--- /srv/rebuilderd/tmp/rebuilderdp2SXh6/inputs/libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb
+++ /srv/rebuilderd/tmp/rebuilderdp2SXh6/out/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 15120 2023-10-07 20:51:37.000000 control.tar.xz
│ --rw-r--r-- 0 0 0 292944 2023-10-07 20:51:37.000000 data.tar.xz
│ +-rw-r--r-- 0 0 0 15116 2023-10-07 20:51:37.000000 control.tar.xz
│ +-rw-r--r-- 0 0 0 293020 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) 14055 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) 739063 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) 26369 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) 11535 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) 8498 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) 6384 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) 203110 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) 65007 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 @@
│ │ │
│ │ │ 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.SmithWaterman
│ │ │ +getScore() - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │
│ │ │ getScore() - Method in class jebl.evolution.align.BartonSternberg
│ │ │
│ │ │ getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
│ │ │
│ │ │ getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
│ │ │
│ │ │ @@ -4236,15 +4236,15 @@
│ │ │
│ │ │ 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
│ │ │ +next(Traceback) - Method in class 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
│ │ │
│ │ │ @@ -4691,15 +4691,15 @@
│ │ │
│ │ │ prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
│ │ │
│ │ │ prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │
│ │ │ prepareAlignment(String, String) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
│ │ │
│ │ │ -prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWaterman
│ │ │ +prepareAlignment(String, String) - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │
│ │ │ 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
│ │ │
│ │ │ @@ -4717,15 +4717,15 @@
│ │ │
│ │ │ Print matrix used to calculate this alignment.
│ │ │
│ │ │ printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │
│ │ │ Print matrix used to calculate this alignment.
│ │ │
│ │ │ -printf(Output) - Method in class jebl.evolution.align.SmithWaterman
│ │ │ +printf(Output) - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │
│ │ │ Print matrix used to calculate this alignment.
│ │ │
│ │ │ printf(Output) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
│ │ │
│ │ │ Print matrix used to calculate this alignment.
│ │ │
│ │ │ @@ -5263,15 +5263,15 @@
│ │ │
│ │ │ 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
│ │ │ +setGapExtend(float) - Method in class 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 jebl.evolution.coalescent.ExponentialGrowth
│ │ │
│ │ │ ├── html2text {}
│ │ │ │ @@ -2502,15 +2502,15 @@
│ │ │ │ get the total number of sampling events.
│ │ │ │ _g_e_t_S_a_m_p_l_e_C_o_u_n_t_(_) - Method in class jebl.evolution.coalescent._I_n_t_e_r_v_a_l_s
│ │ │ │
│ │ │ │ _g_e_t_S_c_o_r_e_(_) - Method in class jebl.evolution.align._A_l_i_g_n
│ │ │ │
│ │ │ │ _g_e_t_S_c_o_r_e_(_) - 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
│ │ │ │
│ │ │ │ - _g_e_t_S_c_o_r_e_(_) - Method in class jebl.evolution.align._S_m_i_t_h_W_a_t_e_r_m_a_n
│ │ │ │ + _g_e_t_S_c_o_r_e_(_) - Method in class jebl.evolution.align._M_a_x_i_m_a_l_S_e_g_m_e_n_t_P_a_i_r
│ │ │ │
│ │ │ │ _g_e_t_S_c_o_r_e_(_) - Method in class jebl.evolution.align._B_a_r_t_o_n_S_t_e_r_n_b_e_r_g
│ │ │ │
│ │ │ │ _g_e_t_S_c_o_r_e_(_) - Method in class jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h
│ │ │ │
│ │ │ │ _g_e_t_S_c_o_r_e_(_) - Method in class jebl.evolution.align._N_e_e_d_l_e_m_a_n_W_u_n_s_c_h_A_f_f_i_n_e
│ │ │ │
│ │ │ │ @@ -3846,15 +3846,15 @@
│ │ │ │ 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._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
│ │ │ │ + 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_L_i_n_e_a_r_S_p_a_c_e
│ │ │ │ Get the next state in the traceback
│ │ │ │ @@ -4237,15 +4237,15 @@
│ │ │ │ _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_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
│ │ │ │ + jebl.evolution.align._M_a_x_i_m_a_l_S_e_g_m_e_n_t_P_a_i_r
│ │ │ │
│ │ │ │ _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_A_f_f_i_n_e
│ │ │ │
│ │ │ │ _p_r_i_n_t_(_) - Method in class jebl.evolution.align._P_r_o_f_i_l_e_C_h_a_r_a_c_t_e_r
│ │ │ │
│ │ │ │ _p_r_i_n_t_(_S_t_r_i_n_g_) - Method in class jebl.evolution.align._O_u_t_p_u_t
│ │ │ │ @@ -4259,15 +4259,15 @@
│ │ │ │ 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
│ │ │ │ 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_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
│ │ │ │ + _p_r_i_n_t_f_(_O_u_t_p_u_t_) - Method in class jebl.evolution.align._M_a_x_i_m_a_l_S_e_g_m_e_n_t_P_a_i_r
│ │ │ │ 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
│ │ │ │
│ │ │ │ _p_r_i_n_t_l_n_(_) - Method in class jebl.evolution.align._S_y_s_t_e_m_O_u_t
│ │ │ │ @@ -4777,15 +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._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
│ │ │ │ + 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 {}
│ │ │ │ @@ -4058,15 +4058,15 @@
│ │ │ │ "l": "getScore()"
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ "c": "OldNeedlemanWunschAffine",
│ │ │ │ "l": "getScore()"
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ - "c": "SmithWaterman",
│ │ │ │ + "c": "MaximalSegmentPair",
│ │ │ │ "l": "getScore()"
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ "c": "BartonSternberg",
│ │ │ │ "l": "getScore()"
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ @@ -6195,15 +6195,15 @@
│ │ │ │ }, {
│ │ │ │ "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)"
│ │ │ │ @@ -6734,15 +6734,15 @@
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ "c": "NonOverlapMultipleLocalAffine",
│ │ │ │ "l": "prepareAlignment(String, String)",
│ │ │ │ "u": "prepareAlignment(java.lang.String,java.lang.String)"
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ - "c": "SmithWaterman",
│ │ │ │ + "c": "MaximalSegmentPair",
│ │ │ │ "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)"
│ │ │ │ @@ -6778,15 +6778,15 @@
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ "c": "SmithWatermanLinearSpaceAffine",
│ │ │ │ "l": "printf(Output)",
│ │ │ │ "u": "printf(jebl.evolution.align.Output)"
│ │ │ │ }, {
│ │ │ │ "p": "jebl.evolution.align",
│ │ │ │ - "c": "SmithWaterman",
│ │ │ │ + "c": "MaximalSegmentPair",
│ │ │ │ "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",