--- /srv/reproducible-results/rbuild-debian/r-b-build.55hnq6KP/b1/biojava-live_1.9.7+dfsg-1_i386.changes
+++ /srv/reproducible-results/rbuild-debian/r-b-build.55hnq6KP/b2/biojava-live_1.9.7+dfsg-1_i386.changes
├── Files
│ @@ -1,4 +1,4 @@
│
│ - f33b8b4356de067753b13638339fd564 4132564 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb
│ + fea2aa4173b98c8ed5c3bf728cf09fdc 4132572 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb
│ ab782163f0e532230201e8c8b6fd1191 5512 java optional libbiojava-java_1.9.7+dfsg-1_all.deb
│ 0088c3dc56fe7264a9179c89ebaae3d1 3154416 java optional libbiojava1.9-java_1.9.7+dfsg-1_all.deb
├── libbiojava-java-doc_1.9.7+dfsg-1_all.deb
│ ├── file list
│ │ @@ -1,3 +1,3 @@
│ │ -rw-r--r-- 0 0 0 4 2023-11-29 07:09:37.000000 debian-binary
│ │ --rw-r--r-- 0 0 0 118540 2023-11-29 07:09:37.000000 control.tar.xz
│ │ --rw-r--r-- 0 0 0 4013832 2023-11-29 07:09:37.000000 data.tar.xz
│ │ +-rw-r--r-- 0 0 0 118536 2023-11-29 07:09:37.000000 control.tar.xz
│ │ +-rw-r--r-- 0 0 0 4013844 2023-11-29 07:09:37.000000 data.tar.xz
│ ├── control.tar.xz
│ │ ├── control.tar
│ │ │ ├── ./md5sums
│ │ │ │ ├── ./md5sums
│ │ │ │ │┄ Files differ
│ ├── data.tar.xz
│ │ ├── data.tar
│ │ │ ├── file list
│ │ │ │ @@ -6,22 +6,22 @@
│ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/
│ │ │ │ -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
│ │ │ │ -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
│ │ │ │ -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
│ │ │ │ -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
│ │ │ │ -rw-r--r-- 0 root (0) root (0) 2568 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/element-list
│ │ │ │ -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
│ │ │ │ --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
│ │ │ │ +-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
│ │ │ │ -rw-r--r-- 0 root (0) root (0) 36274 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/index.html
│ │ │ │ -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
│ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/legal/
│ │ │ │ -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
│ │ │ │ -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
│ │ │ │ -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
│ │ │ │ --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
│ │ │ │ +-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
│ │ │ │ -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
│ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/
│ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2023-11-29 07:09:37.000000 ./usr/share/doc/libbiojava-java/apidocs/org/biojava/
│ │ │ │ -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
│ │ │ │ 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/
│ │ │ │ -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
│ │ │ │ -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
│ │ │ ├── ./usr/share/doc/libbiojava-java/apidocs/index-all.html
│ │ │ │ @@ -3017,21 +3017,21 @@
│ │ │ │
│ │ │ │ Create a bean from an XML file, then attempt to enter it.
│ │ │ │
│ │ │ │ AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
│ │ │ │
│ │ │ │ append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
│ │ │ │
│ │ │ │ -append(T, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ +append(T, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │
│ │ │ │ append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
│ │ │ │
│ │ │ │ Append the specified FASTQ formatted sequences to the specified appendable.
│ │ │ │
│ │ │ │ -append(T, Fastq...) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ +append(T, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │
│ │ │ │ append(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
│ │ │ │
│ │ │ │ Append the specified FASTQ formatted sequences to the specified appendable.
│ │ │ │
│ │ │ │ appendMatrixData(String, Object) - Method in class org.biojavax.bio.phylo.io.nexus.CharactersBlock
│ │ │ │
│ │ │ │ @@ -8350,15 +8350,15 @@
│ │ │ │
│ │ │ │ doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper
│ │ │ │
│ │ │ │ Find out if known tags are retained or dropped.
