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.BlastLikeSAXParser\n+
getErrorHandler() - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
getFeature(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
getNamespacePrefix() - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\n
\n Describe getNamespacePrefix method here.
\n \n-
getNamespacePrefixes() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser\n+
getNamespacePrefixes() - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\n
\n Support SAX2 configuration of namespace support of parser.
\n \n-
getNamespaces() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser\n+
getNamespaces() - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
getProperty(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
getURIFromPrefix(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
iState - Variable in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
oFullNamespacePrefix - Variable in class org.biojava.bio.program.sax.FastaSequenceSAXParser\n
\n-
oHandler - Variable in class org.biojava.bio.program.sax.BlastLikeSAXParser\n+
oHandler - Variable in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
oNamespacePrefix - Variable in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.IlluminaFastqReader\n+
parse(Readable, ParseListener) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\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.BlastLikeSAXParser\n+
parse(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
prefix(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.IlluminaFastqReader\n+
read(File) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\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.IlluminaFastqReader\n+
read(InputStream) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\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.IlluminaFastqReader\n+
read(URL) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\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.BlastLikeSAXParser\n+
setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
setNamespacePrefix(String) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
setProperty(String, Object) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.BlastLikeSAXParser\n+
startElement(QName, Attributes) - Method in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.IlluminaFastqReader\n+
stream(Readable, StreamListener) - Method in class org.biojava.bio.program.fastq.SangerFastqReader\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.BlastLikeSAXParser\n+
tNamespacePrefixes - Variable in class org.biojava.bio.program.sax.FastaSequenceSAXParser\n
\n-
tNamespaces - Variable in class org.biojava.bio.program.sax.BlastLikeSAXParser\n+
tNamespaces - Variable in class org.biojava.bio.program.sax.FastaSequenceSAXParser\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.SimpleGeneticCodeTable\n+
translate(Symbol) - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable\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.IlluminaFastqWriter\n+
write(File, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter\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.IlluminaFastqWriter\n+
write(File, Fastq...) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter\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.IlluminaFastqWriter\n+
write(OutputStream, Iterable<Fastq>) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter\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.IlluminaFastqWriter\n+
write(OutputStream, Fastq...) - Method in class org.biojava.bio.program.fastq.SolexaFastqWriter\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": "@@ -1454,15 +1454,15 @@\n add a search pattern to the searches to be conducted by this object.\n _\ba_\bd_\bd_\bP_\bo_\bs_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class org.biojava.stats.svm._\bD_\bi_\ba_\bg_\bo_\bn_\ba_\bl_\bA_\bd_\bd_\bK_\be_\br_\bn_\be_\bl\n \u00a0\n _\ba_\bd_\bd_\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn_\b(_\bA_\bG_\bA_\bV_\bE_\bM_\ba_\bp_\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bM_\ba_\bp_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n \u00a0\n _\ba_\bd_\bd_\bP_\br_\be_\bf_\bi_\bx_\bM_\ba_\bp_\bp_\bi_\bn_\bg_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Adds a namespace prefix to URI mapping as (key,value) pairs.\n _\ba_\bd_\bd_\bP_\br_\bo_\bp_\b(_\bA_\bG_\bA_\bV_\bE_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bR_\be_\bl_\ba_\bt_\be_\bd_\bA_\bn_\bn_\bo_\bt\n \u00a0\n _\ba_\bd_\bd_\bP_\br_\bo_\bp_\b(_\bA_\bG_\bA_\bV_\bE_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bX_\br_\be_\bf\n \u00a0\n@@ -2779,22 +2779,22 @@\n _\bA_\bp_\bp_\bB_\be_\ba_\bn_\bR_\bu_\bn_\bn_\be_\br - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bu_\bt_\bi_\bl_\bs_\b._\bx_\bm_\bl\n Create a bean from an XML file, then attempt to enter it.\n _\bA_\bp_\bp_\bB_\be_\ba_\bn_\bR_\bu_\bn_\bn_\be_\br_\b(_\b) - Constructor for class org.biojava.utils.xml._\bA_\bp_\bp_\bB_\be_\ba_\bn_\bR_\bu_\bn_\bn_\be_\br\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bN_\bf_\ba_\bS_\bu_\bb_\bM_\bo_\bd_\be_\bl_\b) - Method in class org.biojava.utils.automata._\bN_\bf_\ba_\bS_\bu_\bb_\bM_\bo_\bd_\be_\bl\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Append the specified FASTQ formatted sequences to the specified\n appendable.\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\ba_\bp_\bp_\be_\bn_\bd_\b(_\bT_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Append the specified FASTQ formatted sequences to the specified\n appendable.\n _\ba_\bp_\bp_\be_\bn_\bd_\bM_\ba_\bt_\br_\bi_\bx_\bD_\ba_\bt_\ba_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n org.biojavax.bio.phylo.io.nexus._\bC_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\bB_\bl_\bo_\bc_\bk\n@@ -4471,15 +4471,15 @@\n An implementation that always vetoes everything.