--- /srv/rebuilderd/tmp/rebuilderde4zEF4/inputs/libjebl2-java-doc_0.1+git20230701.b3c0f25-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderde4zEF4/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 292964 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) 738981 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) 203100 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 │ │ │ @@ -332,19 +332,19 @@ │ │ │ │ │ │
beginNextSubtask(String) - Method in class jebl.util.CompositeProgressListener
│ │ │
│ │ │
Convenience method to start the next operation AND set a new message.
│ │ │
│ │ │
beginSubtask() - Method in class jebl.util.CompositeProgressListener
│ │ │
│ │ │ -
Used as an alternative to CompositeProgressListener.beginNextSubtask().
│ │ │ +
Used as an alternative to beginNextSubtask().
│ │ │
│ │ │
beginSubtask(String) - Method in class jebl.util.CompositeProgressListener
│ │ │
│ │ │ -
Used as an alternative to CompositeProgressListener.beginNextSubtask().
│ │ │ +
Used as an alternative to beginNextSubtask().
│ │ │
│ │ │
BilleraMetric - Class in jebl.evolution.treemetrics
│ │ │
│ │ │
Billera tree distance - sum of change in branch lengths required to transform one tree to the second │ │ │ │ │ │ Note that this interface is not optimal for a large set where all pairs are required.
│ │ │
│ │ │ @@ -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.OverlapAlign
│ │ │
 
│ │ │
getScore() - Method in class jebl.evolution.align.BartonSternberg
│ │ │
 
│ │ │
getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
│ │ │
 
│ │ │
getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
│ │ │
 
│ │ │ @@ -4236,23 +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.SmithWatermanLinearSpaceAffine
│ │ │ +
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │
│ │ │
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.SmithWatermanLinearSpace
│ │ │ +
next(Traceback) - Method in class jebl.evolution.align.OverlapAlign
│ │ │
│ │ │
Get the next state in the traceback
│ │ │
│ │ │
next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair
│ │ │
 
│ │ │
nextBoolean() - Static method in class jebl.math.Random
│ │ │
│ │ │ @@ -4687,19 +4687,19 @@ │ │ │
│ │ │
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.SmithWatermanLinearSpaceAffine
│ │ │ +
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │
 
│ │ │
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.OverlapAlign
│ │ │
 
│ │ │
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
│ │ │
 
│ │ │ @@ -4713,19 +4713,19 @@ │ │ │
│ │ │
Print matrix used to calculate this alignment.
│ │ │
│ │ │
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
│ │ │
│ │ │
Print matrix used to calculate this alignment.
│ │ │
│ │ │ -
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
│ │ │ +
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
│ │ │
│ │ │
Print matrix used to calculate this alignment.
│ │ │
│ │ │ -
printf(Output) - Method in class jebl.evolution.align.SmithWaterman
│ │ │ +
printf(Output) - Method in class jebl.evolution.align.OverlapAlign
│ │ │
│ │ │
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.NeedlemanWunschLinearSpaceAffine
│ │ │
 
