{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.55hnq6KP/b1/biojava-live_1.9.7+dfsg-1_i386.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.55hnq6KP/b2/biojava-live_1.9.7+dfsg-1_i386.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,4 +1,4 @@\n \n- f33b8b4356de067753b13638339fd564 4132564 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb\n+ fea2aa4173b98c8ed5c3bf728cf09fdc 4132572 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 118540 2023-11-29 07:09:37.000000 control.tar.xz\n--rw-r--r-- 0 0 0 4013832 2023-11-29 07:09:37.000000 data.tar.xz\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 4013844 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) 5205169 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) 5205190 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) 1398888 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) 1398895 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.SangerFastqWriter
\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.SangerFastqWriter
\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@@ -8350,15 +8350,15 @@\n
 
\n
doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper
\n
\n
Find out if known tags are retained or dropped.
\n
\n
doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
\n
 
\n-
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
\n+
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
\n
\n
this method is expected to translate any symbol\n in the source alphabet.
\n
\n
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
\n
 
\n
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
\n@@ -11756,15 +11756,15 @@\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.SwissprotFileFormer
\n+
formatLocation(Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.EmblFileFormer
\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@@ -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.SolexaFastqReader
\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.FastaSearchSAXParser
\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.SolexaFastqReader
\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.SolexaFastqReader
\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.SolexaFastqReader
\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.SolexaFastqReader
\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.SimpleTranslationTable
\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.SangerFastqWriter
\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.SangerFastqWriter
\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.SangerFastqWriter
\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.SangerFastqWriter
\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": "@@ -2788,22 +2788,22 @@\n AppBeanRunner - Class in org.biojava.utils.xml\n Create a bean from an XML file, then attempt to enter it.\n AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner\n \u00a0\n append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel\n \u00a0\n append(T,_Iterable) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqWriter\n+ org.biojava.bio.program.fastq.IlluminaFastqWriter\n \u00a0\n append(T,_Iterable) - Method in interface\n org.biojava.bio.program.fastq.FastqWriter\n Append the specified FASTQ formatted sequences to the specified\n appendable.\n append(T,_Fastq...) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqWriter\n+ org.biojava.bio.program.fastq.IlluminaFastqWriter\n \u00a0\n append(T,_Fastq...) - Method in interface\n org.biojava.bio.program.fastq.FastqWriter\n Append the specified FASTQ formatted sequences to the specified\n appendable.\n appendMatrixData(String,_Object) - Method in class\n org.biojavax.bio.phylo.io.nexus.CharactersBlock\n@@ -7271,15 +7271,15 @@\n \u00a0\n doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper\n Find out if known tags are retained or dropped.\n doSortPeptides() - Method in class\n org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer\n \u00a0\n doTranslate(Symbol) - Method in class\n- org.biojava.bio.symbol.AbstractManyToOneTranslationTable\n+ org.biojava.bio.symbol.AbstractReversibleTranslationTable\n this method is expected to translate any symbol in the source alphabet.\n doTranslate(Symbol) - Method in class\n org.biojava.bio.symbol.SimpleManyToOneTranslationTable\n \u00a0\n doTranslate(Symbol) - Method in class\n org.biojava.bio.symbol.SimpleReversibleTranslationTable\n \u00a0\n@@ -10279,15 +10279,15 @@\n Deprecated.\n Formats the location of a feature.\n formatLocation(Feature) - Method in class\n org.biojava.bio.seq.io.SwissprotFileFormer\n Deprecated.\n Creates a string representation of the location of a feature\n formatLocation(Location,_StrandedFeature.Strand) - Method in class\n- org.biojava.bio.seq.io.SwissprotFileFormer\n+ org.biojava.bio.seq.io.EmblFileFormer\n formatLocation creates an EMBL/Genbank style representation of a\n Location.\n formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair\n \u00a0\n formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair\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@@ -25058,15 +25058,15 @@\n \u00a0\n parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser\n \u00a0\n parse(Object) - Method in interface\n org.biojava.bio.program.tagvalue.TagValueParser\n \u00a0\n parse(Readable,_ParseListener) - Method in class\n- org.biojava.bio.program.fastq.SolexaFastqReader\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n parse(Readable,_ParseListener) - Method in interface\n org.biojava.bio.program.fastq.FastqReader\n Parse the specified readable.\n parse(String) - Method in class\n org.biojava.bio.program.sax.FastaSearchSAXParser\n Full implementation of interface method.\n@@ -26560,26 +26560,27 @@\n Reads an alignment in FASTA format.\n read(BufferedReader) - Method in class\n org.biojava.bio.seq.io.MSFAlignmentFormat\n Reads an MSF Alignment File\n read(BufferedReader,_TagValueParser,_TagValueListener) - Method in class\n org.biojava.bio.program.tagvalue.Parser\n \u00a0\n- read(File) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader\n+ read(File) - Method in class\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader\n Read zero or more FASTQ formatted sequences from the specified file.