│ │ │ │
│ │ │ │ doSortPeptides() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
│ │ │ │
│ │ │ │ -doTranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
│ │ │ │ +doTranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
│ │ │ │
│ │ │ │ this method is expected to translate any symbol
│ │ │ │ in the source alphabet.
│ │ │ │
│ │ │ │ doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
│ │ │ │
│ │ │ │ doTranslate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
│ │ │ │ @@ -11756,15 +11756,15 @@
│ │ │ │ Formats the location of a feature.
│ │ │ │
│ │ │ │ formatLocation(Feature) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
│ │ │ │
│ │ │ │ Deprecated.
│ │ │ │ Creates a string representation of the location of a feature
│ │ │ │
│ │ │ │ -formatLocation(Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
│ │ │ │ +formatLocation(Location, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.EmblFileFormer
│ │ │ │
│ │ │ │ formatLocation creates an EMBL/Genbank style
│ │ │ │ representation of a Location.
│ │ │ │
│ │ │ │ formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair
│ │ │ │
│ │ │ │ formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair
│ │ │ │ @@ -29486,15 +29486,15 @@
│ │ │ │
│ │ │ │ parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
│ │ │ │
│ │ │ │ parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser
│ │ │ │
│ │ │ │ parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser
│ │ │ │
│ │ │ │ -parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ +parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │
│ │ │ │ parse(Readable, ParseListener) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │
│ │ │ │ Parse the specified readable.
│ │ │ │
│ │ │ │ parse(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
│ │ │ │
│ │ │ │ @@ -31237,27 +31237,27 @@
│ │ │ │
│ │ │ │ read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
│ │ │ │
│ │ │ │ Reads an MSF Alignment File
│ │ │ │
│ │ │ │ read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
│ │ │ │
│ │ │ │ -read(File) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ +read(File) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │
│ │ │ │ read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │
│ │ │ │ Read zero or more FASTQ formatted sequences from the specified file.
│ │ │ │
│ │ │ │ -read(InputStream) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ +read(InputStream) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │
│ │ │ │ read(InputStream) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │
│ │ │ │ Read zero or more FASTQ formatted sequences from the specified input stream.
│ │ │ │
│ │ │ │ -read(URL) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ +read(URL) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │
│ │ │ │ read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │
│ │ │ │ Read zero or more FASTQ formatted sequences from the specified url.
│ │ │ │
│ │ │ │ readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
│ │ │ │
│ │ │ │ @@ -41034,15 +41034,15 @@
│ │ │ │
│ │ │ │ StrandParser - Class in org.biojava.bio.seq
│ │ │ │
│ │ │ │ Process strings and return strand objects.
│ │ │ │
│ │ │ │ StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
│ │ │ │
│ │ │ │ -stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ +stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │
│ │ │ │ stream(Readable, StreamListener) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │
│ │ │ │ Stream the specified readable.
│ │ │ │
│ │ │ │ StreamListener - Interface in org.biojava.bio.program.fastq
│ │ │ │
│ │ │ │ @@ -43108,15 +43108,15 @@
│ │ │ │
│ │ │ │ Takes this position and returns a copy translated by 'distance' bases.
│ │ │ │
│ │ │ │ translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
│ │ │ │
│ │ │ │ Create a location that is a translation of this location.
│ │ │ │
│ │ │ │ -translate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
│ │ │ │ +translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
│ │ │ │
│ │ │ │ translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable
│ │ │ │
│ │ │ │ Translate a single symbol from source alphabet to the target alphabet.
│ │ │ │
│ │ │ │ translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes
│ │ │ │
│ │ │ │ @@ -44284,39 +44284,39 @@
│ │ │ │
│ │ │ │ WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
│ │ │ │
│ │ │ │ Caenorhabditis elegans codon preferences
│ │ │ │
│ │ │ │ Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper
│ │ │ │
│ │ │ │ -write(File, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ +write(File, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │
│ │ │ │ write(File, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
│ │ │ │
│ │ │ │ Write the specified FASTQ formatted sequences to the specified file.
