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.ClustalWAlignmentSAXParser\n+
getErrorHandler() - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
getFeature(String) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
getNamespacePrefix() - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n
\n Describe getNamespacePrefix method here.
\n \n-
getNamespacePrefixes() - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+
getNamespacePrefixes() - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n
\n Support SAX2 configuration of namespace support of parser.
\n \n-
getNamespaces() - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+
getNamespaces() - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
getProperty(String) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
getURIFromPrefix(String) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
iState - Variable in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
oFullNamespacePrefix - Variable in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n
\n-
oHandler - Variable in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+
oHandler - Variable in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
oNamespacePrefix - Variable in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -29486,21 +29486,21 @@\n \n
parse(Object) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser\n
\n
parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser\n
\n
parse(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueParser\n
\n-
parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+
parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n
\n
parse(Readable, ParseListener) - Method in interface org.biojava.bio.program.fastq.FastqReader\n
\n Parse the specified readable.
\n \n-
parse(String) - Method in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+
parse(String) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
prefix(String) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -31237,27 +31237,27 @@\n \n
read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat\n
\n Reads an MSF Alignment File
\n \n
read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser\n
\n-
read(File) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+
read(File) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n
\n
read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader\n
\n Read zero or more FASTQ formatted sequences from the specified file.
\n \n-
read(InputStream) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+
read(InputStream) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n
\n
read(InputStream) - Method in interface org.biojava.bio.program.fastq.FastqReader\n
\n Read zero or more FASTQ formatted sequences from the specified input stream.
\n \n-
read(URL) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+
read(URL) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n
\n
read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader\n
\n Read zero or more FASTQ formatted sequences from the specified url.
\n \n
readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat\n
\n@@ -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.ClustalWAlignmentSAXParser\n+
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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
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.ClustalWAlignmentSAXParser\n+
setNamespacePrefix(String) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+
startElement(QName, Attributes) - Method in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -41034,15 +41034,15 @@\n \n
StrandParser - Class in org.biojava.bio.seq\n
\n Process strings and return strand objects.
\n \n
StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser\n
\n-
stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+
stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n
\n
stream(Readable, StreamListener) - Method in interface org.biojava.bio.program.fastq.FastqReader\n
\n Stream the specified readable.
\n \n
StreamListener - Interface in org.biojava.bio.program.fastq\n
\n@@ -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.ClustalWAlignmentSAXParser\n+
tNamespacePrefixes - Variable in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n
\n-
tNamespaces - Variable in class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+
tNamespaces - Variable in class org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.AbstractManyToOneTranslationTable\n+
translate(Symbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable\n
\n
translate(Symbol) - Method in interface org.biojava.bio.symbol.TranslationTable\n
\n Translate a single symbol from source alphabet to the target alphabet.
\n \n
translate(SymbolList) - Static method in class org.biojava.bio.seq.GeneticCodes\n
\n", "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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -4480,15 +4480,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +4572,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +7271,15 @@\n \u00a0\n doRetain() - Method in class org.biojava.bio.program.tagvalue.TagDropper\n Find out if known tags are retained or dropped.\n doSortPeptides() - Method in class\n org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer\n \u00a0\n doTranslate(Symbol) - Method in class\n- org.biojava.bio.symbol.AbstractManyToOneTranslationTable\n+ org.biojava.bio.symbol.AbstractReversibleTranslationTable\n this method is expected to translate any symbol in the source alphabet.\n doTranslate(Symbol) - Method in class\n org.biojava.bio.symbol.SimpleManyToOneTranslationTable\n \u00a0\n doTranslate(Symbol) - Method in class\n org.biojava.bio.symbol.SimpleReversibleTranslationTable\n \u00a0\n@@ -8033,15 +8033,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +12491,21 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -13274,15 +13274,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +13426,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -13457,15 +13457,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -13542,15 +13542,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +15526,21 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n Describe getNamespacePrefix method here.\n getNamespacePrefixes() - Method in class\n- org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n Support SAX2 configuration of namespace support of parser.\n getNamespaces() - Method in class\n- org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +16357,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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 +18655,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -21013,15 +21013,15 @@\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\n- org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -23599,23 +23599,23 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n \u00a0\n oHandler - Variable in class\n- org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -25060,21 +25060,21 @@\n \u00a0\n parse(Object) - Method in class org.biojava.bio.program.tagvalue.RegexParser\n \u00a0\n parse(Object) - Method in interface\n org.biojava.bio.program.tagvalue.TagValueParser\n \u00a0\n parse(Readable,_ParseListener) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqReader\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n parse(Readable,_ParseListener) - Method in interface\n org.biojava.bio.program.fastq.FastqReader\n Parse the specified readable.