·]Affine</a></dt> |
| 5271 | <dd> </dd> | 5271 | <dd> </dd> |
| 5272 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 5272 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 5273 | <dd> </dd> | 5273 | <dd> </dd> |
| 5274 | <dt><a·href="jebl/evolution/align/Align.html#setGapOpen(float)"·class="member-name-link">setGapOpen(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 5274 | <dt><a·href="jebl/evolution/align/Align.html#setGapOpen(float)"·class="member-name-link">setGapOpen(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 5275 | <dd> </dd> | 5275 | <dd> </dd> |
| 5276 | <dt><a·href="jebl/evolution/coalescent/ExponentialGrowth.html#setGrowthRate(double)"·class="member-name-link">setGrowthRate(double)</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/ExponentialGrowth.html"·title="class·in·jebl.evolution.coalescent">ExponentialGrowth</a></dt> | 5276 | <dt><a·href="jebl/evolution/coalescent/ExponentialGrowth.html#setGrowthRate(double)"·class="member-name-link">setGrowthRate(double)</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/ExponentialGrowth.html"·title="class·in·jebl.evolution.coalescent">ExponentialGrowth</a></dt> |
| 5277 | <dd> | 5277 | <dd> |
| Offset 2502, 15 lines modified | Offset 2502, 15 lines modified | ||
| 2502 | ······get·the·total·number·of·sampling·events. | 2502 | ······get·the·total·number·of·sampling·events. |
| 2503 | ··_\x8g_\x8e_\x8t_\x8S_\x8a_\x8m_\x8p_\x8l_\x8e_\x8C_\x8o_\x8u_\x8n_\x8t_\x8(_\x8)·-·Method·in·class·jebl.evolution.coalescent._\x8I_\x8n_\x8t_\x8e_\x8r_\x8v_\x8a_\x8l_\x8s | 2503 | ··_\x8g_\x8e_\x8t_\x8S_\x8a_\x8m_\x8p_\x8l_\x8e_\x8C_\x8o_\x8u_\x8n_\x8t_\x8(_\x8)·-·Method·in·class·jebl.evolution.coalescent._\x8I_\x8n_\x8t_\x8e_\x8r_\x8v_\x8a_\x8l_\x8s |
| 2504 | ······ | 2504 | ······ |
| 2505 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n | 2505 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n |
| 2506 | ······ | 2506 | ······ |
| 2507 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8O_\x8l_\x8d_\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 2507 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8O_\x8l_\x8d_\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 2508 | ······ | 2508 | ······ |
| 2509 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8 | 2509 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_.m_.i_.t_.h_.W_.a_.t_.e_.r_.m_.a_.n |
| 2510 | ······ | 2510 | ······ |
| 2511 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8B_\x8a_\x8r_\x8t_\x8o_\x8n_\x8S_\x8t_\x8e_\x8r_\x8n_\x8b_\x8e_\x8r_\x8g | 2511 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8B_\x8a_\x8r_\x8t_\x8o_\x8n_\x8S_\x8t_\x8e_\x8r_\x8n_\x8b_\x8e_\x8r_\x8g |
| 2512 | ······ | 2512 | ······ |
| 2513 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h | 2513 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h |
| 2514 | ······ | 2514 | ······ |
| 2515 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 2515 | ··_\x8g_\x8e_\x8t_\x8S_\x8c_\x8o_\x8r_\x8e_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 2516 | ······ | 2516 | ······ |
| Offset 3845, 20 lines modified | Offset 3845, 21 lines modified | ||
| 3845 | ··_\x8n_\x8e_\x8w_\x8T_\x8r_\x8a_\x8c_\x8e_\x8B_\x8a_\x8c_\x8k_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·interface | 3845 | ··_\x8n_\x8e_\x8w_\x8T_\x8r_\x8a_\x8c_\x8e_\x8B_\x8a_\x8c_\x8k_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·interface |