│ │ │ │
│ │ │ │ -write(File, Fastq...) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ +write(File, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │
│ │ │ │ write(File, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
│ │ │ │
│ │ │ │ Write the specified FASTQ formatted sequences to the specified file.
│ │ │ │
│ │ │ │ -write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ +write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │
│ │ │ │ write(OutputStream, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
│ │ │ │
│ │ │ │ Write the specified FASTQ formatted sequences to the specified output stream.
│ │ │ │
│ │ │ │ write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
│ │ │ │
│ │ │ │ Writes out the alignment to an FASTA file.
│ │ │ │
│ │ │ │ write(OutputStream, Alignment, int) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
│ │ │ │
│ │ │ │ -write(OutputStream, Fastq...) - Method in class org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ +write(OutputStream, Fastq...) - Method in class org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │
│ │ │ │ write(OutputStream, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
│ │ │ │
│ │ │ │ Write the specified FASTQ formatted sequences to the specified output stream.
│ │ │ │
│ │ │ │ write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
│ │ │ │
│ │ │ │ ├── html2text {}
│ │ │ │ │ @@ -2788,22 +2788,22 @@
│ │ │ │ │ AppBeanRunner - Class in org.biojava.utils.xml
│ │ │ │ │ Create a bean from an XML file, then attempt to enter it.
│ │ │ │ │ AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
│ │ │ │ │
│ │ │ │ │ append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
│ │ │ │ │
│ │ │ │ │ append(T,_Iterable) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │ │
│ │ │ │ │ append(T,_Iterable) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqWriter
│ │ │ │ │ Append the specified FASTQ formatted sequences to the specified
│ │ │ │ │ appendable.
│ │ │ │ │ append(T,_Fastq...) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │ │
│ │ │ │ │ append(T,_Fastq...) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqWriter
│ │ │ │ │ Append the specified FASTQ formatted sequences to the specified
│ │ │ │ │ appendable.
│ │ │ │ │ appendMatrixData(String,_Object) - Method in class
│ │ │ │ │ org.biojavax.bio.phylo.io.nexus.CharactersBlock
│ │ │ │ │ @@ -7271,15 +7271,15 @@
│ │ │ │ │
│ │ │ │ │ doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper
│ │ │ │ │ Find out if known tags are retained or dropped.
│ │ │ │ │ doSortPeptides() - Method in class
│ │ │ │ │ org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
│ │ │ │ │
│ │ │ │ │ doTranslate(Symbol) - Method in class
│ │ │ │ │ - org.biojava.bio.symbol.AbstractManyToOneTranslationTable
│ │ │ │ │ + org.biojava.bio.symbol.AbstractReversibleTranslationTable
│ │ │ │ │ this method is expected to translate any symbol in the source alphabet.
│ │ │ │ │ doTranslate(Symbol) - Method in class
│ │ │ │ │ org.biojava.bio.symbol.SimpleManyToOneTranslationTable
│ │ │ │ │
│ │ │ │ │ doTranslate(Symbol) - Method in class
│ │ │ │ │ org.biojava.bio.symbol.SimpleReversibleTranslationTable
│ │ │ │ │
│ │ │ │ │ @@ -10279,15 +10279,15 @@
│ │ │ │ │ Deprecated.
│ │ │ │ │ Formats the location of a feature.
│ │ │ │ │ formatLocation(Feature) - Method in class
│ │ │ │ │ org.biojava.bio.seq.io.SwissprotFileFormer
│ │ │ │ │ Deprecated.
│ │ │ │ │ Creates a string representation of the location of a feature
│ │ │ │ │ formatLocation(Location,_StrandedFeature.Strand) - Method in class
│ │ │ │ │ - org.biojava.bio.seq.io.SwissprotFileFormer
│ │ │ │ │ + org.biojava.bio.seq.io.EmblFileFormer
│ │ │ │ │ formatLocation creates an EMBL/Genbank style representation of a
│ │ │ │ │ Location.
