--- /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 @@
│ │ │ │
│ │ │ │ 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.NeedlemanWunschLinearSpaceAffine
│ │ │ │ +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
│ │ │ │
│ │ │ │ -next(Traceback) - Method in class jebl.evolution.align.SmithWaterman
│ │ │ │ +next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
│ │ │ │
│ │ │ │ Get the next state in the traceback
│ │ │ │
│ │ │ │ next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │ │
│ │ │ │ nextBoolean() - Static method in class jebl.math.Random
│ │ │ │
│ │ │ │ @@ -4685,17 +4685,17 @@
│ │ │ │
│ │ │ │ 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
│ │ │ │ +prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
│ │ │ │
│ │ │ │ -prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │ │ +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.NeedlemanWunschAffine
│ │ │ │
│ │ │ │ @@ -4709,19 +4709,19 @@
│ │ │ │
│ │ │ │ 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
│ │ │ │ +printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpace
│ │ │ │
│ │ │ │ Print matrix used to calculate this alignment.
│ │ │ │
│ │ │ │ -printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │ │ +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
│ │ │ │
│ │ │ │ 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.NeedlemanWunschLinearSpaceAffine
│ │ │ │ +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 {}
│ │ │ │ │ @@ -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",