| 3846 | ··jebl.evolution.align._\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8P_\x8l_\x8o_\x8t_\x8t_\x8e_\x8r | 3846 | ··jebl.evolution.align._\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8P_\x8l_\x8o_\x8t_\x8t_\x8e_\x8r |
| 3847 | ······ | 3847 | ······ |
| 3848 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8)·-·Method·in·class·jebl.evolution.io._\x8I_\x8m_\x8p_\x8o_\x8r_\x8t_\x8H_\x8e_\x8l_\x8p_\x8e_\x8r | 3848 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8)·-·Method·in·class·jebl.evolution.io._\x8I_\x8m_\x8p_\x8o_\x8r_\x8t_\x8H_\x8e_\x8l_\x8p_\x8e_\x8r |
| 3849 | ······ | 3849 | ······ |
| 3850 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n | 3850 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n |
| 3851 | ······Get·the·next·state·in·the·traceback | 3851 | ······Get·the·next·state·in·the·traceback |
| 3852 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class | 3852 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class |
| 3853 | ··jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8L_\x8i_\x8n_\x8e_\x8a_\x8r_\x8S_\x8p_\x8a_\x8c_\x8e_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | ||
| 3853 | ······Get·the·next·state·in·the·traceback | 3854 | ······Get·the·next·state·in·the·traceback |
| 3854 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class | 3855 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class |
| 3855 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 3856 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 3856 | ······Get·the·next·state·in·the·traceback | 3857 | ······Get·the·next·state·in·the·traceback |
| 3857 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class·jebl.evolution.align._\x8 | 3858 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_.m_.i_.t_.h_.W_.a_.t_.e_.r_.m_.a_.n |
| 3858 | ······Get·the·next·state·in·the·traceback | 3859 | ······Get·the·next·state·in·the·traceback |
| 3859 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class·jebl.evolution.align._\x8M_\x8a_\x8x_\x8i_\x8m_\x8a_\x8l_\x8S_\x8e_\x8g_\x8m_\x8e_\x8n_\x8t_\x8P_\x8a_\x8i_\x8r | 3860 | ··_\x8n_\x8e_\x8x_\x8t_\x8(_\x8T_\x8r_\x8a_\x8c_\x8e_\x8b_\x8a_\x8c_\x8k_\x8)·-·Method·in·class·jebl.evolution.align._\x8M_\x8a_\x8x_\x8i_\x8m_\x8a_\x8l_\x8S_\x8e_\x8g_\x8m_\x8e_\x8n_\x8t_\x8P_\x8a_\x8i_\x8r |
| 3860 | ······ | 3861 | ······ |
| 3861 | ··_\x8n_\x8e_\x8x_\x8t_\x8B_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8(_\x8)·-·Static·method·in·class·jebl.math._\x8R_\x8a_\x8n_\x8d_\x8o_\x8m | 3862 | ··_\x8n_\x8e_\x8x_\x8t_\x8B_\x8o_\x8o_\x8l_\x8e_\x8a_\x8n_\x8(_\x8)·-·Static·method·in·class·jebl.math._\x8R_\x8a_\x8n_\x8d_\x8o_\x8m |
| 3862 | ······Access·a·default·instance·of·this·class,·access·is·synchronized | 3863 | ······Access·a·default·instance·of·this·class,·access·is·synchronized |
| 3863 | ··_\x8n_\x8e_\x8x_\x8t_\x8B_\x8y_\x8t_\x8e_\x8(_\x8)·-·Static·method·in·class·jebl.math._\x8R_\x8a_\x8n_\x8d_\x8o_\x8m | 3864 | ··_\x8n_\x8e_\x8x_\x8t_\x8B_\x8y_\x8t_\x8e_\x8(_\x8)·-·Static·method·in·class·jebl.math._\x8R_\x8a_\x8n_\x8d_\x8o_\x8m |
| 3864 | ······Access·a·default·instance·of·this·class,·access·is·synchronized | 3865 | ······Access·a·default·instance·of·this·class,·access·is·synchronized |
