{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.Cner0qaY/b1/biojava-live_1.9.7+dfsg-1_armhf.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.Cner0qaY/b2/biojava-live_1.9.7+dfsg-1_armhf.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,4 +1,4 @@\n \n- e3136fd99076cf0169758b480a5169e2 4132568 doc optional libbiojava-java-doc_1.9.7+dfsg-1_all.deb\n+ 64d03df34cd66d34b3e8a6a46cf8517c 4132504 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 4013832 2023-11-29 07:09:37.000000 data.tar.xz\n+-rw-r--r-- 0 0 0 118560 2023-11-29 07:09:37.000000 control.tar.xz\n+-rw-r--r-- 0 0 0 4013752 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": "./control", "source2": "./control", "unified_diff": "@@ -1,13 +1,13 @@\n Package: libbiojava-java-doc\n Source: biojava-live\n Version: 1:1.9.7+dfsg-1\n Architecture: all\n Maintainer: Debian Med Packaging Team \n-Installed-Size: 103816\n+Installed-Size: 103814\n Depends: default-jdk-doc\n Suggests: libbiojava-java\n Section: doc\n Priority: optional\n Multi-Arch: foreign\n Homepage: https://www.biojava.org\n Description: [Biology] Documentation for BioJava\n"}, {"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) 5205187 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) 5204512 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) 1398894 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) 1398669 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": "@@ -1559,15 +1559,15 @@\n
add a search pattern to the searches to be conducted\n by this object.
\n \n
addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
\n
 
\n
addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
\n
 
\n-
addPrefixMapping(String, String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
addPrefixMapping(String, String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Adds a namespace prefix to URI mapping as (key,value) pairs.
\n
\n
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
\n
 
\n
addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
\n
 
\n@@ -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@@ -5096,15 +5096,15 @@\n
\n
A listener that remembers the ChangeEvent of the last change.
\n
\n
ChangeListener.LoggingListener - Class in org.biojava.utils
\n
\n
A listener that writes information about the event stream to a PrintStream.
\n
\n-
changeState(int) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
changeState(int) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Centralise chaining of iState field to help\n with debugging.
\n
\n
changeSupport() - Method in class org.biojava.utils.ChangeForwarder
\n
\n
Return the underlying ChangeSupport instance that can be used to\n@@ -5221,15 +5221,15 @@\n
\n
CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
\n
 
\n
characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
\n
\n
Describe characters method here.
\n
\n-
characters(char[], int, int) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
characters(char[], int, int) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Utility method to centralize the sending of a SAX characters\n message a document handler.
\n
\n
characters(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
\n
 
\n
characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
\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.AbstractReversibleTranslationTable
\n+
doTranslate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
\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@@ -9283,15 +9283,15 @@\n
 
\n
endElement(String, String, String, StAXContentHandler) - Method in interface org.biojava.utils.stax.StAXContentHandler
\n
 
\n
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
\n
 
\n
endElement(String, String, String, StAXContentHandler) - Method in class org.biojava.utils.stax.StringElementHandlerBase
\n
 
\n-
endElement(QName) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
endElement(QName) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Utility method to centralize the sending of a SAX endElement\n message a document handler.
\n
\n
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
\n
 
\n
endElementHandler(String, String, String, StAXContentHandler) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
\n@@ -14395,23 +14395,23 @@\n \n
getContainingClass() - Method in class org.biojava.utils.bytecode.GeneratedCodeMethod
\n
 
\n
getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
\n
\n
Gets the default CONTAINS term used for defining the relationship between features.
\n
\n-
getContentHandler() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getContentHandler() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Return the content handler.
\n
\n
getContentHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
\n
correct this later
\n
\n-
getContentStream(InputSource) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getContentStream(InputSource) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Create a stream from an an InputSource, picking the\n correct stream according to order of precedance.
\n
\n
getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
\n
 
\n
getContext() - Method in class org.biojava.stats.svm.TrainingEvent
\n@@ -15333,15 +15333,15 @@\n end type produced by the primary (intra-site or downstream)\n cut.\n \n
getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
\n
 
\n
getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
\n
 
\n-
getDTDHandler() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getDTDHandler() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
getDTDHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
getE() - Method in class org.biojava.bio.proteomics.StructureTools
\n
 
\n@@ -15505,15 +15505,15 @@\n
\n
Get the current string indicating that a record has ended.
\n
\n
getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser
\n
\n
Get the explicit end-of-record string.
\n
\n-
getEntityResolver() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getEntityResolver() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
getEntityResolver() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
\n
This class has an EntityResolver that\n resolves the public ID specifying the\n@@ -15549,15 +15549,15 @@\n
\n
Find the error handler used by this parser.
\n
\n
getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser
\n
\n
Find the error handler used by this parser.
\n
\n-
getErrorHandler() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getErrorHandler() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
getErrorHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess
\n
\n@@ -15660,15 +15660,15 @@\n
\n
Retrieves the feature this location is associated with.
\n
\n
getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation
\n
\n
Retrieves the feature this location is associated with.
\n
\n-
getFeature(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getFeature(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
getFeature(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
\n
\n@@ -18024,23 +18024,23 @@\n
Returns the namespace of this bioentry.
\n
\n
getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
\n
\n
Return the namespace id for this identifier\n within the authority.
\n
\n-
getNamespacePrefix() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getNamespacePrefix() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Describe getNamespacePrefix method here.
\n
\n-
getNamespacePrefixes() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getNamespacePrefixes() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Support SAX2 configuration of namespace support of parser.
\n
\n-
getNamespaces() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getNamespaces() - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Support SAX2 configuration of namespace support of parser.
\n
\n
getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization
\n
 
