--- /srv/reproducible-results/rbuild-debian/r-b-build.rwMZWJbv/b1/jebl2_0.1+git20230701.b3c0f25-1_armhf.changes
+++ /srv/reproducible-results/rbuild-debian/r-b-build.rwMZWJbv/b2/jebl2_0.1+git20230701.b3c0f25-1_armhf.changes
├── Files
│ @@ -1,3 +1,3 @@
│  
│ - 3591efe14d8cf6c9acd0729fc0492db5 308272 doc optional libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb
│ + e70f1736644b875a6adb6accfb86f5a1 308204 doc optional libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb
│   433f66e6d264470aa4a35fc3faba46fb 531736 java optional libjebl2-java_0.1+git20230701.b3c0f25-1_all.deb
├── libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb
│ ├── file list
│ │ @@ -1,3 +1,3 @@
│ │  -rw-r--r--   0        0        0        4 2023-10-07 20:51:37.000000 debian-binary
│ │  -rw-r--r--   0        0        0    15100 2023-10-07 20:51:37.000000 control.tar.xz
│ │ --rw-r--r--   0        0        0   292980 2023-10-07 20:51:37.000000 data.tar.xz
│ │ +-rw-r--r--   0        0        0   292912 2023-10-07 20:51:37.000000 data.tar.xz
│ ├── control.tar.xz
│ │ ├── control.tar
│ │ │ ├── ./md5sums
│ │ │ │ ├── ./md5sums
│ │ │ │ │┄ Files differ
│ ├── data.tar.xz
│ │ ├── data.tar
│ │ │ ├── file list
│ │ │ │ @@ -6,15 +6,15 @@
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    89486 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/allclasses-index.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     5808 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/allpackages-index.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    13991 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/constant-values.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     7240 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/deprecated-list.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      410 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/element-list
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    10483 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/help-doc.html
│ │ │ │ --rw-r--r--   0 root         (0) root         (0)   739054 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index-all.html
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)   739009 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index-all.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     7337 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index.html
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    26145 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/Align.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    11391 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/AlignCommand.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     8402 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html
│ │ │ │ @@ -613,15 +613,15 @@
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     6336 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/util/package-tree.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    12680 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jebl/util/package-use.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1498 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/jquery-ui.overrides.css
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1522 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/ASSEMBLY_EXCEPTION
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     2936 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/jquery.md
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)     1870 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/legal/jqueryUI.md
│ │ │ │ --rw-r--r--   0 root         (0) root         (0)   203107 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/member-search-index.js
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)   203092 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/member-search-index.js
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)       45 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/module-search-index.js
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      823 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/overview-summary.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)    64815 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/overview-tree.html
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      649 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/package-search-index.js
│ │ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/resources/
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      499 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/resources/glass.png
│ │ │ │  -rw-r--r--   0 root         (0) root         (0)      394 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/resources/x.png
│ │ │ ├── ./usr/share/doc/libjebl2-java/api/index-all.html
│ │ │ │ @@ -2783,15 +2783,15 @@
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/MaximalSegmentPair.html#getScore()" class="member-name-link">getScore()</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/MaximalSegmentPair.html" title="class in jebl.evolution.align">MaximalSegmentPair</a></dt>
│ │ │ │ +<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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ @@ -4236,23 +4236,23 @@
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Get the next state in the traceback</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#next(jebl.evolution.align.Traceback)" class="member-name-link">next(Traceback)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
│ │ │ │ +<dt><a href="jebl/evolution/align/OldNeedlemanWunschAffine.html#next(jebl.evolution.align.Traceback)" class="member-name-link">next(Traceback)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/OldNeedlemanWunschAffine.html" title="class in jebl.evolution.align">OldNeedlemanWunschAffine</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Get the next state in the traceback</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Get the next state in the traceback</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/NeedlemanWunsch.html#next(jebl.evolution.align.Traceback)" class="member-name-link">next(Traceback)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/NeedlemanWunsch.html" title="class in jebl.evolution.align">NeedlemanWunsch</a></dt>