| Offset 4226, 45 lines modified | Offset 4227, 46 lines modified | ||
| 4226 | ······ | 4227 | ······ |
| 4227 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n | 4228 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n |
| 4228 | ······Initialises·the·matrices·for·the·alignment. | 4229 | ······Initialises·the·matrices·for·the·alignment. |
| 4229 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class | 4230 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class |
| 4230 | ··jebl.evolution.align._\x8O_\x8l_\x8d_\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 4231 | ··jebl.evolution.align._\x8O_\x8l_\x8d_\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4231 | ······ | 4232 | ······ |
| 4232 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class | 4233 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class |
| 4233 | ··jebl.evolution.align._\x8 | 4234 | ··jebl.evolution.align._\x8N_.e_.e_.d_.l_.e_.m_.a_.n_.W_.u_.n_.s_.c_.h_\x8L_\x8i_\x8n_\x8e_\x8a_\x8r_\x8S_\x8p_\x8a_\x8c_\x8e |
| 4234 | ······ | 4235 | ······ |
| 4235 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class | 4236 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class |
| 4236 | ··jebl.evolution.align._\x8 | 4237 | ··jebl.evolution.align._\x8N_.e_.e_.d_.l_.e_.m_.a_.n_.W_.u_.n_.s_.c_.h_\x8L_\x8i_\x8n_\x8e_\x8a_\x8r_\x8S_\x8p_\x8a_\x8c_\x8e_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4237 | ······ | 4238 | ······ |
| 4238 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class | 4239 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class |
| 4239 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 4240 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4240 | ······ | 4241 | ······ |
| 4241 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class | 4242 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class |
| 4242 | ··jebl.evolution.align._\x8 | 4243 | ··jebl.evolution.align._\x8S_.m_.i_.t_.h_.W_.a_.t_.e_.r_.m_.a_.n |
| 4243 | ······ | 4244 | ······ |
| 4244 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class | 4245 | ··_\x8p_\x8r_\x8e_\x8p_\x8a_\x8r_\x8e_\x8A_\x8l_\x8i_\x8g_\x8n_\x8m_\x8e_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8,_\x8·_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class |
| 4245 | ··jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 4246 | ··jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4246 | ······ | 4247 | ······ |
| 4247 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8P_\x8r_\x8o_\x8f_\x8i_\x8l_\x8e_\x8C_\x8h_\x8a_\x8r_\x8a_\x8c_\x8t_\x8e_\x8r | 4248 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8P_\x8r_\x8o_\x8f_\x8i_\x8l_\x8e_\x8C_\x8h_\x8a_\x8r_\x8a_\x8c_\x8t_\x8e_\x8r |
| 4248 | ······ | 4249 | ······ |
| 4249 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.align._\x8O_\x8u_\x8t_\x8p_\x8u_\x8t | 4250 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.align._\x8O_\x8u_\x8t_\x8p_\x8u_\x8t |
| 4250 | ······ | 4251 | ······ |
| 4251 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_\x8y_\x8s_\x8t_\x8e_\x8m_\x8O_\x8u_\x8t | 4252 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8(_\x8S_\x8t_\x8r_\x8i_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_\x8y_\x8s_\x8t_\x8e_\x8m_\x8O_\x8u_\x8t |
| 4252 | ······ | 4253 | ······ |
