{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.N57Zao4f/b1/biojava-live_1.9.7+dfsg-1_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.N57Zao4f/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- 81f6d07d313aae34b7855b3025d9e73b 4132572 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb\n+ f85072dd7156bd31e6aec3b3c7370f32 4132564 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 118544 2023-11-29 07:09:37.000000 control.tar.xz\n--rw-r--r-- 0 0 0 4013836 2023-11-29 07:09:37.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 118564 2023-11-29 07:09:37.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 4013808 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) 5205421 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) 5205454 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) 1398972 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) 1398983 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.SolexaFastqWriter
\n+
append(T, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\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.SolexaFastqWriter
\n+
append(T, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\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@@ -29486,15 +29486,15 @@\n \n
parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
\n
 
\n
parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser
\n
 
\n
parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser
\n
 
\n-
parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.SangerFastqReader
\n+
parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
\n
 
\n
parse(Readable, ParseListener) - Method in interface org.biojava.bio.program.fastq.FastqReader
\n
\n
Parse the specified readable.
\n
\n
parse(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser
\n
\n@@ -31237,27 +31237,27 @@\n
\n
read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
\n
\n
Reads an MSF Alignment File
\n
\n
read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
\n
 
\n-
read(File) - Method in class org.biojava.bio.program.fastq.SangerFastqReader
\n+
read(File) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
\n
 
\n
read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader
\n
\n
Read zero or more FASTQ formatted sequences from the specified file.
\n
\n-
read(InputStream) - Method in class org.biojava.bio.program.fastq.SangerFastqReader
\n+
read(InputStream) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
\n
 
\n
read(InputStream) - Method in interface org.biojava.bio.program.fastq.FastqReader
\n
\n
Read zero or more FASTQ formatted sequences from the specified input stream.
\n
\n-
read(URL) - Method in class org.biojava.bio.program.fastq.SangerFastqReader
\n+
read(URL) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
\n
 
\n
read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader
\n
\n
Read zero or more FASTQ formatted sequences from the specified url.
\n
\n
readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
\n
 
\n@@ -41034,15 +41034,15 @@\n \n
StrandParser - Class in org.biojava.bio.seq
\n
\n
Process strings and return strand objects.
\n
\n
StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
\n
 
\n-
stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.SangerFastqReader
\n+
stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
\n
 