\n
getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
\n
\n@@ -19076,15 +19076,15 @@\n
\n Retrieve the value of a property by key.
\n
\n
getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
\n
\n
Deprecated. 
\n
\n-
getProperty(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getProperty(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
getProperty(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
getProperty(Annotation, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
\n
 
\n@@ -21840,15 +21840,15 @@\n
\n
If the namespace has a URI, this will return it.
\n
\n
getURI() - Method in class org.biojavax.SimpleNamespace
\n
\n
If the namespace has a URI, this will return it.
\n
\n-
getURIFromPrefix(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
getURIFromPrefix(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Gets the URI for a namespace prefix, given that prefix,\n or null if the prefix is not recognised.
\n
\n
getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
\n
\n
getURL returns the hotspot URL.
\n@@ -24560,15 +24560,15 @@\n
\n
The issue of the journal.
\n
\n
issueSupplement - Variable in class org.biojava.bibliography.BiblioJournalArticle
\n
\n
Suplement.
\n
\n-
iState - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
iState - Variable in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n
isTaxonHidden() - Method in interface org.biojavax.bio.taxa.NCBITaxon
\n
\n
used in getNameHierarchy() to determine whether this taxonomy level is displayed
\n
\n
isTaxonHidden() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
\n
\n@@ -27710,23 +27710,23 @@\n
 
\n
OffsetRulerRenderer(int, int) - Constructor for class org.biojava.bio.gui.sequence.OffsetRulerRenderer
\n
 
\n
OFFSETS - Static variable in interface org.biojava.bio.chromatogram.Chromatogram
\n
\n
The sequence label for the trace offsets of the called bases.
\n
\n-
oFullNamespacePrefix - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
oFullNamespacePrefix - Variable in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n-
oHandler - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
oHandler - Variable in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n
Omono - Static variable in class org.biojava.bio.proteomics.MassCalc
\n
\n
Constant value of Oxygen monoisotopic mass
\n
\n-
oNamespacePrefix - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
oNamespacePrefix - Variable in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n
one() - Static method in class org.biojavax.ga.util.GATools
\n
 
\n
ONE - Static variable in class org.biojava.bio.CardinalityConstraint
\n
\n
The property should have exactly one value.
\n
\n@@ -29492,15 +29492,15 @@\n
 
\n
parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
\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+
parse(String) - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
\n
\n
Full implementation of interface method.
\n
\n
parse(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
parse(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n@@ -30124,15 +30124,15 @@\n
preChange(ChangeEvent) - Method in class org.biojava.utils.ChangeListener.LoggingListener
\n
 
\n
preChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener
\n
\n
\n Called before a change takes place.
\n
\n-
prefix(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
prefix(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Given an unprefixed element name, returns\n a new element name with a namespace prefix
\n
\n
press() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
\n
 
\n
press() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
\n@@ -35451,15 +35451,15 @@\n \n
setConstraints(Object, PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
\n
 
\n
setConstraints(Object, PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
\n
\n
Set the constraints associated with a property.
\n
\n-
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Allow an application to register a content event handler.
\n
\n
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
\n
\n
sets the ContentHandler for this object
\n
\n@@ -35929,15 +35929,15 @@\n
 
\n
setDoubleValue(double) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
\n
\n
\n Override this method to do something useful with the\n double we collect.
\n
\n-
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
\n
 
\n@@ -36018,15 +36018,15 @@\n
\n
Set the string indicating that a record has ended.
\n
\n
setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.RegexParser
\n
\n
Set the explicit end-of-record string.
\n
\n-
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
\n
This class has an EntityResolver that\n resolves the public ID specifying the\n@@ -36050,15 +36050,15 @@\n
Set the error handler used by this parser.
\n
\n
setErrorHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
\n
\n
Sets the output error handler which is responsible for the standard error\n output of the external process.
\n
\n-
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
setEvents(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
\n
\n@@ -36087,15 +36087,15 @@\n
\n
Set the feature to feature.
\n
\n
setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
\n
\n
Set the feature type to type.
\n
\n-
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Handles support for ReasoningDomain and Namespace-prefixes
\n
\n
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
\n
by default, we set the parser to non-validating.
\n
\n@@ -36938,15 +36938,15 @@\n the namespace of the record being read.\n \n
setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
\n
\n
Call back method so the event emitter can tell the listener\n the namespace of the record being read.
\n
\n-
setNamespacePrefix(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setNamespacePrefix(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n
setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
\n
\n
Set the Shape to represent the negative points.
\n
\n
setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel
\n
 
