{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.ZZigbBEn/b1/biojava-live_1.9.7+dfsg-1_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.ZZigbBEn/b2/biojava-live_1.9.7+dfsg-1_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,4 +1,4 @@\n \n- f40a9f49091e35daf529b95c4719a1dc 4132544 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb\n+ 1a1c81d107588db85d95be8fb88f3c0e 4132624 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb\n ab782163f0e532230201e8c8b6fd1191 5512 java optional libbiojava-java_1.9.7+dfsg-1_all.deb\n 0088c3dc56fe7264a9179c89ebaae3d1 3154416 java optional libbiojava1.9-java_1.9.7+dfsg-1_all.deb\n"}, {"source1": "libbiojava-java-doc_1.9.7+dfsg-1_all.deb", "source2": "libbiojava-java-doc_1.9.7+dfsg-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 2023-11-29 07:09:37.000000 debian-binary\n--rw-r--r-- 0 0 0 118536 2023-11-29 07:09:37.000000 control.tar.xz\n--rw-r--r-- 0 0 0 4013816 2023-11-29 07:09:37.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 118532 2023-11-29 07:09:37.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 4013900 2023-11-29 07:09:37.000000 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": "@@ -6,22 +6,22 @@\n drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/\n -rw-r--r-- 0 root (0) root (0) 588936 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/allclasses-index.html\n -rw-r--r-- 0 root (0) root (0) 27769 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/allpackages-index.html\n -rw-r--r-- 0 root (0) root (0) 460903 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/constant-values.html\n -rw-r--r-- 0 root (0) root (0) 39572 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/deprecated-list.html\n -rw-r--r-- 0 root (0) root (0) 2568 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/element-list\n -rw-r--r-- 0 root (0) root (0) 10486 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/help-doc.html\n--rw-r--r-- 0 root (0) root (0) 5205004 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/index-all.html\n+-rw-r--r-- 0 root (0) root (0) 5205028 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/index-all.html\n -rw-r--r-- 0 root (0) root (0) 36274 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/index.html\n -rw-r--r-- 0 root (0) root (0) 1498 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/jquery-ui.overrides.css\n drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/legal/\n -rw-r--r-- 0 root (0) root (0) 1522 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/legal/ASSEMBLY_EXCEPTION\n -rw-r--r-- 0 root (0) root (0) 2936 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/legal/jquery.md\n -rw-r--r-- 0 root (0) root (0) 1870 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/legal/jqueryUI.md\n--rw-r--r-- 0 root (0) root (0) 1398833 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/member-search-index.js\n+-rw-r--r-- 0 root (0) root (0) 1398841 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/member-search-index.js\n -rw-r--r-- 0 root (0) root (0) 45 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/module-search-index.js\n drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/\n drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/biojava/\n -rw-r--r-- 0 root (0) root (0) 10002 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/biojava/App.html\n drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/\n -rw-r--r-- 0 root (0) root (0) 34030 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/BibRef.html\n -rw-r--r-- 0 root (0) root (0) 14355 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/biojava/bibliography/BibRefException.html\n"}, {"source1": "./usr/share/doc/libbiojava-java/apidocs/index-all.html", "source2": "./usr/share/doc/libbiojava-java/apidocs/index-all.html", "unified_diff": "@@ -3017,21 +3017,21 @@\n
\n
Create a bean from an XML file, then attempt to enter it.
\n
\n
AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
\n
 
\n
append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
\n
 
\n-
append(T, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\n+
append(T, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
\n
 
\n
append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
\n
\n
Append the specified FASTQ formatted sequences to the specified appendable.
\n
\n-
append(T, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\n+
append(T, Fastq...) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
\n
 
\n
append(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
\n
\n
Append the specified FASTQ formatted sequences to the specified appendable.
\n
\n
appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
\n
 