│ │ │ │ │ formatOutput() - Method in class org.biojava.bio.alignment.AlignmentPair
│ │ │ │ │
│ │ │ │ │ formatOutput(int) - Method in class org.biojava.bio.alignment.AlignmentPair
│ │ │ │ │ This method provides a BLAST-like formated alignment from the given
│ │ │ │ │ Strings, in which the sequence coordinates and the information "Query" or
│ │ │ │ │ @@ -25058,15 +25058,15 @@
│ │ │ │ │
│ │ │ │ │ parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser
│ │ │ │ │
│ │ │ │ │ parse(Object) - Method in interface
│ │ │ │ │ org.biojava.bio.program.tagvalue.TagValueParser
│ │ │ │ │
│ │ │ │ │ parse(Readable,_ParseListener) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │ │
│ │ │ │ │ parse(Readable,_ParseListener) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqReader
│ │ │ │ │ Parse the specified readable.
│ │ │ │ │ parse(String) - Method in class
│ │ │ │ │ org.biojava.bio.program.sax.FastaSearchSAXParser
│ │ │ │ │ Full implementation of interface method.
│ │ │ │ │ @@ -26560,26 +26560,27 @@
│ │ │ │ │ Reads an alignment in FASTA format.
│ │ │ │ │ read(BufferedReader) - Method in class
│ │ │ │ │ org.biojava.bio.seq.io.MSFAlignmentFormat
│ │ │ │ │ Reads an MSF Alignment File
│ │ │ │ │ read(BufferedReader,_TagValueParser,_TagValueListener) - Method in class
│ │ │ │ │ org.biojava.bio.program.tagvalue.Parser
│ │ │ │ │
│ │ │ │ │ - read(File) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ │ + read(File) - Method in class
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │ │
│ │ │ │ │ read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │ │ Read zero or more FASTQ formatted sequences from the specified file.
│ │ │ │ │ read(InputStream) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │ │
│ │ │ │ │ read(InputStream) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqReader
│ │ │ │ │ Read zero or more FASTQ formatted sequences from the specified input
│ │ │ │ │ stream.
│ │ │ │ │ - read(URL) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ │ + read(URL) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │ │
│ │ │ │ │ read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader
│ │ │ │ │ Read zero or more FASTQ formatted sequences from the specified url.
│ │ │ │ │ readableFileNames - Static variable in class
│ │ │ │ │ org.biojavax.bio.seq.io.EMBLFormat
│ │ │ │ │
│ │ │ │ │ readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat
│ │ │ │ │ @@ -35011,15 +35012,15 @@
│ │ │ │ │ org.biojava.bio.seq.FeatureFilter.StrandFilter
│ │ │ │ │ Build a new filter that matches all features of a given strand.
│ │ │ │ │ StrandParser - Class in org.biojava.bio.seq
│ │ │ │ │ Process strings and return strand objects.
│ │ │ │ │ StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
│ │ │ │ │
│ │ │ │ │ stream(Readable,_StreamListener) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SolexaFastqReader
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqReader
│ │ │ │ │
│ │ │ │ │ stream(Readable,_StreamListener) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqReader
│ │ │ │ │ Stream the specified readable.
│ │ │ │ │ StreamListener - Interface in org.biojava.bio.program.fastq
│ │ │ │ │ Event based parser callback.
│ │ │ │ │ streamNext(SeqIOListener) - Method in class
│ │ │ │ │ @@ -36763,15 +36764,15 @@
│ │ │ │ │ translate(int) - Method in interface org.biojavax.bio.seq.Position
│ │ │ │ │ Takes this position and returns a copy translated by 'distance' bases.
│ │ │ │ │ translate(int) - Method in class org.biojavax.bio.seq.SimplePosition
│ │ │ │ │ Takes this position and returns a copy translated by 'distance' bases.
│ │ │ │ │ translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
│ │ │ │ │ Create a location that is a translation of this location.