\n@@ -37308,15 +37308,15 @@\n
\n Set the value of a property.
\n \n
setProperty(Object, Object) - Method in class org.biojavax.SimpleRichAnnotation
\n
\n
Deprecated. 
\n
\n-
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Do-nothing implementation of interface method
\n
\n
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
\n
 
\n
setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
\n
 
\n@@ -40333,15 +40333,15 @@\n
 
\n
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
\n
 
\n
startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StringElementHandlerBase
\n
 
\n
startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
\n
 
\n-
startElement(QName, Attributes) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
startElement(QName, Attributes) - Method in class org.biojava.bio.program.sax.PdbSAXParser
\n
\n
Utility method to centralize sending of a SAX\n startElement message to document handler
\n
\n
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
\n
 
\n
startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
\n@@ -42295,17 +42295,17 @@\n
 
\n
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
\n
 
\n
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
\n
 
\n
TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
\n
 
\n-
tNamespacePrefixes - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
tNamespacePrefixes - Variable in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n-
tNamespaces - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser
\n+
tNamespaces - Variable in class org.biojava.bio.program.sax.PdbSAXParser
\n
 
\n
to - Variable in class org.biojava.bio.dp.TrainerTransition
\n
 
\n
to - Variable in class org.biojava.bio.dp.Transition
\n
 
\n
TO_A_LEAF - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree
\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.AbstractReversibleTranslationTable
\n+
translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
\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": "@@ -1463,15 +1463,15 @@\n add a search pattern to the searches to be conducted by this object.\n addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel\n \u00a0\n addPosition(AGAVEMapPosition) - Method in class\n org.biojava.bio.seq.io.agave.AGAVEMapLocation\n \u00a0\n addPrefixMapping(String,_String) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Adds a namespace prefix to URI mapping as (key,value) pairs.\n addProp(AGAVEProperty) - Method in class\n org.biojava.bio.seq.io.agave.AGAVERelatedAnnot\n \u00a0\n addProp(AGAVEProperty) - Method in class\n org.biojava.bio.seq.io.agave.AGAVEXref\n \u00a0\n@@ -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.SolexaFastqWriter\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.SolexaFastqWriter\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@@ -4479,16 +4479,15 @@\n ChangeListener.AlwaysVetoListener - Class in org.biojava.utils\n An implementation that always vetoes everything.\n ChangeListener.ChangeEventRecorder - Class in org.biojava.utils\n A listener that remembers the ChangeEvent of the last change.\n ChangeListener.LoggingListener - Class in org.biojava.utils\n A listener that writes information about the event stream to a\n PrintStream.\n- changeState(int) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ changeState(int) - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Centralise chaining of iState field to help with debugging.\n changeSupport() - Method in class org.biojava.utils.ChangeForwarder\n Return the underlying ChangeSupport instance that can be used to fire\n ChangeEvents and mannage listeners.\n ChangeSupport - Class in org.biojava.utils\n A utility class to provide management for informing ChangeListeners of\n ChangeEvents.\n@@ -4572,15 +4571,15 @@\n CHARACTER - Static variable in interface\n org.biojava.bio.seq.io.SymbolTokenization\n \u00a0\n characters(char[],_int,_int) - Method in class\n org.biojava.bio.program.blast2html.Blast2HTMLHandler\n Describe characters method here.\n characters(char[],_int,_int) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Utility method to centralize the sending of a SAX characters message a\n document handler.\n characters(char[],_int,_int) - Method in class\n org.biojava.bio.program.ssbind.SeqSimilarityAdapter\n \u00a0\n characters(char[],_int,_int) - Method in class\n org.biojava.bio.program.xml.SimpleXMLEmitter\n@@ -7271,15 +7270,15 @@\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.AbstractReversibleTranslationTable\n+ org.biojava.bio.symbol.AbstractManyToOneTranslationTable\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@@ -8032,16 +8031,15 @@\n \u00a0\n endElement(String,_String,_String,_StAXContentHandler) - Method in class\n org.biojava.utils.stax.StAXContentHandlerBase\n \u00a0\n endElement(String,_String,_String,_StAXContentHandler) - Method in class\n org.biojava.utils.stax.StringElementHandlerBase\n \u00a0\n- endElement(QName) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ endElement(QName) - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Utility method to centralize the sending of a SAX endElement message a\n document handler.\n endElementHandler(String,_String,_String,_StAXContentHandler) - Method in\n class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler\n \u00a0\n endElementHandler(String,_String,_String,_StAXContentHandler) - Method in\n class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler\n@@ -12491,21 +12489,21 @@\n org.biojava.utils.bytecode.GeneratedCodeMethod\n \u00a0\n getContainsTerm() - Static method in class\n org.biojavax.bio.seq.SimpleRichFeatureRelationship\n Gets the default CONTAINS term used for defining the relationship between\n features.