\n@@ -11725,15 +11725,15 @@\n \n
formatLocation(StringBuffer, Location) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
\n
\n
Deprecated.
\n
formatLocation creates a String representation of\n a Location.
\n
\n-
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.EmblFileFormer
\n+
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
\n
\n
formatLocation creates an EMBL/Genbank style\n representation of a Location.
\n
\n
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
\n
\n
Deprecated.
\n@@ -11742,29 +11742,29 @@\n
\n
formatLocation(StringBuffer, Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
\n
\n
Deprecated.
\n
formatLocation creates a String representation of\n a Location.
\n
\n-
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.EmblFileFormer
\n+
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
\n
\n
Formats the location of a feature.
\n
\n
formatLocation(Feature) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
\n
\n
Deprecated.
\n
Formats the location of a feature.
\n
\n
formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
\n
\n
Deprecated.
\n
Creates a string representation of the location of a feature
\n
\n-
formatLocation(Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.EmblFileFormer
\n+
formatLocation(Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
\n
\n
formatLocation creates an EMBL/Genbank style\n representation of a Location.
\n
\n
formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair
\n
 
\n
formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair
\n@@ -43108,15 +43108,15 @@\n
\n
Takes this position and returns a copy translated by 'distance' bases.
\n
\n
translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
\n
\n
Create a location that is a translation of this location.
\n
\n-
translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
\n+
translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
\n
 
\n
translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable
\n
\n
Translate a single symbol from source alphabet to the target alphabet.
\n
\n
translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes
\n
\n@@ -44284,39 +44284,39 @@\n
\n
WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
\n
\n
Caenorhabditis elegans codon preferences
\n
\n
Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper
\n
 
\n-
write(File, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\n+
write(File, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
\n
 
\n
write(File, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
\n
\n
Write the specified FASTQ formatted sequences to the specified file.
\n
\n-
write(File, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\n+
write(File, Fastq...) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
\n
 
\n
write(File, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
\n
\n
Write the specified FASTQ formatted sequences to the specified file.
\n
\n-
write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\n+
write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
\n
 
\n
write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
\n
\n
Write the specified FASTQ formatted sequences to the specified output stream.
\n
\n
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
\n
\n
Writes out the alignment to an FASTA file.
\n
\n
write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
\n
 
\n-
write(OutputStream, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\n+
write(OutputStream, Fastq...) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter
\n
 