│ │ │ │ +<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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Get the next state in the traceback</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │ @@ -4685,21 +4685,21 @@
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Initialises the matrices for the alignment.</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/SmithWatermanLinearSpace.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/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
│ │ │ │ +<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="class in jebl.evolution.align">NeedlemanWunschLinearSpace</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.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/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
│ │ │ │ +<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.html" title="class in jebl.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/NeedlemanWunsch.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/NeedlemanWunsch.html" title="class in jebl.evolution.align">NeedlemanWunsch</a></dt>
│ │ │ │ +<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.align">SmithWaterman</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ @@ -4709,23 +4709,23 @@
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print the matrix (matrices) used to compute the alignment</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print matrix used to calculate this alignment.</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/SmithWatermanLinearSpace.html#printf(jebl.evolution.align.Output)" class="member-name-link">printf(Output)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/SmithWatermanLinearSpace.html" title="class in jebl.evolution.align">SmithWatermanLinearSpace</a></dt>
│ │ │ │ +<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">NeedlemanWunschLinearSpace</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print matrix used to calculate this alignment.</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#printf(jebl.evolution.align.Output)" class="member-name-link">printf(Output)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
│ │ │ │ +<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.evolution.align">NeedlemanWunschLinearSpaceAffine</a></dt>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print matrix used to calculate this alignment.</div>
│ │ │ │  </dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/NeedlemanWunsch.html#printf(jebl.evolution.align.Output)" class="member-name-link">printf(Output)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/NeedlemanWunsch.html" title="class in jebl.evolution.align">NeedlemanWunsch</a></dt>
│ │ │ │ +<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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print matrix used to calculate this alignment.</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print matrix used to calculate this alignment.</div>
│ │ │ │  </dd>
│ │ │ │ @@ -5263,15 +5263,15 @@
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Set edge distance between two adjacent nodes.</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │ -<dt><a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#setGapExtend(float)" class="member-name-link">setGapExtend(float)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html" title="class in jebl.evolution.align">SmithWatermanLinearSpaceAffine</a></dt>
│ │ │ │ +<dt><a href="jebl/evolution/align/OldNeedlemanWunschAffine.html#setGapExtend(float)" class="member-name-link">setGapExtend(float)</a> - Method in class jebl.evolution.align.<a href="jebl/evolution/align/OldNeedlemanWunschAffine.html" title="class in jebl.evolution.align">OldNeedlemanWunschAffine</a></dt>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>&nbsp;</dd>
│ │ │ │  <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>
│ │ │ │  <dd>
│ │ │ │ ├── html2text {}
│ │ │ │ │ @@ -2512,15 +2512,15 @@
│ │ │ │ │        get the total number of sampling events.
│ │ │ │ │    getSampleCount() - Method in class jebl.evolution.coalescent.Intervals
│ │ │ │ │         
│ │ │ │ │    getScore() - Method in class jebl.evolution.align.Align
│ │ │ │ │         
│ │ │ │ │    getScore() - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
│ │ │ │ │         
│ │ │ │ │ -  getScore() - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │ │ │ +  getScore() - Method in class jebl.evolution.align.SmithWaterman
│ │ │ │ │         
│ │ │ │ │    getScore() - Method in class jebl.evolution.align.BartonSternberg
│ │ │ │ │         
│ │ │ │ │    getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
│ │ │ │ │         
│ │ │ │ │    getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
│ │ │ │ │         
│ │ │ │ │ @@ -3856,20 +3856,20 @@
│ │ │ │ │    jebl.evolution.align.TracebackPlotter
│ │ │ │ │         
│ │ │ │ │    next() - Method in class jebl.evolution.io.ImportHelper
│ │ │ │ │         
│ │ │ │ │    next(Traceback) - Method in class jebl.evolution.align.Align
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │    next(Traceback) - Method in class
│ │ │ │ │ -  jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │ │ │ +  jebl.evolution.align.OldNeedlemanWunschAffine
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │    next(Traceback) - Method in class
│ │ │ │ │    jebl.evolution.align.NonOverlapMultipleLocalAffine
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │ -  next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunsch
│ │ │ │ │ +  next(Traceback) - Method in class jebl.evolution.align.SmithWaterman
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │    next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │ │ │         
│ │ │ │ │    nextBoolean() - Static method in class jebl.math.Random
│ │ │ │ │        Access a default instance of this class, access is synchronized
│ │ │ │ │    nextByte() - Static method in class jebl.math.Random
│ │ │ │ │        Access a default instance of this class, access is synchronized
│ │ │ │ │ @@ -4237,24 +4237,24 @@
│ │ │ │ │         
│ │ │ │ │    prepareAlignment(String,_String) - Method in class jebl.evolution.align.Align
│ │ │ │ │        Initialises the matrices for the alignment.