│ │ │ │ │ translate(Symbol) - Method in class
│ │ │ │ │ - org.biojava.bio.symbol.AbstractManyToOneTranslationTable
│ │ │ │ │ + org.biojava.bio.symbol.SimpleTranslationTable
│ │ │ │ │
│ │ │ │ │ translate(Symbol) - Method in interface
│ │ │ │ │ org.biojava.bio.symbol.TranslationTable
│ │ │ │ │ Translate a single symbol from source alphabet to the target alphabet.
│ │ │ │ │ translate(SymbolList) - Static method in class
│ │ │ │ │ org.biojava.bio.seq.GeneticCodes
│ │ │ │ │ Translate RNA into protein (with termination symbols).
│ │ │ │ │ @@ -37688,40 +37689,40 @@
│ │ │ │ │ width.
│ │ │ │ │ WORM_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
│ │ │ │ │ Caenorhabditis elegans codon preferences
│ │ │ │ │ Wrapper(SearchListener) - Constructor for class
│ │ │ │ │ org.biojava.bio.program.ssaha.SearchListener.Wrapper
│ │ │ │ │
│ │ │ │ │ write(File,_Iterable) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │ │
│ │ │ │ │ write(File,_Iterable) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqWriter
│ │ │ │ │ Write the specified FASTQ formatted sequences to the specified file.
│ │ │ │ │ write(File,_Fastq...) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │ │
│ │ │ │ │ write(File,_Fastq...) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqWriter
│ │ │ │ │ Write the specified FASTQ formatted sequences to the specified file.
│ │ │ │ │ write(OutputStream,_Iterable) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │ │
│ │ │ │ │ write(OutputStream,_Iterable) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqWriter
│ │ │ │ │ Write the specified FASTQ formatted sequences to the specified output
│ │ │ │ │ stream.
│ │ │ │ │ write(OutputStream,_Alignment,_int) - Method in class
│ │ │ │ │ org.biojava.bio.seq.io.FastaAlignmentFormat
│ │ │ │ │ Writes out the alignment to an FASTA file.
│ │ │ │ │ write(OutputStream,_Alignment,_int) - Method in class
│ │ │ │ │ org.biojava.bio.seq.io.MSFAlignmentFormat
│ │ │ │ │
│ │ │ │ │ write(OutputStream,_Fastq...) - Method in class
│ │ │ │ │ - org.biojava.bio.program.fastq.SangerFastqWriter
│ │ │ │ │ + org.biojava.bio.program.fastq.IlluminaFastqWriter
│ │ │ │ │
│ │ │ │ │ write(OutputStream,_Fastq...) - Method in interface
│ │ │ │ │ org.biojava.bio.program.fastq.FastqWriter
│ │ │ │ │ Write the specified FASTQ formatted sequences to the specified output
│ │ │ │ │ stream.
│ │ │ │ │ write(Sequence) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
│ │ │ │ │ Writing Sequence.