\n
write(OutputStream, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
\n
\n
Write the specified FASTQ formatted sequences to the specified output stream.
\n
\n
write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
\n
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -2779,22 +2779,22 @@\n _\bA_\bp_\bp_\bB_\be_\ba_\bn_\bR_\bu_\bn_\bn_\be_\br - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bu_\bt_\bi_\bl_\bs_\b._\bx_\bm_\bl\n Create a bean from an XML file, then attempt to enter it.\n _\bA_\bp_\bp_\bB_\be_\ba_\bn_\bR_\bu_\bn_\bn_\be_\br_\b(_\b) - Constructor for class org.biojava.utils.xml._\bA_\bp_\bp_\bB_\be_\ba_\bn_\bR_\bu_\bn_\bn_\be_\br\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bN_\bf_\ba_\bS_\bu_\bb_\bM_\bo_\bd_\be_\bl_\b) - Method in class org.biojava.utils.automata._\bN_\bf_\ba_\bS_\bu_\bb_\bM_\bo_\bd_\be_\bl\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Append the specified FASTQ formatted sequences to the specified\n appendable.\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Append the specified FASTQ formatted sequences to the specified\n appendable.\n _\ba_\bp_\bp_\be_\bn_\bd_\bM_\ba_\bt_\br_\bi_\bx_\bD_\ba_\bt_\ba_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n org.biojavax.bio.phylo.io.nexus._\bC_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\bB_\bl_\bo_\bc_\bk\n@@ -10247,38 +10247,38 @@\n _\bF_\bo_\br_\bm_\ba_\bt - Interface in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bb_\bi_\bo_\b._\bp_\br_\bo_\bg_\br_\ba_\bm_\b._\bf_\bo_\br_\bm_\ba_\bt_\bs\n A file format supported by the tag-value event-based parsing system.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b) - Method in class\n org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n formatLocation creates a String representation of a Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in\n- class org.biojava.bio.seq.io._\bE_\bm_\bb_\bl_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n+ class org.biojava.bio.seq.io._\bG_\be_\bn_\bb_\ba_\bn_\bk_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n formatLocation creates an EMBL/Genbank style representation of a\n Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in\n interface org.biojava.bio.seq.io._\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n formatLocation creates a String representation of a Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in\n class org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n formatLocation creates a String representation of a Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in class\n- org.biojava.bio.seq.io._\bE_\bm_\bb_\bl_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n+ org.biojava.bio.seq.io._\bG_\be_\bn_\bb_\ba_\bn_\bk_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Formats the location of a feature.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in interface\n org.biojava.bio.seq.io._\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n Formats the location of a feature.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in class\n org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n Creates a string representation of the location of a feature\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in class\n- org.biojava.bio.seq.io._\bE_\bm_\bb_\bl_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n+ org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n formatLocation creates an EMBL/Genbank style representation of a\n Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bO_\bu_\bt_\bp_\bu_\bt_\b(_\b) - Method in class org.biojava.bio.alignment._\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bP_\ba_\bi_\br\n \u00a0\n _\bf_\bo_\br_\bm_\ba_\bt_\bO_\bu_\bt_\bp_\bu_\bt_\b(_\bi_\bn_\bt_\b) - Method in class org.biojava.bio.alignment._\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bP_\ba_\bi_\br\n This method provides a BLAST-like formated alignment from the given\n Strings, in which the sequence coordinates and the information \"Query\" or\n@@ -36755,15 +36755,15 @@\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in interface org.biojavax.bio.seq._\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn\n Takes this position and returns a copy translated by 'distance' bases.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in class org.biojavax.bio.seq._\bS_\bi_\bm_\bp_\bl_\be_\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn\n Takes this position and returns a copy translated by 'distance' bases.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in class org.biojavax.bio.seq._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n Create a location that is a translation of this location.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in class\n- org.biojava.bio.symbol._\bS_\bi_\bm_\bp_\bl_\be_\bG_\be_\bn_\be_\bt_\bi_\bc_\bC_\bo_\bd_\be_\bT_\ba_\bb_\bl_\be\n+ org.biojava.bio.symbol._\bS_\bi_\bm_\bp_\bl_\be_\bM_\ba_\bn_\by_\bT_\bo_\bO_\bn_\be_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n \u00a0\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in interface\n org.biojava.bio.symbol._\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n Translate a single symbol from source alphabet to the target alphabet.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\bL_\bi_\bs_\bt_\b) - Static method in class\n org.biojava.bio.seq._\bG_\be_\bn_\be_\bt_\bi_\bc_\bC_\bo_\bd_\be_\bs\n Translate RNA into protein (with termination symbols).\n@@ -37680,40 +37680,40 @@\n width.