| 4253 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n | 4254 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n |
| 4254 | ······Print·the·matrix·(matrices)·used·to·compute·the·alignment | 4255 | ······Print·the·matrix·(matrices)·used·to·compute·the·alignment |
| 4255 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class | 4256 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class |
| 4257 | ··jebl.evolution.align._\x8O_\x8l_\x8d_\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | ||
| 4256 | ······Print·matrix·used·to·calculate·this·alignment. | 4258 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4257 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class | 4259 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class |
| 4258 | ··jebl.evolution.align._\x8 | 4260 | ··jebl.evolution.align._\x8N_.e_.e_.d_.l_.e_.m_.a_.n_.W_.u_.n_.s_.c_.h_\x8L_\x8i_\x8n_\x8e_\x8a_\x8r_\x8S_\x8p_\x8a_\x8c_\x8e |
| 4259 | ······Print·matrix·used·to·calculate·this·alignment. | 4261 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4260 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class | 4262 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class |
| 4261 | ··jebl.evolution.align._\x8 | 4263 | ··jebl.evolution.align._\x8N_.e_.e_.d_.l_.e_.m_.a_.n_.W_.u_.n_.s_.c_.h_\x8L_\x8i_\x8n_\x8e_\x8a_\x8r_\x8S_\x8p_\x8a_\x8c_\x8e_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4262 | ······Print·matrix·used·to·calculate·this·alignment. | 4264 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4263 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class·jebl.evolution.align._\x8 | 4265 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_.m_.i_.t_.h_.W_.a_.t_.e_.r_.m_.a_.n |
| 4264 | ······Print·matrix·used·to·calculate·this·alignment. | 4266 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4265 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class | 4267 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8f_\x8(_\x8O_\x8u_\x8t_\x8p_\x8u_\x8t_\x8)·-·Method·in·class |
| 4266 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 4268 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4267 | ······Print·matrix·used·to·calculate·this·alignment. | 4269 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4268 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8l_\x8n_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8O_\x8u_\x8t_\x8p_\x8u_\x8t | 4270 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8l_\x8n_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8O_\x8u_\x8t_\x8p_\x8u_\x8t |
| 4269 | ······ | 4271 | ······ |
| 4270 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8l_\x8n_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_\x8y_\x8s_\x8t_\x8e_\x8m_\x8O_\x8u_\x8t | 4272 | ··_\x8p_\x8r_\x8i_\x8n_\x8t_\x8l_\x8n_\x8(_\x8)·-·Method·in·class·jebl.evolution.align._\x8S_\x8y_\x8s_\x8t_\x8e_\x8m_\x8O_\x8u_\x8t |
| Offset 4774, 15 lines modified | Offset 4776, 15 lines modified | ||
| 4774 | ······Change·length·of·an·existing·edge. | 4776 | ······Change·length·of·an·existing·edge. |
| 4775 | ··_\x8s_\x8e_\x8t_\x8E_\x8d_\x8g_\x8e_\x8L_\x8e_\x8n_\x8g_\x8t_\x8h_\x8(_\x8N_\x8o_\x8d_\x8e_\x8,_\x8·_\x8N_\x8o_\x8d_\x8e_\x8,_\x8·_\x8d_\x8o_\x8u_\x8b_\x8l_\x8e_\x8)·-·Method·in·class | 4777 | ··_\x8s_\x8e_\x8t_\x8E_\x8d_\x8g_\x8e_\x8L_\x8e_\x8n_\x8g_\x8t_\x8h_\x8(_\x8N_\x8o_\x8d_\x8e_\x8,_\x8·_\x8N_\x8o_\x8d_\x8e_\x8,_\x8·_\x8d_\x8o_\x8u_\x8b_\x8l_\x8e_\x8)·-·Method·in·class |