│ │ │ │ │    prepareAlignment(String,_String) - Method in class
│ │ │ │ │    jebl.evolution.align.OldNeedlemanWunschAffine
│ │ │ │ │         
│ │ │ │ │    prepareAlignment(String,_String) - Method in class
│ │ │ │ │ -  jebl.evolution.align.SmithWatermanLinearSpace
│ │ │ │ │ +  jebl.evolution.align.NeedlemanWunschLinearSpace
│ │ │ │ │         
│ │ │ │ │    prepareAlignment(String,_String) - Method in class
│ │ │ │ │ -  jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │ │ │ +  jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │ │ │         
│ │ │ │ │    prepareAlignment(String,_String) - Method in class
│ │ │ │ │    jebl.evolution.align.NonOverlapMultipleLocalAffine
│ │ │ │ │         
│ │ │ │ │    prepareAlignment(String,_String) - Method in class
│ │ │ │ │ -  jebl.evolution.align.NeedlemanWunsch
│ │ │ │ │ +  jebl.evolution.align.SmithWaterman
│ │ │ │ │         
│ │ │ │ │    prepareAlignment(String,_String) - Method in class
│ │ │ │ │    jebl.evolution.align.NeedlemanWunschAffine
│ │ │ │ │         
│ │ │ │ │    print() - Method in class jebl.evolution.align.ProfileCharacter
│ │ │ │ │         
│ │ │ │ │    print(String) - Method in class jebl.evolution.align.Output
│ │ │ │ │ @@ -4263,20 +4263,20 @@
│ │ │ │ │         
│ │ │ │ │    printf(Output) - Method in class jebl.evolution.align.Align
│ │ │ │ │        Print the matrix (matrices) used to compute the alignment
│ │ │ │ │    printf(Output) - Method in class
│ │ │ │ │    jebl.evolution.align.OldNeedlemanWunschAffine
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    printf(Output) - Method in class
│ │ │ │ │ -  jebl.evolution.align.SmithWatermanLinearSpace
│ │ │ │ │ +  jebl.evolution.align.NeedlemanWunschLinearSpace
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    printf(Output) - Method in class
│ │ │ │ │ -  jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │ │ │ +  jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │ -  printf(Output) - Method in class jebl.evolution.align.NeedlemanWunsch
│ │ │ │ │ +  printf(Output) - Method in class jebl.evolution.align.SmithWaterman
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    printf(Output) - Method in class
│ │ │ │ │    jebl.evolution.align.NonOverlapMultipleLocalAffine
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    println() - Method in class jebl.evolution.align.Output
│ │ │ │ │         
│ │ │ │ │    println() - Method in class jebl.evolution.align.SystemOut
│ │ │ │ │ @@ -4786,15 +4786,15 @@
│ │ │ │ │        Change length of an existing edge.
│ │ │ │ │    setEdgeLength(Node,_Node,_double) - Method in class
│ │ │ │ │    jebl.evolution.trees.SimpleTree
│ │ │ │ │        Set edge distance between two adjacent nodes.