\n parse(String) - Method in class\n- org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -25623,15 +25623,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -26562,26 +26562,27 @@\n Reads an alignment in FASTA format.\n read(BufferedReader) - Method in class\n org.biojava.bio.seq.io.MSFAlignmentFormat\n Reads an MSF Alignment File\n read(BufferedReader,_TagValueParser,_TagValueListener) - Method in class\n org.biojava.bio.program.tagvalue.Parser\n \u00a0\n- read(File) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+ read(File) - Method in class\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader\n Read zero or more FASTQ formatted sequences from the specified file.\n read(InputStream) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqReader\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n read(InputStream) - Method in interface\n org.biojava.bio.program.fastq.FastqReader\n Read zero or more FASTQ formatted sequences from the specified input\n stream.\n- read(URL) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\n+ read(URL) - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader\n Read zero or more FASTQ formatted sequences from the specified url.\n readableFileNames - Static variable in class\n org.biojavax.bio.seq.io.EMBLFormat\n \u00a0\n readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat\n@@ -30140,15 +30141,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -30576,15 +30577,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -30655,15 +30656,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -30680,15 +30681,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -30709,15 +30710,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -31438,15 +31439,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -31742,15 +31743,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -34327,15 +34328,15 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -35013,15 +35014,15 @@\n org.biojava.bio.seq.FeatureFilter.StrandFilter\n Build a new filter that matches all features of a given strand.\n StrandParser - Class in org.biojava.bio.seq\n Process strings and return strand objects.\n StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser\n \u00a0\n stream(Readable,_StreamListener) - Method in class\n- org.biojava.bio.program.fastq.SangerFastqReader\n+ org.biojava.bio.program.fastq.IlluminaFastqReader\n \u00a0\n stream(Readable,_StreamListener) - Method in interface\n org.biojava.bio.program.fastq.FastqReader\n Stream the specified readable.\n StreamListener - Interface in org.biojava.bio.program.fastq\n Event based parser callback.\n streamNext(SeqIOListener) - Method in class\n@@ -36035,18 +36036,18 @@\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.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\n \u00a0\n tNamespaces - Variable in class\n- org.biojava.bio.program.sax.ClustalWAlignmentSAXParser\n+ org.biojava.bio.program.sax.SequenceAlignmentSAXParser\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@@ -36765,15 +36766,15 @@\n translate(int) - Method in interface org.biojavax.bio.seq.Position\n Takes this position and returns a copy translated by 'distance' bases.\n translate(int) - Method in class org.biojavax.bio.seq.SimplePosition\n Takes this position and returns a copy translated by 'distance' bases.\n translate(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation\n Create a location that is a translation of this location.\n translate(Symbol) - Method in class\n- org.biojava.bio.symbol.AbstractManyToOneTranslationTable\n+ org.biojava.bio.symbol.SimpleManyToOneTranslationTable\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"}]}, {"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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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@@ -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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"AbstractManyToOneTranslationTable\",\n+ \"c\": \"AbstractReversibleTranslationTable\",\n \"l\": \"doTranslate(Symbol)\",\n \"u\": \"doTranslate(org.biojava.bio.symbol.Symbol)\"\n }, {\n \"p\": \"org.biojava.bio.symbol\",\n \"c\": \"SimpleManyToOneTranslationTable\",\n \"l\": \"doTranslate(Symbol)\",\n \"u\": \"doTranslate(org.biojava.bio.symbol.Symbol)\"\n@@ -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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\n \"l\": \"getNamespacePrefix()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\n \"l\": \"getNamespacePrefixes()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\n \"l\": \"oFullNamespacePrefix\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\n \"l\": \"oNamespacePrefix\"\n }, {\n \"p\": \"org.biojava.bio\",\n \"c\": \"CardinalityConstraint\",\n \"l\": \"ONE\"\n }, {\n \"p\": \"org.biojava.bio\",\n@@ -36584,25 +36584,25 @@\n }, {\n \"p\": \"org.biojavax.bio.phylo.io.phylip\",\n \"c\": \"PHYLIPFileFormat\",\n \"l\": \"parse(PHYLIPFileListener, BufferedReader)\",\n \"u\": \"parse(org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener,java.io.BufferedReader)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"parse(Readable, ParseListener)\",\n \"u\": \"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"parse(Readable, ParseListener)\",\n \"u\": \"parse(java.lang.Readable,org.biojava.bio.program.fastq.ParseListener)\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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@@ -38670,35 +38670,35 @@\n }, {\n \"p\": \"org.biojava.utils.io\",\n \"c\": \"RandomAccessReader\",\n \"l\": \"read(char[], int, int)\",\n \"u\": \"read(char[],int,int)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"read(File)\",\n \"u\": \"read(java.io.File)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"read(File)\",\n \"u\": \"read(java.io.File)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"read(InputStream)\",\n \"u\": \"read(java.io.InputStream)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"read(InputStream)\",\n \"u\": \"read(java.io.InputStream)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"read(URL)\",\n \"u\": \"read(java.net.URL)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"read(URL)\",\n \"u\": \"read(java.net.URL)\"\n@@ -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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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@@ -50748,15 +50748,15 @@\n }, {\n \"p\": \"org.biojava.bio.seq\",\n \"c\": \"StrandParser\",\n \"l\": \"StrandParser()\",\n \"u\": \"%3Cinit%3E()\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n- \"c\": \"SangerFastqReader\",\n+ \"c\": \"IlluminaFastqReader\",\n \"l\": \"stream(Readable, StreamListener)\",\n \"u\": \"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)\"\n }, {\n \"p\": \"org.biojava.bio.program.fastq\",\n \"c\": \"FastqReader\",\n \"l\": \"stream(Readable, StreamListener)\",\n \"u\": \"stream(java.lang.Readable,org.biojava.bio.program.fastq.StreamListener)\"\n@@ -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\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\n \"l\": \"tNamespacePrefixes\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"ClustalWAlignmentSAXParser\",\n+ \"c\": \"SequenceAlignmentSAXParser\",\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\": \"AbstractManyToOneTranslationTable\",\n+ \"c\": \"SimpleManyToOneTranslationTable\",\n \"l\": \"translate(Symbol)\",\n \"u\": \"translate(org.biojava.bio.symbol.Symbol)\"\n }, {\n \"p\": \"org.biojava.bio.symbol\",\n \"c\": \"TranslationTable\",\n \"l\": \"translate(Symbol)\",\n \"u\": \"translate(org.biojava.bio.symbol.Symbol)\"\n"}]}]}]}]}]}