| 4776 | ··jebl.evolution.trees._\x8S_\x8i_\x8m_\x8p_\x8l_\x8e_\x8T_\x8r_\x8e_\x8e | 4778 | ··jebl.evolution.trees._\x8S_\x8i_\x8m_\x8p_\x8l_\x8e_\x8T_\x8r_\x8e_\x8e |
| 4777 | ······Set·edge·distance·between·two·adjacent·nodes. | 4779 | ······Set·edge·distance·between·two·adjacent·nodes. |
| 4778 | ··_\x8s_\x8e_\x8t_\x8E_\x8x_\x8p_\x8e_\x8c_\x8t_\x8e_\x8d_\x8I_\x8n_\x8p_\x8u_\x8t_\x8L_\x8e_\x8n_\x8g_\x8t_\x8h_\x8(_\x8l_\x8o_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.io._\x8I_\x8m_\x8p_\x8o_\x8r_\x8t_\x8H_\x8e_\x8l_\x8p_\x8e_\x8r | 4780 | ··_\x8s_\x8e_\x8t_\x8E_\x8x_\x8p_\x8e_\x8c_\x8t_\x8e_\x8d_\x8I_\x8n_\x8p_\x8u_\x8t_\x8L_\x8e_\x8n_\x8g_\x8t_\x8h_\x8(_\x8l_\x8o_\x8n_\x8g_\x8)·-·Method·in·class·jebl.evolution.io._\x8I_\x8m_\x8p_\x8o_\x8r_\x8t_\x8H_\x8e_\x8l_\x8p_\x8e_\x8r |
| 4779 | ······ | 4781 | ······ |
| 4780 | ··_\x8s_\x8e_\x8t_\x8G_\x8a_\x8p_\x8E_\x8x_\x8t_\x8e_\x8n_\x8d_\x8(_\x8f_\x8l_\x8o_\x8a_\x8t_\x8)·-·Method·in·class | 4782 | ··_\x8s_\x8e_\x8t_\x8G_\x8a_\x8p_\x8E_\x8x_\x8t_\x8e_\x8n_\x8d_\x8(_\x8f_\x8l_\x8o_\x8a_\x8t_\x8)·-·Method·in·class |
| 4781 | ··jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 4783 | ··jebl.evolution.align._\x8N_\x8e_\x8e_\x8d_\x8l_\x8e_\x8m_\x8a_\x8n_\x8W_\x8u_\x8n_\x8s_\x8c_\x8h_\x8L_.i_.n_.e_.a_.r_.S_.p_.a_.c_.e_.A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4782 | ······ | 4784 | ······ |
| 4783 | ··_\x8s_\x8e_\x8t_\x8G_\x8a_\x8p_\x8E_\x8x_\x8t_\x8e_\x8n_\x8d_\x8(_\x8f_\x8l_\x8o_\x8a_\x8t_\x8)·-·Method·in·class | 4785 | ··_\x8s_\x8e_\x8t_\x8G_\x8a_\x8p_\x8E_\x8x_\x8t_\x8e_\x8n_\x8d_\x8(_\x8f_\x8l_\x8o_\x8a_\x8t_\x8)·-·Method·in·class |
| 4784 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e | 4786 | ··jebl.evolution.align._\x8N_\x8o_\x8n_\x8O_\x8v_\x8e_\x8r_\x8l_\x8a_\x8p_\x8M_\x8u_\x8l_\x8t_\x8i_\x8p_\x8l_\x8e_\x8L_\x8o_\x8c_\x8a_\x8l_\x8A_\x8f_\x8f_\x8i_\x8n_\x8e |
| 4785 | ······ | 4787 | ······ |
| 4786 | ··_\x8s_\x8e_\x8t_\x8G_\x8a_\x8p_\x8O_\x8p_\x8e_\x8n_\x8(_\x8f_\x8l_\x8o_\x8a_\x8t_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n | 4788 | ··_\x8s_\x8e_\x8t_\x8G_\x8a_\x8p_\x8O_\x8p_\x8e_\x8n_\x8(_\x8f_\x8l_\x8o_\x8a_\x8t_\x8)·-·Method·in·class·jebl.evolution.align._\x8A_\x8l_\x8i_\x8g_\x8n |
| 4787 | ······ | 4789 | ······ |
| 4788 | ··_\x8s_\x8e_\x8t_\x8G_\x8r_\x8o_\x8w_\x8t_\x8h_\x8R_\x8a_\x8t_\x8e_\x8(_\x8d_\x8o_\x8u_\x8b_\x8l_\x8e_\x8)·-·Method·in·class | 4790 | ··_\x8s_\x8e_\x8t_\x8G_\x8r_\x8o_\x8w_\x8t_\x8h_\x8R_\x8a_\x8t_\x8e_\x8(_\x8d_\x8o_\x8u_\x8b_\x8l_\x8e_\x8)·-·Method·in·class |
| Offset 4058, 15 lines modified | Offset 4058, 15 lines modified | ||
| 4058 | ····"l":·"getScore()" | 4058 | ····"l":·"getScore()" |
| 4059 | },·{ | 4059 | },·{ |
| 4060 | ····"p":·"jebl.evolution.align", | 4060 | ····"p":·"jebl.evolution.align", |
| 4061 | ····"c":·"OldNeedlemanWunschAffine", | 4061 | ····"c":·"OldNeedlemanWunschAffine", |
| 4062 | ····"l":·"getScore()" | 4062 | ····"l":·"getScore()" |
| 4063 | },·{ | 4063 | },·{ |
| 4064 | ····"p":·"jebl.evolution.align", | 4064 | ····"p":·"jebl.evolution.align", |
| 4065 | ····"c":·" | 4065 | ····"c":·"SmithWaterman", |
| 4066 | ····"l":·"getScore()" | 4066 | ····"l":·"getScore()" |
| 4067 | },·{ | 4067 | },·{ |