│ │ │ │ │    setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
│ │ │ │ │         
│ │ │ │ │    setGapExtend(float) - Method in class
│ │ │ │ │ -  jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │ │ │ +  jebl.evolution.align.OldNeedlemanWunschAffine
│ │ │ │ │         
│ │ │ │ │    setGapExtend(float) - Method in class
│ │ │ │ │    jebl.evolution.align.NonOverlapMultipleLocalAffine
│ │ │ │ │         
│ │ │ │ │    setGapOpen(float) - Method in class jebl.evolution.align.Align
│ │ │ │ │         
│ │ │ │ │    setGrowthRate(double) - Method in class
│ │ │ ├── ./usr/share/doc/libjebl2-java/api/member-search-index.js
│ │ │ │ ├── js-beautify {}
│ │ │ │ │ @@ -4058,15 +4058,15 @@
│ │ │ │ │      "l": "getScore()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "OldNeedlemanWunschAffine",
│ │ │ │ │      "l": "getScore()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "MaximalSegmentPair",
│ │ │ │ │ +    "c": "SmithWaterman",
│ │ │ │ │      "l": "getScore()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "BartonSternberg",
│ │ │ │ │      "l": "getScore()"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ @@ -6195,25 +6195,25 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "Align",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ │ +    "c": "OldNeedlemanWunschAffine",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "NonOverlapMultipleLocalAffine",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "NeedlemanWunsch",
│ │ │ │ │ +    "c": "SmithWaterman",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "MaximalSegmentPair",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │ @@ -6719,30 +6719,30 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "OldNeedlemanWunschAffine",
│ │ │ │ │      "l": "prepareAlignment(String, String)",
│ │ │ │ │      "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "SmithWatermanLinearSpace",
│ │ │ │ │ +    "c": "NeedlemanWunschLinearSpace",
│ │ │ │ │      "l": "prepareAlignment(String, String)",
│ │ │ │ │      "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ │ +    "c": "NeedlemanWunschLinearSpaceAffine",
│ │ │ │ │      "l": "prepareAlignment(String, String)",
│ │ │ │ │      "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "NonOverlapMultipleLocalAffine",
│ │ │ │ │      "l": "prepareAlignment(String, String)",
│ │ │ │ │      "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "NeedlemanWunsch",
│ │ │ │ │ +    "c": "SmithWaterman",
│ │ │ │ │      "l": "prepareAlignment(String, String)",
│ │ │ │ │      "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "NeedlemanWunschAffine",
│ │ │ │ │      "l": "prepareAlignment(String, String)",
│ │ │ │ │      "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ │ @@ -6768,25 +6768,25 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "OldNeedlemanWunschAffine",
│ │ │ │ │      "l": "printf(Output)",
│ │ │ │ │      "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "SmithWatermanLinearSpace",
│ │ │ │ │ +    "c": "NeedlemanWunschLinearSpace",
│ │ │ │ │      "l": "printf(Output)",
│ │ │ │ │      "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ │ +    "c": "NeedlemanWunschLinearSpaceAffine",
│ │ │ │ │      "l": "printf(Output)",
│ │ │ │ │      "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "NeedlemanWunsch",
│ │ │ │ │ +    "c": "SmithWaterman",
│ │ │ │ │      "l": "printf(Output)",
│ │ │ │ │      "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "NonOverlapMultipleLocalAffine",
│ │ │ │ │      "l": "printf(Output)",
│ │ │ │ │      "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ │ @@ -7566,15 +7566,15 @@
│ │ │ │ │      "u": "setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.io",
│ │ │ │ │      "c": "ImportHelper",
│ │ │ │ │      "l": "setExpectedInputLength(long)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ │ +    "c": "OldNeedlemanWunschAffine",
│ │ │ │ │      "l": "setGapExtend(float)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "NonOverlapMultipleLocalAffine",
│ │ │ │ │      "l": "setGapExtend(float)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",