\n read(InputStream) - Method in class\n- org.biojava.bio.program.fastq.SolexaFastqReader\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n read(InputStream) - Method in interface\n org.biojava.bio.program.fastq.FastqReader\n Read zero or more FASTQ formatted sequences from the specified input\n stream.\n- read(URL) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader\n+ read(URL) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader\n Read zero or more FASTQ formatted sequences from the specified url.\n readableFileNames - Static variable in class\n org.biojavax.bio.seq.io.EMBLFormat\n \u00a0\n readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat\n@@ -35011,15 +35012,15 @@\n org.biojava.bio.seq.FeatureFilter.StrandFilter\n Build a new filter that matches all features of a given strand.\n StrandParser - Class in org.biojava.bio.seq\n Process strings and return strand objects.\n StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser\n \u00a0\n stream(Readable,_StreamListener) - Method in class\n- org.biojava.bio.program.fastq.SolexaFastqReader\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n stream(Readable,_StreamListener) - Method in interface\n org.biojava.bio.program.fastq.FastqReader\n Stream the specified readable.\n StreamListener - Interface in org.biojava.bio.program.fastq\n Event based parser callback.\n streamNext(SeqIOListener) - Method in class\n@@ -36763,15 +36764,15 @@\n translate(int) - Method in interface org.biojavax.bio.seq.Position\n Takes this position and returns a copy translated by 'distance' bases.\n translate(int) - Method in class org.biojavax.bio.seq.SimplePosition\n Takes this position and returns a copy translated by 'distance' bases.\n translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation\n Create a location that is a translation of this location.\n translate(Symbol) - Method in class\n- org.biojava.bio.symbol.AbstractManyToOneTranslationTable\n+ org.biojava.bio.symbol.SimpleTranslationTable\n \u00a0\n translate(Symbol) - Method in interface\n org.biojava.bio.symbol.TranslationTable\n Translate a single symbol from source alphabet to the target alphabet.\n translate(SymbolList) - Static method in class\n org.biojava.bio.seq.GeneticCodes\n Translate RNA into protein (with termination symbols).\n@@ -37688,40 +37689,40 @@\n width.\n WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools\n Caenorhabditis elegans codon preferences\n Wrapper(SearchListener) - Constructor for class\n org.biojava.bio.program.ssaha.SearchListener.Wrapper\n \u00a0\n write(File,_Iterable) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqWriter\n+ org.biojava.bio.program.fastq.IlluminaFastqWriter\n \u00a0\n write(File,_Iterable) - Method in interface\n org.biojava.bio.program.fastq.FastqWriter\n Write the specified FASTQ formatted sequences to the specified file.\n write(File,_Fastq...) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqWriter\n+ org.biojava.bio.program.fastq.IlluminaFastqWriter\n \u00a0\n write(File,_Fastq...) - Method in interface\n org.biojava.bio.program.fastq.FastqWriter\n Write the specified FASTQ formatted sequences to the specified file.\n write(OutputStream,_Iterable) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqWriter\n+ org.biojava.bio.program.fastq.IlluminaFastqWriter\n \u00a0\n write(OutputStream,_Iterable) - Method in interface\n org.biojava.bio.program.fastq.FastqWriter\n Write the specified FASTQ formatted sequences to the specified output\n stream.\n write(OutputStream,_Alignment,_int) - Method in class\n org.biojava.bio.seq.io.FastaAlignmentFormat\n Writes out the alignment to an FASTA file.\n write(OutputStream,_Alignment,_int) - Method in class\n org.biojava.bio.seq.io.MSFAlignmentFormat\n \u00a0\n write(OutputStream,_Fastq...) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqWriter\n+ org.biojava.bio.program.fastq.IlluminaFastqWriter\n \u00a0\n write(OutputStream,_Fastq...) - Method in interface\n org.biojava.bio.program.fastq.FastqWriter\n Write the specified FASTQ formatted sequences to the specified output\n stream.\n write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter\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\": \"SangerFastqWriter\",\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\": \"SangerFastqWriter\",\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@@ -10199,15 +10199,15 @@\n \"l\": \"doRetain()\"\n }, {\n \"p\": \"org.biojava.bio.gui.sequence\",\n \"c\": \"AbstractPeptideDigestRenderer\",\n \"l\": \"doSortPeptides()\"\n }, {\n \"p\": \"org.biojava.bio.symbol\",\n- \"c\": \"AbstractManyToOneTranslationTable\",\n+ \"c\": \"AbstractReversibleTranslationTable\",\n \"l\": \"doTranslate(Symbol)\",\n \"u\": \"doTranslate(org.biojava.bio.symbol.Symbol)\"\n }, {\n \"p\": \"org.biojava.bio.symbol\",\n \"c\": \"SimpleManyToOneTranslationTable\",\n \"l\": \"doTranslate(Symbol)\",\n \"u\": \"doTranslate(org.biojava.bio.symbol.Symbol)\"\n@@ -14445,15 +14445,15 @@\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\": \"SwissprotFileFormer\",\n+ \"c\": \"EmblFileFormer\",\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@@ -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\": \"SolexaFastqReader\",\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\": \"SolexaFastqReader\",\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\": \"SolexaFastqReader\",\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\": \"SolexaFastqReader\",\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\": \"SolexaFastqReader\",\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\": \"SimpleTranslationTable\",\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\": \"SangerFastqWriter\",\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\": \"SangerFastqWriter\",\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\": \"SangerFastqWriter\",\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\": \"SangerFastqWriter\",\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"}]}]}]}]}]}