\n getContentHandler() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Return the content handler.\n getContentHandler() - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n correct this later\n getContentStream(InputSource) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Create a stream from an an InputSource, picking the correct stream\n according to order of precedance.\n getContext() - Method in class\n org.biojava.bio.seq.projection.ProjectedFeatureHolder\n \u00a0\n getContext() - Method in class org.biojava.stats.svm.TrainingEvent\n \u00a0\n@@ -13273,16 +13271,15 @@\n org.biojava.bio.molbio.RestrictionEnzyme\n getDownstreamEndType returns the double-stranded end type produced by the\n primary (intra-site or downstream) cut.\n getDP() - Method in class org.biojava.bio.dp.AbstractTrainer\n \u00a0\n getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm\n \u00a0\n- getDTDHandler() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ getDTDHandler() - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n getDTDHandler() - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n getE() - Method in class org.biojava.bio.proteomics.StructureTools\n \u00a0\n getEcNumber(Annotation) - Method in class\n@@ -13426,15 +13423,15 @@\n getEndOfRecord() - Method in class\n org.biojava.bio.program.tagvalue.LineSplitParser\n Get the current string indicating that a record has ended.\n getEndOfRecord() - Method in class\n org.biojava.bio.program.tagvalue.RegexParser\n Get the explicit end-of-record string.\n getEntityResolver() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n getEntityResolver() - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n This class has an EntityResolver that resolves the public ID specifying\n the NCBI DTDs to resource files within the BioJava libraries.\n getEntryByName(String) - Method in interface\n org.biojava.utils.candy.CandyVocabulary\n@@ -13456,16 +13453,15 @@\n getEquates() - Method in class\n org.biojavax.bio.phylo.io.nexus.CharactersBlock\n \u00a0\n getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser\n Find the error handler used by this parser.\n getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser\n Find the error handler used by this parser.\n- getErrorHandler() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ getErrorHandler() - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n getErrorHandler() - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess\n Gets the output error handler which is responsible for the standard error\n output of the external process.\n@@ -13541,16 +13537,15 @@\n \u00a0\n getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation\n Retrieves the feature this location is associated with.\n getFeature() - Method in interface org.biojavax.bio.seq.RichLocation\n Retrieves the feature this location is associated with.\n getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation\n Retrieves the feature this location is associated with.\n- getFeature(String) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ getFeature(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n getFeature(String) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n getFeatureDescTerm() - Static method in class\n org.biojavax.bio.seq.RichSequence.Terms\n Getter for the FeatureDesc term\n@@ -15526,21 +15521,20 @@\n Getter for property namespace.\n getNamespace() - Method in class org.biojavax.bio.SimpleBioEntry\n Returns the namespace of this bioentry.\n getNamespaceId() - Method in class\n org.biojava.utils.lsid.LifeScienceIdentifier\n Return the namespace id for this identifier within the authority.\n getNamespacePrefix() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Describe getNamespacePrefix method here.\n getNamespacePrefixes() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Support SAX2 configuration of namespace support of parser.\n- getNamespaces() - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ getNamespaces() - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Support SAX2 configuration of namespace support of parser.\n getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization\n \u00a0\n getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon\n Gets the NCBI taxon ID.\n getNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon\n Gets the NCBI taxon ID.\n@@ -16357,15 +16351,15 @@\n getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation\n \u00a0\n getProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation\n Retrieve the value of a property by key.\n getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation\n Deprecated.\u00a0\n getProperty(String) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n getProperty(String) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n getProperty(Annotation,_Object) - Method in class\n org.biojava.bio.AnnotationType.Abstract\n \u00a0\n@@ -18655,15 +18649,15 @@\n getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type\n Get the URI for this type.\n getURI() - Method in interface org.biojavax.Namespace\n If the namespace has a URI, this will return it.\n getURI() - Method in class org.biojavax.SimpleNamespace\n If the namespace has a URI, this will return it.