--- /srv/reproducible-results/rbuild-debian/r-b-build.wcjF3PKt/b1/jebl2_0.1+git20230701.b3c0f25-1_i386.changes
+++ /srv/reproducible-results/rbuild-debian/r-b-build.wcjF3PKt/b2/jebl2_0.1+git20230701.b3c0f25-1_i386.changes
├── Files
│ @@ -1,3 +1,3 @@
│  
│ - 633fb5724180b06a7b0f85e49838650e 308228 doc optional libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb
│ + c1a7707891f638cb9c823971232a139e 308208 doc optional libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb
│   5a7a03d1c3d5e2eccc0552ab1ba50840 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    15096 2023-10-07 20:51:37.000000 control.tar.xz
│ │ --rw-r--r--   0        0        0   292940 2023-10-07 20:51:37.000000 data.tar.xz
│ │ +-rw-r--r--   0        0        0   292920 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)   739045 2023-10-07 20:51:37.000000 ./usr/share/doc/libjebl2-java/api/index-all.html
│ │ │ │ +-rw-r--r--   0 root         (0) root         (0)   739036 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)   203104 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)   203101 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
│ │ │ │ @@ -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/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">NeedlemanWunschLinearSpaceAffine</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/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>
│ │ │ │ +<dt><a href="jebl/evolution/align/NeedlemanWunschLinearSpace.html#next(jebl.evolution.align.Traceback)" class="member-name-link">next(Traceback)</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">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>
│ │ │ │ @@ -4685,17 +4685,17 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <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/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>
│ │ │ │ @@ -4709,19 +4709,19 @@
│ │ │ │  <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/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>
│ │ │ │ +<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>
│ │ │ │  <dd>
│ │ │ │  <div class="block">Print matrix used to calculate this alignment.</div>
│ │ │ │  </dd>
│ │ │ │  <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>
│ │ │ │ @@ -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/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">NeedlemanWunschLinearSpaceAffine</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 {}
│ │ │ │ │ @@ -3846,20 +3846,21 @@
│ │ │ │ │    jebl.evolution.align._T_r_a_c_e_b_a_c_k_P_l_o_t_t_e_r
│ │ │ │ │         
│ │ │ │ │    _n_e_x_t_(_) - Method in class jebl.evolution.io._I_m_p_o_r_t_H_e_l_p_e_r
│ │ │ │ │         
│ │ │ │ │    _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class jebl.evolution.align._A_l_i_g_n
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │    _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class
│ │ │ │ │ -  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e_A_f_f_i_n_e
│ │ │ │ │ +  jebl.evolution.align._O_l_d_N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_A_f_f_i_n_e
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │    _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class
│ │ │ │ │    jebl.evolution.align._N_o_n_O_v_e_r_l_a_p_M_u_l_t_i_p_l_e_L_o_c_a_l_A_f_f_i_n_e
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │ -  _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n
│ │ │ │ │ +  _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class
│ │ │ │ │ +  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e
│ │ │ │ │        Get the next state in the traceback
│ │ │ │ │    _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class jebl.evolution.align._M_a_x_i_m_a_l_S_e_g_m_e_n_t_P_a_i_r
│ │ │ │ │         
│ │ │ │ │    _n_e_x_t_B_o_o_l_e_a_n_(_) - Static method in class jebl.math._R_a_n_d_o_m
│ │ │ │ │        Access a default instance of this class, access is synchronized
│ │ │ │ │    _n_e_x_t_B_y_t_e_(_) - Static method in class jebl.math._R_a_n_d_o_m
│ │ │ │ │        Access a default instance of this class, access is synchronized
│ │ │ │ │ @@ -4227,18 +4228,18 @@
│ │ │ │ │         
│ │ │ │ │    _p_r_e_p_a_r_e_A_l_i_g_n_m_e_n_t_(_S_t_r_i_n_g_,_ _S_t_r_i_n_g_) - Method in class jebl.evolution.align._A_l_i_g_n
│ │ │ │ │        Initialises the matrices for the alignment.