│ │ │
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 {} │ │ │ │ @@ -271,17 +271,17 @@ │ │ │ │ Creates a sequence with a name corresponding to the taxon name │ │ │ │ _b_e_g_i_n_N_e_x_t_S_u_b_t_a_s_k_(_) - Method in class jebl.util._C_o_m_p_o_s_i_t_e_P_r_o_g_r_e_s_s_L_i_s_t_e_n_e_r │ │ │ │ begins the next subtask. │ │ │ │ _b_e_g_i_n_N_e_x_t_S_u_b_t_a_s_k_(_S_t_r_i_n_g_) - Method in class │ │ │ │ jebl.util._C_o_m_p_o_s_i_t_e_P_r_o_g_r_e_s_s_L_i_s_t_e_n_e_r │ │ │ │ Convenience method to start the next operation AND set a new message. │ │ │ │ _b_e_g_i_n_S_u_b_t_a_s_k_(_) - Method in class jebl.util._C_o_m_p_o_s_i_t_e_P_r_o_g_r_e_s_s_L_i_s_t_e_n_e_r │ │ │ │ - Used as an alternative to _C_o_m_p_o_s_i_t_e_P_r_o_g_r_e_s_s_L_i_s_t_e_n_e_r_._b_e_g_i_n_N_e_x_t_S_u_b_t_a_s_k_(_). │ │ │ │ + Used as an alternative to _b_e_g_i_n_N_e_x_t_S_u_b_t_a_s_k_(_). │ │ │ │ _b_e_g_i_n_S_u_b_t_a_s_k_(_S_t_r_i_n_g_) - Method in class jebl.util._C_o_m_p_o_s_i_t_e_P_r_o_g_r_e_s_s_L_i_s_t_e_n_e_r │ │ │ │ - Used as an alternative to _C_o_m_p_o_s_i_t_e_P_r_o_g_r_e_s_s_L_i_s_t_e_n_e_r_._b_e_g_i_n_N_e_x_t_S_u_b_t_a_s_k_(_). │ │ │ │ + Used as an alternative to _b_e_g_i_n_N_e_x_t_S_u_b_t_a_s_k_(_). │ │ │ │ _B_i_l_l_e_r_a_M_e_t_r_i_c - Class in _j_e_b_l_._e_v_o_l_u_t_i_o_n_._t_r_e_e_m_e_t_r_i_c_s │ │ │ │ Billera tree distance - sum of change in branch lengths required to │ │ │ │ transform one tree to the second Note that this interface is not optimal │ │ │ │ for a large set where all pairs are required. │ │ │ │ _B_i_l_l_e_r_a_M_e_t_r_i_c_(_) - Constructor for class │ │ │ │ jebl.evolution.treemetrics._B_i_l_l_e_r_a_M_e_t_r_i_c │ │ │ │   │ │ │ │ @@ -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._O_v_e_r_l_a_p_A_l_i_g_n │ │ │ │   │ │ │ │ _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 │ │ │ │   │ │ │ │ @@ -3846,21 +3846,20 @@ │ │ │ │ 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._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 │ │ │ │ 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 │ │ │ │ + _n_e_x_t_(_T_r_a_c_e_b_a_c_k_) - Method in class jebl.evolution.align._O_v_e_r_l_a_p_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._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 │ │ │ │ @@ -4231,21 +4230,21 @@ │ │ │ │ _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 │ │ │ │   │ │ │ │ _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 │ │ │ │ + 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 │ │ │ │   │ │ │ │ _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._O_v_e_r_l_a_p_A_l_i_g_n │ │ │ │   │ │ │ │ _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 │ │ │ │ @@ -4257,17 +4256,17 @@ │ │ │ │ _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 │ │ │ │ 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 │ │ │ │ + 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 │ │ │ │ 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._O_v_e_r_l_a_p_A_l_i_g_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 │ │ │ │   │ │ │ │ _p_r_i_n_t_l_n_(_) - Method in class jebl.evolution.align._S_y_s_t_e_m_O_u_t │ │ │ │ @@ -4777,15 +4776,15 @@ │ │ │ │ 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._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 │ │ │ │   │ │ │ │ _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": "OverlapAlign", │ │ │ │ "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": "NeedlemanWunschLinearSpaceAffine", │ │ │ │ "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": "SmithWatermanLinearSpace", │ │ │ │ + "c": "OverlapAlign", │ │ │ │ "l": "next(Traceback)", │ │ │ │ "u": "next(jebl.evolution.align.Traceback)" │ │ │ │ }, { │ │ │ │ "p": "jebl.evolution.align", │ │ │ │ "c": "MaximalSegmentPair", │ │ │ │ "l": "next(Traceback)", │ │ │ │ "u": "next(jebl.evolution.align.Traceback)" │ │ │ │ @@ -6724,25 +6724,25 @@ │ │ │ │ }, { │ │ │ │ "p": "jebl.evolution.align", │ │ │ │ "c": "SmithWatermanLinearSpace", │ │ │ │ "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": "SmithWaterman", │ │ │ │ + "c": "OverlapAlign", │ │ │ │ "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)" │ │ │ │ @@ -6773,20 +6773,20 @@ │ │ │ │ }, { │ │ │ │ "p": "jebl.evolution.align", │ │ │ │ "c": "SmithWatermanLinearSpace", │ │ │ │ "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": "SmithWaterman", │ │ │ │ + "c": "OverlapAlign", │ │ │ │ "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": "NeedlemanWunschLinearSpaceAffine", │ │ │ │ "l": "setGapExtend(float)" │ │ │ │ }, { │ │ │ │ "p": "jebl.evolution.align", │ │ │ │ "c": "NonOverlapMultipleLocalAffine", │ │ │ │ "l": "setGapExtend(float)" │ │ │ │ }, { │ │ │ │ "p": "jebl.evolution.align",