{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.eDWQR2jJ/b1/jebl2_0.1+git20201011.969bd4b-1_armhf.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.eDWQR2jJ/b2/jebl2_0.1+git20201011.969bd4b-1_armhf.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,3 +1,3 @@\n \n- f9e6816cad70888cc98c61fc4a1a61db 304736 doc optional libjebl2-java-doc_0.1+git20201011.969bd4b-1_all.deb\n+ 7609ab07cd891310467f6f7cd1421e74 304760 doc optional libjebl2-java-doc_0.1+git20201011.969bd4b-1_all.deb\n 0b9ff1dc96e87b702a85528e83a59e2f 522224 java optional libjebl2-java_0.1+git20201011.969bd4b-1_all.deb\n"}, {"source1": "libjebl2-java-doc_0.1+git20201011.969bd4b-1_all.deb", "source2": "libjebl2-java-doc_0.1+git20201011.969bd4b-1_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r-- 0 0 0 4 2020-10-12 19:24:22.000000 debian-binary\n--rw-r--r-- 0 0 0 15100 2020-10-12 19:24:22.000000 control.tar.xz\n--rw-r--r-- 0 0 0 289444 2020-10-12 19:24:22.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 15104 2020-10-12 19:24:22.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 289464 2020-10-12 19:24:22.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -6,15 +6,15 @@\n drwxr-xr-x 0 root (0) root (0) 0 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/\n -rw-r--r-- 0 root (0) root (0) 89376 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/allclasses-index.html\n -rw-r--r-- 0 root (0) root (0) 5808 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/allpackages-index.html\n -rw-r--r-- 0 root (0) root (0) 13991 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/constant-values.html\n -rw-r--r-- 0 root (0) root (0) 7240 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/deprecated-list.html\n -rw-r--r-- 0 root (0) root (0) 410 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/element-list\n -rw-r--r-- 0 root (0) root (0) 10483 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/help-doc.html\n--rw-r--r-- 0 root (0) root (0) 719384 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/index-all.html\n+-rw-r--r-- 0 root (0) root (0) 719369 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/index-all.html\n -rw-r--r-- 0 root (0) root (0) 7337 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/index.html\n drwxr-xr-x 0 root (0) root (0) 0 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/\n drwxr-xr-x 0 root (0) root (0) 0 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/\n drwxr-xr-x 0 root (0) root (0) 0 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/\n -rw-r--r-- 0 root (0) root (0) 26145 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/Align.html\n -rw-r--r-- 0 root (0) root (0) 11391 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/AlignCommand.html\n -rw-r--r-- 0 root (0) root (0) 8402 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/evolution/align/AlignmentTreeBuilderFactory.Result.html\n@@ -613,15 +613,15 @@\n -rw-r--r-- 0 root (0) root (0) 6336 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/util/package-tree.html\n -rw-r--r-- 0 root (0) root (0) 12680 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jebl/util/package-use.html\n -rw-r--r-- 0 root (0) root (0) 1498 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/jquery-ui.overrides.css\n drwxr-xr-x 0 root (0) root (0) 0 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/legal/\n -rw-r--r-- 0 root (0) root (0) 1522 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/legal/ASSEMBLY_EXCEPTION\n -rw-r--r-- 0 root (0) root (0) 2936 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/legal/jquery.md\n -rw-r--r-- 0 root (0) root (0) 1870 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/legal/jqueryUI.md\n--rw-r--r-- 0 root (0) root (0) 196614 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/member-search-index.js\n+-rw-r--r-- 0 root (0) root (0) 196609 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/member-search-index.js\n -rw-r--r-- 0 root (0) root (0) 45 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/module-search-index.js\n -rw-r--r-- 0 root (0) root (0) 823 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/overview-summary.html\n -rw-r--r-- 0 root (0) root (0) 65234 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/overview-tree.html\n -rw-r--r-- 0 root (0) root (0) 649 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/package-search-index.js\n drwxr-xr-x 0 root (0) root (0) 0 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/resources/\n -rw-r--r-- 0 root (0) root (0) 499 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/resources/glass.png\n -rw-r--r-- 0 root (0) root (0) 394 2020-10-12 19:24:22.000000 ./usr/share/doc/libjebl2-java/api/resources/x.png\n"}, {"source1": "./usr/share/doc/libjebl2-java/api/index-all.html", "source2": "./usr/share/doc/libjebl2-java/api/index-all.html", "unified_diff": "@@ -2684,15 +2684,15 @@\n \n
getSampleCount() - Method in class jebl.evolution.coalescent.Intervals
\n
 