│ │ │ │ │    _p_r_e_p_a_r_e_A_l_i_g_n_m_e_n_t_(_S_t_r_i_n_g_,_ _S_t_r_i_n_g_) - Method in class
│ │ │ │ │    jebl.evolution.align._O_l_d_N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_A_f_f_i_n_e
│ │ │ │ │         
│ │ │ │ │    _p_r_e_p_a_r_e_A_l_i_g_n_m_e_n_t_(_S_t_r_i_n_g_,_ _S_t_r_i_n_g_) - Method in class
│ │ │ │ │ -  jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n_L_i_n_e_a_r_S_p_a_c_e
│ │ │ │ │ +  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e
│ │ │ │ │         
│ │ │ │ │    _p_r_e_p_a_r_e_A_l_i_g_n_m_e_n_t_(_S_t_r_i_n_g_,_ _S_t_r_i_n_g_) - Method in class
│ │ │ │ │ -  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e_A_f_f_i_n_e
│ │ │ │ │ +  jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n_L_i_n_e_a_r_S_p_a_c_e_A_f_f_i_n_e
│ │ │ │ │         
│ │ │ │ │    _p_r_e_p_a_r_e_A_l_i_g_n_m_e_n_t_(_S_t_r_i_n_g_,_ _S_t_r_i_n_g_) - Method in class
│ │ │ │ │    jebl.evolution.align._N_o_n_O_v_e_r_l_a_p_M_u_l_t_i_p_l_e_L_o_c_a_l_A_f_f_i_n_e
│ │ │ │ │         
│ │ │ │ │    _p_r_e_p_a_r_e_A_l_i_g_n_m_e_n_t_(_S_t_r_i_n_g_,_ _S_t_r_i_n_g_) - Method in class
│ │ │ │ │    jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n
│ │ │ │ │         
│ │ │ │ │ @@ -4253,18 +4254,18 @@
│ │ │ │ │         
│ │ │ │ │    _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class jebl.evolution.align._A_l_i_g_n
│ │ │ │ │        Print the matrix (matrices) used to compute the alignment
│ │ │ │ │    _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class
│ │ │ │ │    jebl.evolution.align._O_l_d_N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_A_f_f_i_n_e
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class
│ │ │ │ │ -  jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n_L_i_n_e_a_r_S_p_a_c_e
│ │ │ │ │ +  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class
│ │ │ │ │ -  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e_A_f_f_i_n_e
│ │ │ │ │ +  jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n_L_i_n_e_a_r_S_p_a_c_e_A_f_f_i_n_e
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class
│ │ │ │ │    jebl.evolution.align._N_o_n_O_v_e_r_l_a_p_M_u_l_t_i_p_l_e_L_o_c_a_l_A_f_f_i_n_e
│ │ │ │ │        Print matrix used to calculate this alignment.
│ │ │ │ │    _p_r_i_n_t_l_n_(_) - Method in class jebl.evolution.align._O_u_t_p_u_t
│ │ │ │ │ @@ -4776,15 +4777,15 @@
│ │ │ │ │        Change length of an existing edge.
│ │ │ │ │    _s_e_t_E_d_g_e_L_e_n_g_t_h_(_N_o_d_e_,_ _N_o_d_e_,_ _d_o_u_b_l_e_) - Method in class
│ │ │ │ │    jebl.evolution.trees._S_i_m_p_l_e_T_r_e_e
│ │ │ │ │        Set edge distance between two adjacent nodes.
│ │ │ │ │    _s_e_t_E_x_p_e_c_t_e_d_I_n_p_u_t_L_e_n_g_t_h_(_l_o_n_g_) - Method in class jebl.evolution.io._I_m_p_o_r_t_H_e_l_p_e_r
│ │ │ │ │         
│ │ │ │ │    _s_e_t_G_a_p_E_x_t_e_n_d_(_f_l_o_a_t_) - Method in class
│ │ │ │ │ -  jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_L_i_n_e_a_r_S_p_a_c_e_A_f_f_i_n_e
│ │ │ │ │ +  jebl.evolution.align._O_l_d_N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_A_f_f_i_n_e
│ │ │ │ │         
│ │ │ │ │    _s_e_t_G_a_p_E_x_t_e_n_d_(_f_l_o_a_t_) - Method in class
│ │ │ │ │    jebl.evolution.align._N_o_n_O_v_e_r_l_a_p_M_u_l_t_i_p_l_e_L_o_c_a_l_A_f_f_i_n_e
│ │ │ │ │         
│ │ │ │ │    _s_e_t_G_a_p_O_p_e_n_(_f_l_o_a_t_) - Method in class jebl.evolution.align._A_l_i_g_n
│ │ │ │ │         
│ │ │ │ │    _s_e_t_G_r_o_w_t_h_R_a_t_e_(_d_o_u_b_l_e_) - Method in class
│ │ │ ├── ./usr/share/doc/libjebl2-java/api/member-search-index.js
│ │ │ │ ├── js-beautify {}
│ │ │ │ │ @@ -6195,25 +6195,25 @@
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "Align",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │ -    "c": "NeedlemanWunschLinearSpaceAffine",
│ │ │ │ │ +    "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": "SmithWaterman",
│ │ │ │ │ +    "c": "NeedlemanWunschLinearSpace",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "MaximalSegmentPair",
│ │ │ │ │      "l": "next(Traceback)",
│ │ │ │ │      "u": "next(jebl.evolution.align.Traceback)"
│ │ │ │ │ @@ -6719,20 +6719,20 @@
│ │ │ │ │  }, {
│ │ │ │ │      "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": "NeedlemanWunschLinearSpaceAffine",
│ │ │ │ │ +    "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ │      "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)"
│ │ │ │ │ @@ -6768,20 +6768,20 @@
│ │ │ │ │  }, {
│ │ │ │ │      "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": "NeedlemanWunschLinearSpaceAffine",
│ │ │ │ │ +    "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ │      "l": "printf(Output)",
│ │ │ │ │      "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "SmithWaterman",
│ │ │ │ │      "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": "NeedlemanWunschLinearSpaceAffine",
│ │ │ │ │ +    "c": "OldNeedlemanWunschAffine",
│ │ │ │ │      "l": "setGapExtend(float)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",
│ │ │ │ │      "c": "NonOverlapMultipleLocalAffine",
│ │ │ │ │      "l": "setGapExtend(float)"
│ │ │ │ │  }, {
│ │ │ │ │      "p": "jebl.evolution.align",