│ │ │ ├── ./usr/share/doc/libbiojava-java/apidocs/member-search-index.js
│ │ │ │ ├── js-beautify {}
│ │ │ │ │ @@ -3994,25 +3994,25 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.utils.automata",
│ │ │ │ │ "c": "NfaSubModel",
│ │ │ │ │ "l": "append(NfaSubModel)",
│ │ │ │ │ "u": "append(org.biojava.utils.automata.NfaSubModel)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SangerFastqWriter",
│ │ │ │ │ + "c": "IlluminaFastqWriter",
│ │ │ │ │ "l": "append(T, Fastq...)",
│ │ │ │ │ "u": "append(T,org.biojava.bio.program.fastq.Fastq...)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqWriter",
│ │ │ │ │ "l": "append(T, Fastq...)",
│ │ │ │ │ "u": "append(T,org.biojava.bio.program.fastq.Fastq...)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SangerFastqWriter",
│ │ │ │ │ + "c": "IlluminaFastqWriter",
│ │ │ │ │ "l": "append(T, Iterable)",
│ │ │ │ │ "u": "append(T,java.lang.Iterable)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqWriter",
│ │ │ │ │ "l": "append(T, Iterable)",
│ │ │ │ │ "u": "append(T,java.lang.Iterable)"
│ │ │ │ │ @@ -10199,15 +10199,15 @@
│ │ │ │ │ "l": "doRetain()"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.gui.sequence",
│ │ │ │ │ "c": "AbstractPeptideDigestRenderer",
│ │ │ │ │ "l": "doSortPeptides()"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.symbol",
│ │ │ │ │ - "c": "AbstractManyToOneTranslationTable",
│ │ │ │ │ + "c": "AbstractReversibleTranslationTable",
│ │ │ │ │ "l": "doTranslate(Symbol)",
│ │ │ │ │ "u": "doTranslate(org.biojava.bio.symbol.Symbol)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.symbol",
│ │ │ │ │ "c": "SimpleManyToOneTranslationTable",
│ │ │ │ │ "l": "doTranslate(Symbol)",
│ │ │ │ │ "u": "doTranslate(org.biojava.bio.symbol.Symbol)"
│ │ │ │ │ @@ -14445,15 +14445,15 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.seq.io",
│ │ │ │ │ "c": "SwissprotFileFormer",
│ │ │ │ │ "l": "formatLocation(Feature)",
│ │ │ │ │ "u": "formatLocation(org.biojava.bio.seq.Feature)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.seq.io",
│ │ │ │ │ - "c": "SwissprotFileFormer",
│ │ │ │ │ + "c": "EmblFileFormer",
│ │ │ │ │ "l": "formatLocation(Location, StrandedFeature.Strand)",
│ │ │ │ │ "u": "formatLocation(org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.seq.io",
│ │ │ │ │ "c": "SwissprotFileFormer",
│ │ │ │ │ "l": "formatLocation(StringBuffer, Location)",
│ │ │ │ │ "u": "formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)"
│ │ │ │ │ @@ -36584,15 +36584,15 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojavax.bio.phylo.io.phylip",
│ │ │ │ │ "c": "PHYLIPFileFormat",
│ │ │ │ │ "l": "parse(PHYLIPFileListener, BufferedReader)",
│ │ │ │ │ "u": "parse(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener,java.io.BufferedReader)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SolexaFastqReader",
│ │ │ │ │ + "c": "IlluminaFastqReader",
│ │ │ │ │ "l": "parse(Readable, ParseListener)",
│ │ │ │ │ "u": "parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqReader",
│ │ │ │ │ "l": "parse(Readable, ParseListener)",
│ │ │ │ │ "u": "parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)"
│ │ │ │ │ @@ -38670,35 +38670,35 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.utils.io",
│ │ │ │ │ "c": "RandomAccessReader",
│ │ │ │ │ "l": "read(char[], int, int)",
│ │ │ │ │ "u": "read(char[],int,int)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SolexaFastqReader",
│ │ │ │ │ + "c": "IlluminaFastqReader",
│ │ │ │ │ "l": "read(File)",
│ │ │ │ │ "u": "read(java.io.File)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqReader",
│ │ │ │ │ "l": "read(File)",
│ │ │ │ │ "u": "read(java.io.File)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SolexaFastqReader",
│ │ │ │ │ + "c": "IlluminaFastqReader",
│ │ │ │ │ "l": "read(InputStream)",