\n
getScore() - Method in class jebl.evolution.align.Align
\n
 
\n
getScore() - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
\n
 
\n-
getScore() - Method in class jebl.evolution.align.SmithWaterman
\n+
getScore() - Method in class jebl.evolution.align.MaximalSegmentPair
\n
 
\n
getScore() - Method in class jebl.evolution.align.BartonSternberg
\n
 
\n
getScore() - Method in class jebl.evolution.align.NeedlemanWunsch
\n
 
\n
getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine
\n
 
\n@@ -4091,23 +4091,23 @@\n
 
\n
next() - Method in class jebl.evolution.io.ImportHelper
\n
 
\n
next(Traceback) - Method in class jebl.evolution.align.Align
\n
\n
Get the next state in the traceback
\n
\n-
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n+
next(Traceback) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
\n
\n
Get the next state in the traceback
\n
\n
next(Traceback) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
\n
Get the next state in the traceback
\n
\n-
next(Traceback) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
\n+
next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunsch
\n
\n
Get the next state in the traceback
\n
\n
next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair
\n
 
\n
nextBoolean() - Static method in class jebl.math.Random
\n
\n@@ -4542,45 +4542,45 @@\n
\n
Initialises the matrices for the alignment.
\n
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
\n
 
\n-
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n+
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
 
\n-
prepareAlignment(String, String) - Method in class jebl.evolution.align.SmithWaterman
\n+
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunsch
\n
 
\n
prepareAlignment(String, String) - Method in class jebl.evolution.align.NeedlemanWunschAffine
\n
 
\n
print() - Method in class jebl.evolution.align.ProfileCharacter
\n
 
\n
print(String) - Method in class jebl.evolution.align.Output
\n
 
\n
print(String) - Method in class jebl.evolution.align.SystemOut
\n
 
\n
printf(Output) - Method in class jebl.evolution.align.Align
\n
\n
Print the matrix (matrices) used to compute the alignment
\n
\n-
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschAffine
\n+
printf(Output) - Method in class jebl.evolution.align.OldNeedlemanWunschAffine
\n
\n
Print matrix used to calculate this alignment.
\n
\n
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpace
\n
\n
Print matrix used to calculate this alignment.
\n
\n-
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n+
printf(Output) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
\n
\n
Print matrix used to calculate this alignment.
\n
\n-
printf(Output) - Method in class jebl.evolution.align.SmithWaterman
\n+
printf(Output) - Method in class jebl.evolution.align.NeedlemanWunsch
\n
\n
Print matrix used to calculate this alignment.
\n
\n
printf(Output) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
\n
Print matrix used to calculate this alignment.
\n
\n@@ -5107,15 +5107,15 @@\n \n
setEdgeLength(Node, Node, double) - Method in class jebl.evolution.trees.SimpleTree
\n
\n
Set edge distance between two adjacent nodes.
\n
\n
setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper
\n
 
\n-
setGapExtend(float) - Method in class jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
\n+
setGapExtend(float) - Method in class jebl.evolution.align.SmithWatermanLinearSpaceAffine
\n
 
\n
setGapExtend(float) - Method in class jebl.evolution.align.NonOverlapMultipleLocalAffine
\n
 