| 4068 | ····"p":·"jebl.evolution.align", | 4068 | ····"p":·"jebl.evolution.align", |
| 4069 | ····"c":·"BartonSternberg", | 4069 | ····"c":·"BartonSternberg", |
| 4070 | ····"l":·"getScore()" | 4070 | ····"l":·"getScore()" |
| 4071 | },·{ | 4071 | },·{ |
| 4072 | ····"p":·"jebl.evolution.align", | 4072 | ····"p":·"jebl.evolution.align", |
| Offset 6195, 25 lines modified | Offset 6195, 25 lines modified | ||
| 6195 | },·{ | 6195 | },·{ |
| 6196 | ····"p":·"jebl.evolution.align", | 6196 | ····"p":·"jebl.evolution.align", |
| 6197 | ····"c":·"Align", | 6197 | ····"c":·"Align", |
| 6198 | ····"l":·"next(Traceback)", | 6198 | ····"l":·"next(Traceback)", |
| 6199 | ····"u":·"next(jebl.evolution.align.Traceback)" | 6199 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 6200 | },·{ | 6200 | },·{ |
| 6201 | ····"p":·"jebl.evolution.align", | 6201 | ····"p":·"jebl.evolution.align", |
| 6202 | ····"c":·"NeedlemanWunschAffine", | 6202 | ····"c":·"NeedlemanWunschLinearSpaceAffine", |
| 6203 | ····"l":·"next(Traceback)", | 6203 | ····"l":·"next(Traceback)", |
| 6204 | ····"u":·"next(jebl.evolution.align.Traceback)" | 6204 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 6205 | },·{ | 6205 | },·{ |
| 6206 | ····"p":·"jebl.evolution.align", | 6206 | ····"p":·"jebl.evolution.align", |
| 6207 | ····"c":·"NonOverlapMultipleLocalAffine", | 6207 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 6208 | ····"l":·"next(Traceback)", | 6208 | ····"l":·"next(Traceback)", |
| 6209 | ····"u":·"next(jebl.evolution.align.Traceback)" | 6209 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 6210 | },·{ | 6210 | },·{ |
| 6211 | ····"p":·"jebl.evolution.align", | 6211 | ····"p":·"jebl.evolution.align", |
| 6212 | ····"c":·" | 6212 | ····"c":·"SmithWaterman", |
| 6213 | ····"l":·"next(Traceback)", | 6213 | ····"l":·"next(Traceback)", |
| 6214 | ····"u":·"next(jebl.evolution.align.Traceback)" | 6214 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 6215 | },·{ | 6215 | },·{ |
| 6216 | ····"p":·"jebl.evolution.align", | 6216 | ····"p":·"jebl.evolution.align", |
| 6217 | ····"c":·"MaximalSegmentPair", | 6217 | ····"c":·"MaximalSegmentPair", |
| 6218 | ····"l":·"next(Traceback)", | 6218 | ····"l":·"next(Traceback)", |
| 6219 | ····"u":·"next(jebl.evolution.align.Traceback)" | 6219 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| Offset 6719, 30 lines modified | Offset 6719, 30 lines modified | ||
| 6719 | },·{ | 6719 | },·{ |
| 6720 | ····"p":·"jebl.evolution.align", | 6720 | ····"p":·"jebl.evolution.align", |
| 6721 | ····"c":·"OldNeedlemanWunschAffine", | 6721 | ····"c":·"OldNeedlemanWunschAffine", |
| 6722 | ····"l":·"prepareAlignment(String,·String)", | 6722 | ····"l":·"prepareAlignment(String,·String)", |
| 6723 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6723 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6724 | },·{ | 6724 | },·{ |
| 6725 | ····"p":·"jebl.evolution.align", | 6725 | ····"p":·"jebl.evolution.align", |
| 6726 | ····"c":·" | 6726 | ····"c":·"NeedlemanWunschLinearSpace", |
| 6727 | ····"l":·"prepareAlignment(String,·String)", | 6727 | ····"l":·"prepareAlignment(String,·String)", |
| 6728 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6728 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6729 | },·{ | 6729 | },·{ |
| 6730 | ····"p":·"jebl.evolution.align", | 6730 | ····"p":·"jebl.evolution.align", |