\n
stream(Readable, StreamListener) - Method in interface org.biojava.bio.program.fastq.FastqReader
\n
\n
Stream the specified readable.
\n
\n
StreamListener - Interface in org.biojava.bio.program.fastq
\n
\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.AbstractManyToOneTranslationTable
\n+
translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
\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.SolexaFastqWriter
\n+
write(File, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\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.SolexaFastqWriter
\n+
write(File, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\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.SolexaFastqWriter
\n+
write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\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.SolexaFastqWriter
\n+
write(OutputStream, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
\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._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\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 \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._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\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 \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@@ -25050,15 +25050,15 @@\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class org.biojava.bio.program.tagvalue._\bR_\be_\bg_\be_\bx_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in interface\n org.biojava.bio.program.tagvalue._\bT_\ba_\bg_\bV_\ba_\bl_\bu_\be_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bP_\ba_\br_\bs_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n- org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bP_\ba_\br_\bs_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Parse the specified readable.\n _\bp_\ba_\br_\bs_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Full implementation of interface method.\n@@ -26552,26 +26552,27 @@\n Reads an alignment in FASTA format.\n _\br_\be_\ba_\bd_\b(_\bB_\bu_\bf_\bf_\be_\br_\be_\bd_\bR_\be_\ba_\bd_\be_\br_\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 Reads an MSF Alignment File\n _\br_\be_\ba_\bd_\b(_\bB_\bu_\bf_\bf_\be_\br_\be_\bd_\bR_\be_\ba_\bd_\be_\br_\b,_\b _\bT_\ba_\bg_\bV_\ba_\bl_\bu_\be_\bP_\ba_\br_\bs_\be_\br_\b,_\b _\bT_\ba_\bg_\bV_\ba_\bl_\bu_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n org.biojava.bio.program.tagvalue._\bP_\ba_\br_\bs_\be_\br\n \u00a0\n- _\br_\be_\ba_\bd_\b(_\bF_\bi_\bl_\be_\b) - Method in class org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ _\br_\be_\ba_\bd_\b(_\bF_\bi_\bl_\be_\b) - Method in class\n+ org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\br_\be_\ba_\bd_\b(_\bF_\bi_\bl_\be_\b) - Method in interface org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Read zero or more FASTQ formatted sequences from the specified file.\n _\br_\be_\ba_\bd_\b(_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b) - Method in class\n- org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\br_\be_\ba_\bd_\b(_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Read zero or more FASTQ formatted sequences from the specified input\n stream.\n- _\br_\be_\ba_\bd_\b(_\bU_\bR_\bL_\b) - Method in class org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ _\br_\be_\ba_\bd_\b(_\bU_\bR_\bL_\b) - Method in class org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\br_\be_\ba_\bd_\b(_\bU_\bR_\bL_\b) - Method in interface org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Read zero or more FASTQ formatted sequences from the specified url.\n _\br_\be_\ba_\bd_\ba_\bb_\bl_\be_\bF_\bi_\bl_\be_\bN_\ba_\bm_\be_\bs - Static variable in class\n org.biojavax.bio.seq.io._\bE_\bM_\bB_\bL_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\br_\be_\ba_\bd_\ba_\bb_\bl_\be_\bF_\bi_\bl_\be_\bs - Static variable in class org.biojavax.bio.seq.io._\bF_\ba_\bs_\bt_\ba_\bF_\bo_\br_\bm_\ba_\bt\n@@ -35003,15 +35004,15 @@\n org.biojava.bio.seq._\bF_\be_\ba_\bt_\bu_\br_\be_\bF_\bi_\bl_\bt_\be_\br_\b._\bS_\bt_\br_\ba_\bn_\bd_\bF_\bi_\bl_\bt_\be_\br\n Build a new filter that matches all features of a given strand.\n _\bS_\bt_\br_\ba_\bn_\bd_\bP_\ba_\br_\bs_\be_\br - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bb_\bi_\bo_\b._\bs_\be_\bq\n Process strings and return strand objects.\n _\bS_\bt_\br_\ba_\bn_\bd_\bP_\ba_\br_\bs_\be_\br_\b(_\b) - Constructor for class org.biojava.bio.seq._\bS_\bt_\br_\ba_\bn_\bd_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bs_\bt_\br_\be_\ba_\bm_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bS_\bt_\br_\be_\ba_\bm_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n- org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\bs_\bt_\br_\be_\ba_\bm_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bS_\bt_\br_\be_\ba_\bm_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Stream the specified readable.\n _\bS_\bt_\br_\be_\ba_\bm_\bL_\bi_\bs_\bt_\be_\bn_\be_\br - 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_\ba_\bs_\bt_\bq\n Event based parser callback.\n _\bs_\bt_\br_\be_\ba_\bm_\bN_\be_\bx_\bt_\b(_\bS_\be_\bq_\bI_\bO_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n@@ -36755,15 +36756,15 @@\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._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\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+ 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 \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 +37681,40 @@\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._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\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 \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._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\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 \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._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\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 \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._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\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 \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\": \"SolexaFastqWriter\",\n+ \"c\": \"IlluminaFastqWriter\",\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\": \"SolexaFastqWriter\",\n+ \"c\": \"IlluminaFastqWriter\",\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@@ -36584,15 +36584,15 @@\n }, {\n \"p\": \"org.biojavax.bio.phylo.io.phylip\",\n \"c\": \"PHYLIPFileFormat\",\n \"l\": \"parse(PHYLIPFileListener, BufferedReader)\",\n \"u\": \"parse(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener,java.io.BufferedReader)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"parse(Readable, ParseListener)\",\n \"u\": \"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"parse(Readable, ParseListener)\",\n \"u\": \"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)\"\n@@ -38670,35 +38670,35 @@\n }, {\n \"p\": \"org.biojava.utils.io\",\n \"c\": \"RandomAccessReader\",\n \"l\": \"read(char[], int, int)\",\n \"u\": \"read(char[],int,int)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"read(File)\",\n \"u\": \"read(java.io.File)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"read(File)\",\n \"u\": \"read(java.io.File)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"read(InputStream)\",\n \"u\": \"read(java.io.InputStream)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"read(InputStream)\",\n \"u\": \"read(java.io.InputStream)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"read(URL)\",\n \"u\": \"read(java.net.URL)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"read(URL)\",\n \"u\": \"read(java.net.URL)\"\n@@ -50748,15 +50748,15 @@\n }, {\n \"p\": \"org.biojava.bio.seq\",\n \"c\": \"StrandParser\",\n \"l\": \"StrandParser()\",\n \"u\": \"%3Cinit%3E()\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"stream(Readable, StreamListener)\",\n \"u\": \"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"stream(Readable, StreamListener)\",\n \"u\": \"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)\"\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\": \"AbstractManyToOneTranslationTable\",\n+ \"c\": \"SimpleGeneticCodeTable\",\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\": \"SolexaFastqWriter\",\n+ \"c\": \"IlluminaFastqWriter\",\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\": \"SolexaFastqWriter\",\n+ \"c\": \"IlluminaFastqWriter\",\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\": \"SolexaFastqWriter\",\n+ \"c\": \"IlluminaFastqWriter\",\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\": \"SolexaFastqWriter\",\n+ \"c\": \"IlluminaFastqWriter\",\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"}]}]}]}]}]}