\n
setGapOpen(float) - Method in class jebl.evolution.align.Align
\n
 
\n
setGrowthRate(double) - Method in class jebl.evolution.coalescent.ExponentialGrowth
\n
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -2422,15 +2422,15 @@\n get the total number of sampling events.\n getSampleCount() - Method in class jebl.evolution.coalescent.Intervals\n \u00a0\n getScore() - Method in class jebl.evolution.align.Align\n \u00a0\n getScore() - Method in class jebl.evolution.align.OldNeedlemanWunschAffine\n \u00a0\n- getScore() - Method in class jebl.evolution.align.SmithWaterman\n+ getScore() - Method in class jebl.evolution.align.MaximalSegmentPair\n \u00a0\n getScore() - Method in class jebl.evolution.align.BartonSternberg\n \u00a0\n getScore() - Method in class jebl.evolution.align.NeedlemanWunsch\n \u00a0\n getScore() - Method in class jebl.evolution.align.NeedlemanWunschAffine\n \u00a0\n@@ -3722,21 +3722,20 @@\n jebl.evolution.align.TracebackPlotter\n \u00a0\n next() - Method in class jebl.evolution.io.ImportHelper\n \u00a0\n next(Traceback) - Method in class jebl.evolution.align.Align\n Get the next state in the traceback\n next(Traceback) - Method in class\n- jebl.evolution.align.NeedlemanWunschLinearSpaceAffine\n+ jebl.evolution.align.SmithWatermanLinearSpaceAffine\n Get the next state in the traceback\n next(Traceback) - Method in class\n jebl.evolution.align.NonOverlapMultipleLocalAffine\n Get the next state in the traceback\n- next(Traceback) - Method in class\n- jebl.evolution.align.SmithWatermanLinearSpace\n+ next(Traceback) - Method in class jebl.evolution.align.NeedlemanWunsch\n Get the next state in the traceback\n next(Traceback) - Method in class jebl.evolution.align.MaximalSegmentPair\n \u00a0\n nextBoolean() - Static method in class jebl.math.Random\n Access a default instance of this class, access is synchronized\n nextByte() - Static method in class jebl.math.Random\n Access a default instance of this class, access is synchronized\n@@ -4107,42 +4106,43 @@\n prepareAlignment(String,_String) - Method in class\n jebl.evolution.align.OldNeedlemanWunschAffine\n \u00a0\n prepareAlignment(String,_String) - Method in class\n jebl.evolution.align.SmithWatermanLinearSpace\n \u00a0\n prepareAlignment(String,_String) - Method in class\n- jebl.evolution.align.NeedlemanWunschLinearSpaceAffine\n+ jebl.evolution.align.SmithWatermanLinearSpaceAffine\n \u00a0\n prepareAlignment(String,_String) - Method in class\n jebl.evolution.align.NonOverlapMultipleLocalAffine\n \u00a0\n prepareAlignment(String,_String) - Method in class\n- jebl.evolution.align.SmithWaterman\n+ jebl.evolution.align.NeedlemanWunsch\n \u00a0\n prepareAlignment(String,_String) - Method in class\n jebl.evolution.align.NeedlemanWunschAffine\n \u00a0\n print() - Method in class jebl.evolution.align.ProfileCharacter\n \u00a0\n print(String) - Method in class jebl.evolution.align.Output\n \u00a0\n print(String) - Method in class jebl.evolution.align.SystemOut\n \u00a0\n printf(Output) - Method in class jebl.evolution.align.Align\n Print the matrix (matrices) used to compute the alignment\n- printf(Output) - Method in class jebl.evolution.align.NeedlemanWunschAffine\n+ printf(Output) - Method in class\n+ jebl.evolution.align.OldNeedlemanWunschAffine\n Print matrix used to calculate this alignment.\n printf(Output) - Method in class\n jebl.evolution.align.SmithWatermanLinearSpace\n Print matrix used to calculate this alignment.\n printf(Output) - Method in class\n- jebl.evolution.align.NeedlemanWunschLinearSpaceAffine\n+ jebl.evolution.align.SmithWatermanLinearSpaceAffine\n Print matrix used to calculate this alignment.