| 6731 | ····"c":·" | 6731 | ····"c":·"NeedlemanWunschLinearSpaceAffine", |
| 6732 | ····"l":·"prepareAlignment(String,·String)", | 6732 | ····"l":·"prepareAlignment(String,·String)", |
| 6733 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6733 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6734 | },·{ | 6734 | },·{ |
| 6735 | ····"p":·"jebl.evolution.align", | 6735 | ····"p":·"jebl.evolution.align", |
| 6736 | ····"c":·"NonOverlapMultipleLocalAffine", | 6736 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 6737 | ····"l":·"prepareAlignment(String,·String)", | 6737 | ····"l":·"prepareAlignment(String,·String)", |
| 6738 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6738 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6739 | },·{ | 6739 | },·{ |
| 6740 | ····"p":·"jebl.evolution.align", | 6740 | ····"p":·"jebl.evolution.align", |
| 6741 | ····"c":·" | 6741 | ····"c":·"SmithWaterman", |
| 6742 | ····"l":·"prepareAlignment(String,·String)", | 6742 | ····"l":·"prepareAlignment(String,·String)", |
| 6743 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6743 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6744 | },·{ | 6744 | },·{ |
| 6745 | ····"p":·"jebl.evolution.align", | 6745 | ····"p":·"jebl.evolution.align", |
| 6746 | ····"c":·"NeedlemanWunschAffine", | 6746 | ····"c":·"NeedlemanWunschAffine", |
| 6747 | ····"l":·"prepareAlignment(String,·String)", | 6747 | ····"l":·"prepareAlignment(String,·String)", |
| 6748 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6748 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| Offset 6763, 30 lines modified | Offset 6763, 30 lines modified | ||
| 6763 | },·{ | 6763 | },·{ |
| 6764 | ····"p":·"jebl.evolution.align", | 6764 | ····"p":·"jebl.evolution.align", |
| 6765 | ····"c":·"Align", | 6765 | ····"c":·"Align", |
| 6766 | ····"l":·"printf(Output)", | 6766 | ····"l":·"printf(Output)", |
| 6767 | ····"u":·"printf(jebl.evolution.align.Output)" | 6767 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6768 | },·{ | 6768 | },·{ |
| 6769 | ····"p":·"jebl.evolution.align", | 6769 | ····"p":·"jebl.evolution.align", |
| 6770 | ····"c":·"NeedlemanWunschAffine", | 6770 | ····"c":·"OldNeedlemanWunschAffine", |
| 6771 | ····"l":·"printf(Output)", | 6771 | ····"l":·"printf(Output)", |
| 6772 | ····"u":·"printf(jebl.evolution.align.Output)" | 6772 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6773 | },·{ | 6773 | },·{ |
| 6774 | ····"p":·"jebl.evolution.align", | 6774 | ····"p":·"jebl.evolution.align", |
| 6775 | ····"c":·" | 6775 | ····"c":·"NeedlemanWunschLinearSpace", |
| 6776 | ····"l":·"printf(Output)", | 6776 | ····"l":·"printf(Output)", |
| 6777 | ····"u":·"printf(jebl.evolution.align.Output)" | 6777 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6778 | },·{ | 6778 | },·{ |
| 6779 | ····"p":·"jebl.evolution.align", | 6779 | ····"p":·"jebl.evolution.align", |
| 6780 | ····"c":·" | 6780 | ····"c":·"NeedlemanWunschLinearSpaceAffine", |
| 6781 | ····"l":·"printf(Output)", | 6781 | ····"l":·"printf(Output)", |
| 6782 | ····"u":·"printf(jebl.evolution.align.Output)" | 6782 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6783 | },·{ | 6783 | },·{ |
| 6784 | ····"p":·"jebl.evolution.align", | 6784 | ····"p":·"jebl.evolution.align", |
| 6785 | ····"c":·" | 6785 | ····"c":·"SmithWaterman", |