\n getURIFromPrefix(String) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Gets the URI for a namespace prefix, given that prefix, or null if the\n prefix is not recognised.\n getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot\n getURL returns the hotspot URL.\n getURN() - Method in class org.biojava.bio.seq.impl.DummySequence\n \u00a0\n getURN() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence\n@@ -21012,15 +21006,15 @@\n org.biojava.bio.seq.FeatureTypes\n Work out if one type is a sub-type of another.\n issue - Variable in class org.biojava.bibliography.BiblioJournalArticle\n The issue of the journal.\n issueSupplement - Variable in class\n org.biojava.bibliography.BiblioJournalArticle\n Suplement.\n- iState - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser\n+ iState - Variable in class org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n isTaxonHidden() - Method in interface org.biojavax.bio.taxa.NCBITaxon\n used in getNameHierarchy() to determine whether this taxonomy level is\n displayed\n isTaxonHidden() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon\n Returns the taxonomy hierarchy of this taxon entry in the form: most\n specific; less specific; ...; least specific.\n@@ -23598,22 +23592,21 @@\n OffsetRulerRenderer(int,_int) - Constructor for class\n org.biojava.bio.gui.sequence.OffsetRulerRenderer\n \u00a0\n OFFSETS - Static variable in interface\n org.biojava.bio.chromatogram.Chromatogram\n The sequence label for the trace offsets of the called bases.\n oFullNamespacePrefix - Variable in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n- oHandler - Variable in class org.biojava.bio.program.sax.FastaSearchSAXParser\n+ oHandler - Variable in class org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n Omono - Static variable in class org.biojava.bio.proteomics.MassCalc\n Constant value of Oxygen monoisotopic mass\n- oNamespacePrefix - Variable in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ oNamespacePrefix - Variable in class org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n one() - Static method in class org.biojavax.ga.util.GATools\n \u00a0\n ONE - Static variable in class org.biojava.bio.CardinalityConstraint\n The property should have exactly one value.\n ONE_OR_MORE - Static variable in class org.biojava.bio.CardinalityConstraint\n The property should have one or more values.\n@@ -25064,15 +25057,15 @@\n parse(Readable,_ParseListener) - Method in class\n org.biojava.bio.program.fastq.SolexaFastqReader\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+ org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n Full implementation of interface method.\n parse(String) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n parse(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n parse(String) - Method in class org.biojava.naming.ObdaUriParser\n@@ -25620,16 +25613,15 @@\n org.biojava.utils.ChangeListener.ChangeEventRecorder\n \u00a0\n preChange(ChangeEvent) - Method in class\n org.biojava.utils.ChangeListener.LoggingListener\n \u00a0\n preChange(ChangeEvent) - Method in interface org.biojava.utils.ChangeListener\n Called before a change takes place.\n- prefix(String) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ prefix(String) - Method in class org.biojava.bio.program.sax.PdbSAXParser\n Given an unprefixed element name, returns a new element name with a\n namespace prefix\n press() - Method in class\n org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor\n \u00a0\n press() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor\n Returns the minimal context of the DP matrix necessary to compute the\n@@ -30138,15 +30130,15 @@\n setConstraints(Object,_PropertyConstraint,_Location) - Method in class\n org.biojava.bio.AnnotationType.Abstract\n \u00a0\n setConstraints(Object,_PropertyConstraint,_Location) - Method in interface\n org.biojava.bio.AnnotationType\n Set the constraints associated with a property.\n setContentHandler(ContentHandler) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Allow an application to register a content event handler.\n setContentHandler(ContentHandler) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParser\n sets the ContentHandler for this object\n setContentHandler(ContentHandler) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n this sets the ContentHandler that receives SAX events from the internal\n@@ -30574,15 +30566,15 @@\n setDoubleProperty(Symbol,_String) - Method in class\n org.biojava.bio.symbol.SimpleSymbolPropertyTable\n \u00a0\n setDoubleValue(double) - Method in class\n org.biojava.utils.stax.DoubleElementHandlerBase\n Override this method to do something useful with the double we collect.\n setDTDHandler(DTDHandler) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n setDTDHandler(DTDHandler) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n setElementId(String) - Method in class\n org.biojava.bio.seq.io.agave.AGAVEMatchRegion\n \u00a0\n@@ -30653,15 +30645,15 @@\n setEndOfRecord(String) - Method in class\n org.biojava.bio.program.tagvalue.LineSplitParser\n Set the string indicating that a record has ended.\n setEndOfRecord(String) - Method in class\n org.biojava.bio.program.tagvalue.RegexParser\n Set the explicit end-of-record string.\n setEntityResolver(EntityResolver) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n setEntityResolver(EntityResolver) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n This class has an EntityResolver that resolves the public ID specifying\n the NCBI DTDs to resource files within the BioJava libraries.