│ │ │ │ │ "u": "read(java.io.InputStream)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqReader",
│ │ │ │ │ "l": "read(InputStream)",
│ │ │ │ │ "u": "read(java.io.InputStream)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SolexaFastqReader",
│ │ │ │ │ + "c": "IlluminaFastqReader",
│ │ │ │ │ "l": "read(URL)",
│ │ │ │ │ "u": "read(java.net.URL)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqReader",
│ │ │ │ │ "l": "read(URL)",
│ │ │ │ │ "u": "read(java.net.URL)"
│ │ │ │ │ @@ -50748,15 +50748,15 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.seq",
│ │ │ │ │ "c": "StrandParser",
│ │ │ │ │ "l": "StrandParser()",
│ │ │ │ │ "u": "%3Cinit%3E()"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SolexaFastqReader",
│ │ │ │ │ + "c": "IlluminaFastqReader",
│ │ │ │ │ "l": "stream(Readable, StreamListener)",
│ │ │ │ │ "u": "stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqReader",
│ │ │ │ │ "l": "stream(Readable, StreamListener)",
│ │ │ │ │ "u": "stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)"
│ │ │ │ │ @@ -53366,15 +53366,15 @@
│ │ │ │ │ "l": "translate(int)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojavax.bio.seq",
│ │ │ │ │ "c": "SimpleRichLocation",
│ │ │ │ │ "l": "translate(int)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.symbol",
│ │ │ │ │ - "c": "AbstractManyToOneTranslationTable",
│ │ │ │ │ + "c": "SimpleTranslationTable",
│ │ │ │ │ "l": "translate(Symbol)",
│ │ │ │ │ "u": "translate(org.biojava.bio.symbol.Symbol)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.symbol",
│ │ │ │ │ "c": "TranslationTable",
│ │ │ │ │ "l": "translate(Symbol)",
│ │ │ │ │ "u": "translate(org.biojava.bio.symbol.Symbol)"
│ │ │ │ │ @@ -54624,25 +54624,25 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.ssaha",
│ │ │ │ │ "c": "SearchListener.Wrapper",
│ │ │ │ │ "l": "Wrapper(SearchListener)",
│ │ │ │ │ "u": "%3Cinit%3E(org.biojava.bio.program.ssaha.SearchListener)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SangerFastqWriter",
│ │ │ │ │ + "c": "IlluminaFastqWriter",
│ │ │ │ │ "l": "write(File, Fastq...)",
│ │ │ │ │ "u": "write(java.io.File,org.biojava.bio.program.fastq.Fastq...)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqWriter",
│ │ │ │ │ "l": "write(File, Fastq...)",
│ │ │ │ │ "u": "write(java.io.File,org.biojava.bio.program.fastq.Fastq...)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SangerFastqWriter",
│ │ │ │ │ + "c": "IlluminaFastqWriter",
│ │ │ │ │ "l": "write(File, Iterable)",
│ │ │ │ │ "u": "write(java.io.File,java.lang.Iterable)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqWriter",
│ │ │ │ │ "l": "write(File, Iterable)",
│ │ │ │ │ "u": "write(java.io.File,java.lang.Iterable)"
│ │ │ │ │ @@ -54654,25 +54654,25 @@
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.seq.io",
│ │ │ │ │ "c": "MSFAlignmentFormat",
│ │ │ │ │ "l": "write(OutputStream, Alignment, int)",
│ │ │ │ │ "u": "write(java.io.OutputStream,org.biojava.bio.alignment.Alignment,int)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SangerFastqWriter",
│ │ │ │ │ + "c": "IlluminaFastqWriter",
│ │ │ │ │ "l": "write(OutputStream, Fastq...)",
│ │ │ │ │ "u": "write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqWriter",
│ │ │ │ │ "l": "write(OutputStream, Fastq...)",
│ │ │ │ │ "u": "write(java.io.OutputStream,org.biojava.bio.program.fastq.Fastq...)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ - "c": "SangerFastqWriter",
│ │ │ │ │ + "c": "IlluminaFastqWriter",
│ │ │ │ │ "l": "write(OutputStream, Iterable)",
│ │ │ │ │ "u": "write(java.io.OutputStream,java.lang.Iterable)"
│ │ │ │ │ }, {
│ │ │ │ │ "p": "org.biojava.bio.program.fastq",
│ │ │ │ │ "c": "FastqWriter",
│ │ │ │ │ "l": "write(OutputStream, Iterable)",
│ │ │ │ │ "u": "write(java.io.OutputStream,java.lang.Iterable)"