| 6786 | ····"l":·"printf(Output)", | 6786 | ····"l":·"printf(Output)", |
| 6787 | ····"u":·"printf(jebl.evolution.align.Output)" | 6787 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6788 | },·{ | 6788 | },·{ |
| 6789 | ····"p":·"jebl.evolution.align", | 6789 | ····"p":·"jebl.evolution.align", |
| 6790 | ····"c":·"NonOverlapMultipleLocalAffine", | 6790 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 6791 | ····"l":·"printf(Output)", | 6791 | ····"l":·"printf(Output)", |
| 6792 | ····"u":·"printf(jebl.evolution.align.Output)" | 6792 | ····"u":·"printf(jebl.evolution.align.Output)" |
| Offset 7566, 15 lines modified | Offset 7566, 15 lines modified | ||
| 7566 | ····"u":·"setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)" | 7566 | ····"u":·"setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)" |
| 7567 | },·{ | 7567 | },·{ |
| 7568 | ····"p":·"jebl.evolution.io", | 7568 | ····"p":·"jebl.evolution.io", |
| 7569 | ····"c":·"ImportHelper", | 7569 | ····"c":·"ImportHelper", |
| 7570 | ····"l":·"setExpectedInputLength(long)" | 7570 | ····"l":·"setExpectedInputLength(long)" |
| 7571 | },·{ | 7571 | },·{ |
| 7572 | ····"p":·"jebl.evolution.align", | 7572 | ····"p":·"jebl.evolution.align", |
| 7573 | ····"c":·"NeedlemanWunschAffine", | 7573 | ····"c":·"NeedlemanWunschLinearSpaceAffine", |
| 7574 | ····"l":·"setGapExtend(float)" | 7574 | ····"l":·"setGapExtend(float)" |
| 7575 | },·{ | 7575 | },·{ |
| 7576 | ····"p":·"jebl.evolution.align", | 7576 | ····"p":·"jebl.evolution.align", |
| 7577 | ····"c":·"NonOverlapMultipleLocalAffine", | 7577 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 7578 | ····"l":·"setGapExtend(float)" | 7578 | ····"l":·"setGapExtend(float)" |
| 7579 | },·{ | 7579 | },·{ |
| 7580 | ····"p":·"jebl.evolution.align", | 7580 | ····"p":·"jebl.evolution.align", |
| Offset 1, 13 lines modified | Offset 1, 13 lines modified | ||
| 1 | ··Streams:···········1 | 1 | ··Streams:···········1 |
| 2 | ··Blocks:············1 | 2 | ··Blocks:············1 |
| 3 | ··Compressed·size:···286.1·KiB·(2929 | 3 | ··Compressed·size:···286.1·KiB·(292960·B) |
| 4 | ··Uncompressed·size:·8850.0·KiB·(9062400·B) | 4 | ··Uncompressed·size:·8850.0·KiB·(9062400·B) |
| 5 | ··Ratio:·············0.032 | 5 | ··Ratio:·············0.032 |
| 6 | ··Check:·············CRC64 | 6 | ··Check:·············CRC64 |
| 7 | ··Stream·Padding:····0·B | 7 | ··Stream·Padding:····0·B |
| 8 | ··Streams: | 8 | ··Streams: |
| 9 | ····Stream····Blocks······CompOffset····UncompOffset········CompSize······UncompSize··Ratio··Check······Padding | 9 | ····Stream····Blocks······CompOffset····UncompOffset········CompSize······UncompSize··Ratio··Check······Padding |
| 10 | ·········1·········1···············0···············0··········2929 | 10 | ·········1·········1···············0···············0··········292960·········9062400··0.032··CRC64············0 |
| 11 | ··Blocks: | 11 | ··Blocks: |
| 12 | ····Stream·····Block······CompOffset····UncompOffset·······TotalSize······UncompSize··Ratio··Check | 12 | ····Stream·····Block······CompOffset····UncompOffset·······TotalSize······UncompSize··Ratio··Check |
| 13 | ·········1·········1··············12···············0··········2929 | 13 | ·········1·········1··············12···············0··········292920·········9062400··0.032··CRC64 |