\n- printf(Output) - Method in class jebl.evolution.align.SmithWaterman\n+ printf(Output) - Method in class jebl.evolution.align.NeedlemanWunsch\n Print matrix used to calculate this alignment.\n printf(Output) - Method in class\n jebl.evolution.align.NonOverlapMultipleLocalAffine\n Print matrix used to calculate this alignment.\n println() - Method in class jebl.evolution.align.Output\n \u00a0\n println() - Method in class jebl.evolution.align.SystemOut\n@@ -4645,15 +4645,15 @@\n Change length of an existing edge.\n setEdgeLength(Node,_Node,_double) - Method in class\n jebl.evolution.trees.SimpleTree\n Set edge distance between two adjacent nodes.\n setExpectedInputLength(long) - Method in class jebl.evolution.io.ImportHelper\n \u00a0\n setGapExtend(float) - Method in class\n- jebl.evolution.align.NeedlemanWunschLinearSpaceAffine\n+ jebl.evolution.align.SmithWatermanLinearSpaceAffine\n \u00a0\n setGapExtend(float) - Method in class\n jebl.evolution.align.NonOverlapMultipleLocalAffine\n \u00a0\n setGapOpen(float) - Method in class jebl.evolution.align.Align\n \u00a0\n setGrowthRate(double) - Method in class\n"}]}, {"source1": "./usr/share/doc/libjebl2-java/api/member-search-index.js", "source2": "./usr/share/doc/libjebl2-java/api/member-search-index.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -3880,15 +3880,15 @@\n \"l\": \"getScore()\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"OldNeedlemanWunschAffine\",\n \"l\": \"getScore()\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"SmithWaterman\",\n+ \"c\": \"MaximalSegmentPair\",\n \"l\": \"getScore()\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"BartonSternberg\",\n \"l\": \"getScore()\"\n }, {\n \"p\": \"jebl.evolution.align\",\n@@ -5921,25 +5921,25 @@\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"Align\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n+ \"c\": \"SmithWatermanLinearSpaceAffine\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"SmithWatermanLinearSpace\",\n+ \"c\": \"NeedlemanWunsch\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"MaximalSegmentPair\",\n \"l\": \"next(Traceback)\",\n \"u\": \"next(jebl.evolution.align.Traceback)\"\n@@ -6450,25 +6450,25 @@\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"SmithWatermanLinearSpace\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n+ \"c\": \"SmithWatermanLinearSpaceAffine\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"SmithWaterman\",\n+ \"c\": \"NeedlemanWunsch\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NeedlemanWunschAffine\",\n \"l\": \"prepareAlignment(String, String)\",\n \"u\": \"prepareAlignment(java.lang.String,java.lang.String)\"\n@@ -6489,30 +6489,30 @@\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"Align\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunschAffine\",\n+ \"c\": \"OldNeedlemanWunschAffine\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"SmithWatermanLinearSpace\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n+ \"c\": \"SmithWatermanLinearSpaceAffine\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"SmithWaterman\",\n+ \"c\": \"NeedlemanWunsch\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"printf(Output)\",\n \"u\": \"printf(jebl.evolution.align.Output)\"\n@@ -7277,15 +7277,15 @@\n \"u\": \"setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)\"\n }, {\n \"p\": \"jebl.evolution.io\",\n \"c\": \"ImportHelper\",\n \"l\": \"setExpectedInputLength(long)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n- \"c\": \"NeedlemanWunschLinearSpaceAffine\",\n+ \"c\": \"SmithWatermanLinearSpaceAffine\",\n \"l\": \"setGapExtend(float)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n \"c\": \"NonOverlapMultipleLocalAffine\",\n \"l\": \"setGapExtend(float)\"\n }, {\n \"p\": \"jebl.evolution.align\",\n"}]}]}]}]}]}