\n _\bW_\bO_\bR_\bM_\b__\bN_\bU_\bC_\bL_\bE_\bA_\bR - Static variable in class org.biojava.bio.symbol._\bC_\bo_\bd_\bo_\bn_\bP_\br_\be_\bf_\bT_\bo_\bo_\bl_\bs\n Caenorhabditis elegans codon preferences\n _\bW_\br_\ba_\bp_\bp_\be_\br_\b(_\bS_\be_\ba_\br_\bc_\bh_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Constructor for class\n org.biojava.bio.program.ssaha._\bS_\be_\ba_\br_\bc_\bh_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b._\bW_\br_\ba_\bp_\bp_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified file.\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified file.\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified output\n stream.\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.seq.io._\bF_\ba_\bs_\bt_\ba_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bF_\bo_\br_\bm_\ba_\bt\n Writes out the alignment to an FASTA file.\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.seq.io._\bM_\bS_\bF_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified output\n stream.\n _\bw_\br_\bi_\bt_\be_\b(_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b) - Method in class org.biojava.bio.seq.io.agave._\bA_\bg_\ba_\bv_\be_\bW_\br_\bi_\bt_\be_\br\n Writing Sequence.\n"}]}, {"source1": "./usr/share/doc/libbiojava-java/apidocs/member-search-index.js", "source2": "./usr/share/doc/libbiojava-java/apidocs/member-search-index.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -3994,25 +3994,25 @@\n }, {\n \"p\": \"org.biojava.utils.automata\",\n \"c\": \"NfaSubModel\",\n \"l\": \"append(NfaSubModel)\",\n \"u\": \"append(org.biojava.utils.automata.NfaSubModel)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\n \"l\": \"append(T, Fastq...)\",\n \"u\": \"append(T,org.biojava.bio.program.fastq.Fastq...)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqWriter\",\n \"l\": \"append(T, Fastq...)\",\n \"u\": \"append(T,org.biojava.bio.program.fastq.Fastq...)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\n \"l\": \"append(T, Iterable)\",\n \"u\": \"append(T,java.lang.Iterable)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqWriter\",\n \"l\": \"append(T, Iterable)\",\n \"u\": \"append(T,java.lang.Iterable)\"\n@@ -14430,40 +14430,40 @@\n \"l\": \"forIndex(int)\"\n }, {\n \"p\": \"org.biojava.bibliography\",\n \"c\": \"BibRef\",\n \"l\": \"format\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n- \"c\": \"EmblFileFormer\",\n+ \"c\": \"GenbankFileFormer\",\n \"l\": \"formatLocation(Feature)\",\n \"u\": \"formatLocation(org.biojava.bio.seq.Feature)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SeqFileFormer\",\n \"l\": \"formatLocation(Feature)\",\n \"u\": \"formatLocation(org.biojava.bio.seq.Feature)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SwissprotFileFormer\",\n \"l\": \"formatLocation(Feature)\",\n \"u\": \"formatLocation(org.biojava.bio.seq.Feature)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n- \"c\": \"EmblFileFormer\",\n+ \"c\": \"SwissprotFileFormer\",\n \"l\": \"formatLocation(Location, StrandedFeature.Strand)\",\n \"u\": \"formatLocation(org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SwissprotFileFormer\",\n \"l\": \"formatLocation(StringBuffer, Location)\",\n \"u\": \"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n- \"c\": \"EmblFileFormer\",\n+ \"c\": \"GenbankFileFormer\",\n \"l\": \"formatLocation(StringBuffer, Location, StrandedFeature.Strand)\",\n \"u\": \"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SeqFileFormer\",\n \"l\": \"formatLocation(StringBuffer, Location, StrandedFeature.Strand)\",\n \"u\": \"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)\"\n@@ -53366,15 +53366,15 @@\n \"l\": \"translate(int)\"\n }, {\n \"p\": \"org.biojavax.bio.seq\",\n \"c\": \"SimpleRichLocation\",\n \"l\": \"translate(int)\"\n }, {\n \"p\": \"org.biojava.bio.symbol\",\n- \"c\": \"SimpleGeneticCodeTable\",\n+ \"c\": \"SimpleManyToOneTranslationTable\",\n \"l\": \"translate(Symbol)\",\n \"u\": \"translate(org.biojava.bio.symbol.Symbol)\"\n }, {\n \"p\": \"org.biojava.bio.symbol\",\n \"c\": \"TranslationTable\",\n \"l\": \"translate(Symbol)\",\n \"u\": \"translate(org.biojava.bio.symbol.Symbol)\"\n@@ -54624,25 +54624,25 @@\n }, {\n \"p\": \"org.biojava.bio.program.ssaha\",\n \"c\": \"SearchListener.Wrapper\",\n \"l\": \"Wrapper(SearchListener)\",\n \"u\": \"%3Cinit%3E(org.biojava.bio.program.ssaha.SearchListener)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\n \"l\": \"write(File, Fastq...)\",\n \"u\": \"write(java.io.File,org.biojava.bio.program.fastq.Fastq...)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqWriter\",\n \"l\": \"write(File, Fastq...)\",\n \"u\": \"write(java.io.File,org.biojava.bio.program.fastq.Fastq...)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\n \"l\": \"write(File, Iterable)\",\n \"u\": \"write(java.io.File,java.lang.Iterable)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqWriter\",\n \"l\": \"write(File, Iterable)\",\n \"u\": \"write(java.io.File,java.lang.Iterable)\"\n@@ -54654,25 +54654,25 @@\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"MSFAlignmentFormat\",\n \"l\": \"write(OutputStream, Alignment, int)\",\n \"u\": \"write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\n \"l\": \"write(OutputStream, Fastq...)\",\n \"u\": \"write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqWriter\",\n \"l\": \"write(OutputStream, Fastq...)\",\n \"u\": \"write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\n \"l\": \"write(OutputStream, Iterable)\",\n \"u\": \"write(java.io.OutputStream,java.lang.Iterable)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqWriter\",\n \"l\": \"write(OutputStream, Iterable)\",\n \"u\": \"write(java.io.OutputStream,java.lang.Iterable)\"\n"}]}]}]}]}]}