\n setEnvironmentProperties(String[]) - Method in class\n org.biojava.utils.process.ExternalProcess\n@@ -30678,15 +30670,15 @@\n org.biojava.bio.program.gff3.GFF3Parser\n Set the error handler used by this parser.\n setErrorHandler(OutputHandler) - Method in class\n org.biojava.utils.process.ExternalProcess\n Sets the output error handler which is responsible for the standard error\n output of the external process.\n setErrorHandler(ErrorHandler) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n setErrorHandler(ErrorHandler) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n setEvents(List) - Method in class\n org.biojavax.bio.seq.io.UniProtCommentParser\n Setter for property events.\n@@ -30707,15 +30699,15 @@\n setFeature(String) - Method in class\n org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter\n Set the feature to feature.\n setFeature(String) - Method in class\n org.biojava.bio.program.gff.SimpleGFFRecord\n Set the feature type to type.\n setFeature(String,_boolean) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Handles support for ReasoningDomain and Namespace-prefixes\n setFeature(String,_boolean) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n by default, we set the parser to non-validating.\n setFeature(RichFeature) - Method in class\n org.biojavax.bio.seq.CompoundRichLocation\n Sets the feature this location is associated with.\n@@ -31436,15 +31428,15 @@\n Call back method so the event emitter can tell the listener the namespace\n of the record being read.\n setNamespace(Namespace) - Method in class\n org.biojavax.bio.seq.io.SimpleRichSequenceBuilder\n Call back method so the event emitter can tell the listener the namespace\n of the record being read.\n setNamespacePrefix(String) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n setNegShape(Shape) - Method in class\n org.biojava.stats.svm.tools.ClassifierExample.PointClassifier\n Set the Shape to represent the negative points.\n setNestedKernel(SVMKernel) - Method in class\n org.biojava.stats.svm.CachingKernel\n \u00a0\n@@ -31740,15 +31732,15 @@\n setProperty(Object,_Object) - Method in class\n org.biojavax.EmptyRichAnnotation\n Set the value of a property.\n setProperty(Object,_Object) - Method in class\n org.biojavax.SimpleRichAnnotation\n Deprecated.\u00a0\n setProperty(String,_Object) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Do-nothing implementation of interface method\n setProperty(String,_Object) - Method in class\n org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade\n \u00a0\n setProperty(String,_String) - Method in class\n org.biojava.bio.seq.io.agave.StAXPropertyHandler\n \u00a0\n@@ -34325,15 +34317,15 @@\n startElement(String,_String,_String,_Attributes,_DelegationManager) - Method\n in class org.biojava.utils.stax.StringElementHandlerBase\n \u00a0\n startElement(String,_Attributes) - Method in class\n org.biojava.bio.program.xml.BaseXMLWriter\n \u00a0\n startElement(QName,_Attributes) - Method in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n Utility method to centralize sending of a SAX startElement message to\n document handler\n startElementHandler(String,_String,_String,_Attributes) - Method in class\n org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler\n \u00a0\n startElementHandler(String,_String,_String,_Attributes) - Method in class\n org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler\n@@ -36033,18 +36025,17 @@\n TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat\n \u00a0\n TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat\n \u00a0\n TITLE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat\n \u00a0\n tNamespacePrefixes - Variable in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n- tNamespaces - Variable in class\n- org.biojava.bio.program.sax.FastaSearchSAXParser\n+ tNamespaces - Variable in class org.biojava.bio.program.sax.PdbSAXParser\n \u00a0\n to - Variable in class org.biojava.bio.dp.TrainerTransition\n \u00a0\n to - Variable in class org.biojava.bio.dp.Transition\n \u00a0\n TO_A_LEAF - Static variable in class org.biojava.bio.symbol.UkkonenSuffixTree\n \u00a0\n@@ -36763,15 +36754,15 @@\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.AbstractReversibleTranslationTable\n+ org.biojava.bio.symbol.SimpleReversibleTranslationTable\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 +37679,40 @@\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.SolexaFastqWriter\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.SolexaFastqWriter\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.SolexaFastqWriter\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.SolexaFastqWriter\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": "@@ -2253,15 +2253,15 @@\n }, {\n \"p\": \"org.biojava.bio.seq.io.agave\",\n \"c\": \"AGAVEMapLocation\",\n \"l\": \"addPosition(AGAVEMapPosition)\",\n \"u\": \"addPosition(org.biojava.bio.seq.io.agave.AGAVEMapPosition)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"addPrefixMapping(String, String)\",\n \"u\": \"addPrefixMapping(java.lang.String,java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io.agave\",\n \"c\": \"AGAVERelatedAnnot\",\n \"l\": \"addProp(AGAVEProperty)\",\n \"u\": \"addProp(org.biojava.bio.seq.io.agave.AGAVEProperty)\"\n@@ -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@@ -6168,15 +6168,15 @@\n }, {\n \"p\": \"org.biojava.utils\",\n \"c\": \"ChangeForwarder\",\n \"l\": \"ChangeForwarder(Object, ChangeSupport)\",\n \"u\": \"%3Cinit%3E(java.lang.Object,org.biojava.utils.ChangeSupport)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"changeState(int)\"\n }, {\n \"p\": \"org.biojava.utils\",\n \"c\": \"ChangeForwarder\",\n \"l\": \"changeSupport()\"\n }, {\n \"p\": \"org.biojava.utils\",\n@@ -6289,15 +6289,15 @@\n }, {\n \"p\": \"org.biojava.bio.program.blast2html\",\n \"c\": \"Blast2HTMLHandler\",\n \"l\": \"characters(char[], int, int)\",\n \"u\": \"characters(char[],int,int)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"characters(char[], int, int)\",\n \"u\": \"characters(char[],int,int)\"\n }, {\n \"p\": \"org.biojava.bio.program.ssbind\",\n \"c\": \"SeqSimilarityAdapter\",\n \"l\": \"characters(char[], int, int)\",\n \"u\": \"characters(char[],int,int)\"\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\": \"AbstractReversibleTranslationTable\",\n+ \"c\": \"AbstractManyToOneTranslationTable\",\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@@ -11030,15 +11030,15 @@\n \"l\": \"endDocument()\"\n }, {\n \"p\": \"org.biojava.bio.program.xml\",\n \"c\": \"BaseXMLWriter\",\n \"l\": \"endElement()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"endElement(QName)\",\n \"u\": \"endElement(org.biojava.bio.program.sax.QName)\"\n }, {\n \"p\": \"org.biojava.bio.program.blast2html\",\n \"c\": \"Blast2HTMLHandler\",\n \"l\": \"endElement(String, String, String)\",\n \"u\": \"endElement(java.lang.String,java.lang.String,java.lang.String)\"\n@@ -17692,23 +17692,23 @@\n \"l\": \"getContainingClass()\"\n }, {\n \"p\": \"org.biojavax.bio.seq\",\n \"c\": \"SimpleRichFeatureRelationship\",\n \"l\": \"getContainsTerm()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getContentHandler()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"getContentHandler()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getContentStream(InputSource)\",\n \"u\": \"getContentStream(org.xml.sax.InputSource)\"\n }, {\n \"p\": \"org.biojava.bio.seq.projection\",\n \"c\": \"ProjectedFeatureHolder\",\n \"l\": \"getContext()\"\n }, {\n@@ -18898,15 +18898,15 @@\n \"l\": \"getDP()\"\n }, {\n \"p\": \"org.biojava.bio.dp\",\n \"c\": \"TrainingAlgorithm\",\n \"l\": \"getDP()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getDTDHandler()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"getDTDHandler()\"\n }, {\n \"p\": \"org.biojava.bio.proteomics\",\n@@ -19128,15 +19128,15 @@\n \"l\": \"getEndOfRecord()\"\n }, {\n \"p\": \"org.biojava.bio.program.tagvalue\",\n \"c\": \"RegexParser\",\n \"l\": \"getEndOfRecord()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getEntityResolver()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"getEntityResolver()\"\n }, {\n \"p\": \"org.biojava.utils.candy\",\n@@ -19178,15 +19178,15 @@\n \"l\": \"getErrorHandler()\"\n }, {\n \"p\": \"org.biojava.bio.program.gff3\",\n \"c\": \"GFF3Parser\",\n \"l\": \"getErrorHandler()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getErrorHandler()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"getErrorHandler()\"\n }, {\n \"p\": \"org.biojava.utils.process\",\n@@ -19310,15 +19310,15 @@\n \"l\": \"getFeature()\"\n }, {\n \"p\": \"org.biojavax.bio.seq\",\n \"c\": \"SimpleRichLocation\",\n \"l\": \"getFeature()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getFeature(String)\",\n \"u\": \"getFeature(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"getFeature(String)\",\n \"u\": \"getFeature(java.lang.String)\"\n@@ -22557,23 +22557,23 @@\n \"l\": \"getNamespace()\"\n }, {\n \"p\": \"org.biojava.utils.lsid\",\n \"c\": \"LifeScienceIdentifier\",\n \"l\": \"getNamespaceId()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getNamespacePrefix()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getNamespacePrefixes()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getNamespaces()\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"NameTokenization\",\n \"l\": \"getNameToSymbol()\"\n }, {\n \"p\": \"org.biojavax.bio.taxa\",\n@@ -23883,15 +23883,15 @@\n }, {\n \"p\": \"org.biojavax\",\n \"c\": \"SimpleRichAnnotation\",\n \"l\": \"getProperty(Object)\",\n \"u\": \"getProperty(java.lang.Object)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getProperty(String)\",\n \"u\": \"getProperty(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"getProperty(String)\",\n \"u\": \"getProperty(java.lang.String)\"\n@@ -27387,15 +27387,15 @@\n \"l\": \"getURI()\"\n }, {\n \"p\": \"org.biojavax\",\n \"c\": \"SimpleNamespace\",\n \"l\": \"getURI()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"getURIFromPrefix(String)\",\n \"u\": \"getURIFromPrefix(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.gui.sequence\",\n \"c\": \"ImageMap.HotSpot\",\n \"l\": \"getURL()\"\n }, {\n@@ -30825,15 +30825,15 @@\n \"l\": \"issue\"\n }, {\n \"p\": \"org.biojava.bibliography\",\n \"c\": \"BiblioJournalArticle\",\n \"l\": \"issueSupplement\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"iState\"\n }, {\n \"p\": \"org.biojavax.bio.taxa\",\n \"c\": \"NCBITaxon\",\n \"l\": \"isTaxonHidden()\"\n }, {\n \"p\": \"org.biojavax.bio.taxa\",\n@@ -34740,27 +34740,27 @@\n \"u\": \"%3Cinit%3E(int,int)\"\n }, {\n \"p\": \"org.biojava.bio.chromatogram\",\n \"c\": \"Chromatogram\",\n \"l\": \"OFFSETS\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"oFullNamespacePrefix\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"oHandler\"\n }, {\n \"p\": \"org.biojava.bio.proteomics\",\n \"c\": \"MassCalc\",\n \"l\": \"Omono\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"oNamespacePrefix\"\n }, {\n \"p\": \"org.biojava.bio\",\n \"c\": \"CardinalityConstraint\",\n \"l\": \"ONE\"\n }, {\n \"p\": \"org.biojava.bio\",\n@@ -36594,15 +36594,15 @@\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 }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"ClustalWAlignmentSAXParser\",\n \"l\": \"parse(String)\",\n \"u\": \"parse(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"parse(String)\",\n \"u\": \"parse(java.lang.String)\"\n@@ -37341,15 +37341,15 @@\n }, {\n \"p\": \"org.biojava.utils\",\n \"c\": \"ChangeListener\",\n \"l\": \"preChange(ChangeEvent)\",\n \"u\": \"preChange(org.biojava.utils.ChangeEvent)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"prefix(String)\",\n \"u\": \"prefix(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.dp.twohead\",\n \"c\": \"AbstractMatrixPairDPCursor\",\n \"l\": \"press()\"\n }, {\n@@ -43603,15 +43603,15 @@\n }, {\n \"p\": \"org.biojava.bio\",\n \"c\": \"AnnotationType\",\n \"l\": \"setConstraints(Object, PropertyConstraint, Location)\",\n \"u\": \"setConstraints(java.lang.Object,org.biojava.bio.PropertyConstraint,org.biojava.bio.symbol.Location)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setContentHandler(ContentHandler)\",\n \"u\": \"setContentHandler(org.xml.sax.ContentHandler)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParser\",\n \"l\": \"setContentHandler(ContentHandler)\",\n \"u\": \"setContentHandler(org.xml.sax.ContentHandler)\"\n@@ -44285,15 +44285,15 @@\n \"u\": \"setDoubleProperty(org.biojava.bio.symbol.Symbol,java.lang.String)\"\n }, {\n \"p\": \"org.biojava.utils.stax\",\n \"c\": \"DoubleElementHandlerBase\",\n \"l\": \"setDoubleValue(double)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setDTDHandler(DTDHandler)\",\n \"u\": \"setDTDHandler(org.xml.sax.DTDHandler)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"setDTDHandler(DTDHandler)\",\n \"u\": \"setDTDHandler(org.xml.sax.DTDHandler)\"\n@@ -44400,15 +44400,15 @@\n }, {\n \"p\": \"org.biojava.bio.program.tagvalue\",\n \"c\": \"RegexParser\",\n \"l\": \"setEndOfRecord(String)\",\n \"u\": \"setEndOfRecord(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setEntityResolver(EntityResolver)\",\n \"u\": \"setEntityResolver(org.xml.sax.EntityResolver)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"setEntityResolver(EntityResolver)\",\n \"u\": \"setEntityResolver(org.xml.sax.EntityResolver)\"\n@@ -44423,15 +44423,15 @@\n \"l\": \"setEpsilon(double)\"\n }, {\n \"p\": \"org.biojava.stats.svm\",\n \"c\": \"SMOTrainer\",\n \"l\": \"setEpsilon(double)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setErrorHandler(ErrorHandler)\",\n \"u\": \"setErrorHandler(org.xml.sax.ErrorHandler)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"setErrorHandler(ErrorHandler)\",\n \"u\": \"setErrorHandler(org.xml.sax.ErrorHandler)\"\n@@ -44502,15 +44502,15 @@\n }, {\n \"p\": \"org.biojava.bio.program.gff\",\n \"c\": \"SimpleGFFRecord\",\n \"l\": \"setFeature(String)\",\n \"u\": \"setFeature(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setFeature(String, boolean)\",\n \"u\": \"setFeature(java.lang.String,boolean)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"setFeature(String, boolean)\",\n \"u\": \"setFeature(java.lang.String,boolean)\"\n@@ -45672,15 +45672,15 @@\n }, {\n \"p\": \"org.biojavax.bio.seq.io\",\n \"c\": \"SimpleRichSequenceBuilder\",\n \"l\": \"setNamespace(Namespace)\",\n \"u\": \"setNamespace(org.biojavax.Namespace)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setNamespacePrefix(String)\",\n \"u\": \"setNamespacePrefix(java.lang.String)\"\n }, {\n \"p\": \"org.biojava.stats.svm.tools\",\n \"c\": \"ClassifierExample.PointClassifier\",\n \"l\": \"setNegShape(Shape)\",\n \"u\": \"setNegShape(java.awt.Shape)\"\n@@ -46172,15 +46172,15 @@\n }, {\n \"p\": \"org.biojavax\",\n \"c\": \"SimpleRichAnnotation\",\n \"l\": \"setProperty(Object, Object)\",\n \"u\": \"setProperty(java.lang.Object,java.lang.Object)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"setProperty(String, Object)\",\n \"u\": \"setProperty(java.lang.String,java.lang.Object)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax.blastxml\",\n \"c\": \"BlastXMLParserFacade\",\n \"l\": \"setProperty(String, Object)\",\n \"u\": \"setProperty(java.lang.String,java.lang.Object)\"\n@@ -49568,15 +49568,15 @@\n }, {\n \"p\": \"org.biojava.utils\",\n \"c\": \"ActivityListener\",\n \"l\": \"startedActivity(Object)\",\n \"u\": \"startedActivity(java.lang.Object)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"startElement(QName, Attributes)\",\n \"u\": \"startElement(org.biojava.bio.program.sax.QName,org.xml.sax.Attributes)\"\n }, {\n \"p\": \"org.biojava.bio.program.xml\",\n \"c\": \"BaseXMLWriter\",\n \"l\": \"startElement(String)\",\n \"u\": \"startElement(java.lang.String)\"\n@@ -52159,19 +52159,19 @@\n \"l\": \"TITLE_TAG\"\n }, {\n \"p\": \"org.biojavax.bio.seq.io\",\n \"c\": \"UniProtXMLFormat\",\n \"l\": \"TITLE_TAG\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"tNamespacePrefixes\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"FastaSearchSAXParser\",\n+ \"c\": \"PdbSAXParser\",\n \"l\": \"tNamespaces\"\n }, {\n \"p\": \"org.biojava.bio.dp\",\n \"c\": \"TrainerTransition\",\n \"l\": \"to\"\n }, {\n \"p\": \"org.biojava.bio.dp\",\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\": \"AbstractReversibleTranslationTable\",\n+ \"c\": \"SimpleReversibleTranslationTable\",\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"}]}]}]}]}]}