--- /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 @@
│ │ │ │
│ │ │ │
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
│ │ │ │
│ │ │ │ @@ -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.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
│ │ │ │
│ │ │ │ @@ -4685,21 +4685,21 @@
│ │ │ │
│ │ │ │ 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.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.NeedlemanWunsch
│ │ │ │ +prepareAlignment(String, String) - Method in class 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
│ │ │ │
│ │ │ │ @@ -4709,23 +4709,23 @@
│ │ │ │
│ │ │ │ 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.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.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.
│ │ │ │
│ │ │ │ @@ -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 {}
│ │ │ │ │ @@ -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",