\n _\bC_\bh_\ba_\bn_\bg_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b._\bC_\bh_\ba_\bn_\bg_\be_\bE_\bv_\be_\bn_\bt_\bR_\be_\bc_\bo_\br_\bd_\be_\br - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bu_\bt_\bi_\bl_\bs\n A listener that remembers the ChangeEvent of the last change.\n _\bC_\bh_\ba_\bn_\bg_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b._\bL_\bo_\bg_\bg_\bi_\bn_\bg_\bL_\bi_\bs_\bt_\be_\bn_\be_\br - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bu_\bt_\bi_\bl_\bs\n A listener that writes information about the event stream to a\n PrintStream.\n _\bc_\bh_\ba_\bn_\bg_\be_\bS_\bt_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Centralise chaining of iState field to help with debugging.\n _\bc_\bh_\ba_\bn_\bg_\be_\bS_\bu_\bp_\bp_\bo_\br_\bt_\b(_\b) - Method in class org.biojava.utils._\bC_\bh_\ba_\bn_\bg_\be_\bF_\bo_\br_\bw_\ba_\br_\bd_\be_\br\n Return the underlying ChangeSupport instance that can be used to fire\n ChangeEvents and mannage listeners.\n _\bC_\bh_\ba_\bn_\bg_\be_\bS_\bu_\bp_\bp_\bo_\br_\bt - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bu_\bt_\bi_\bl_\bs\n A utility class to provide management for informing ChangeListeners of\n ChangeEvents.\n@@ -4563,15 +4563,15 @@\n _\bC_\bH_\bA_\bR_\bA_\bC_\bT_\bE_\bR - Static variable in interface\n org.biojava.bio.seq.io._\bS_\by_\bm_\bb_\bo_\bl_\bT_\bo_\bk_\be_\bn_\bi_\bz_\ba_\bt_\bi_\bo_\bn\n \u00a0\n _\bc_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\b(_\bc_\bh_\ba_\br_\b[_\b]_\b,_\b _\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.program.blast2html._\bB_\bl_\ba_\bs_\bt_\b2_\bH_\bT_\bM_\bL_\bH_\ba_\bn_\bd_\bl_\be_\br\n Describe characters method here.\n _\bc_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\b(_\bc_\bh_\ba_\br_\b[_\b]_\b,_\b _\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Utility method to centralize the sending of a SAX characters message a\n document handler.\n _\bc_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\b(_\bc_\bh_\ba_\br_\b[_\b]_\b,_\b _\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.program.ssbind._\bS_\be_\bq_\bS_\bi_\bm_\bi_\bl_\ba_\br_\bi_\bt_\by_\bA_\bd_\ba_\bp_\bt_\be_\br\n \u00a0\n _\bc_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\b(_\bc_\bh_\ba_\br_\b[_\b]_\b,_\b _\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.program.xml._\bS_\bi_\bm_\bp_\bl_\be_\bX_\bM_\bL_\bE_\bm_\bi_\bt_\bt_\be_\br\n@@ -7262,15 +7262,15 @@\n \u00a0\n _\bd_\bo_\bR_\be_\bt_\ba_\bi_\bn_\b(_\b) - Method in class org.biojava.bio.program.tagvalue._\bT_\ba_\bg_\bD_\br_\bo_\bp_\bp_\be_\br\n Find out if known tags are retained or dropped.\n _\bd_\bo_\bS_\bo_\br_\bt_\bP_\be_\bp_\bt_\bi_\bd_\be_\bs_\b(_\b) - Method in class\n org.biojava.bio.gui.sequence._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\bP_\be_\bp_\bt_\bi_\bd_\be_\bD_\bi_\bg_\be_\bs_\bt_\bR_\be_\bn_\bd_\be_\br_\be_\br\n \u00a0\n _\bd_\bo_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in class\n- org.biojava.bio.symbol._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\bR_\be_\bv_\be_\br_\bs_\bi_\bb_\bl_\be_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n+ org.biojava.bio.symbol._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\bM_\ba_\bn_\by_\bT_\bo_\bO_\bn_\be_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n this method is expected to translate any symbol in the source alphabet.\n _\bd_\bo_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in class\n org.biojava.bio.symbol._\bS_\bi_\bm_\bp_\bl_\be_\bM_\ba_\bn_\by_\bT_\bo_\bO_\bn_\be_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n \u00a0\n _\bd_\bo_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in class\n org.biojava.bio.symbol._\bS_\bi_\bm_\bp_\bl_\be_\bR_\be_\bv_\be_\br_\bs_\bi_\bb_\bl_\be_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n \u00a0\n@@ -8024,15 +8024,15 @@\n _\be_\bn_\bd_\bE_\bl_\be_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\bA_\bX_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.utils.stax._\bS_\bt_\bA_\bX_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\bB_\ba_\bs_\be\n \u00a0\n _\be_\bn_\bd_\bE_\bl_\be_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\bA_\bX_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.utils.stax._\bS_\bt_\br_\bi_\bn_\bg_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\bB_\ba_\bs_\be\n \u00a0\n _\be_\bn_\bd_\bE_\bl_\be_\bm_\be_\bn_\bt_\b(_\bQ_\bN_\ba_\bm_\be_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Utility method to centralize the sending of a SAX endElement message a\n document handler.\n _\be_\bn_\bd_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\bA_\bX_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in\n class org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bB_\bi_\bo_\bS_\be_\bq_\bH_\ba_\bn_\bd_\bl_\be_\br\n \u00a0\n _\be_\bn_\bd_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\bA_\bX_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in\n class org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bC_\bh_\br_\bo_\bm_\bo_\bs_\bo_\bm_\be_\bH_\ba_\bn_\bd_\bl_\be_\br\n@@ -10247,38 +10247,38 @@\n _\bF_\bo_\br_\bm_\ba_\bt - Interface in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bb_\bi_\bo_\b._\bp_\br_\bo_\bg_\br_\ba_\bm_\b._\bf_\bo_\br_\bm_\ba_\bt_\bs\n A file format supported by the tag-value event-based parsing system.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b) - Method in class\n org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n formatLocation creates a String representation of a Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in\n- class org.biojava.bio.seq.io._\bE_\bm_\bb_\bl_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n+ class org.biojava.bio.seq.io._\bP_\br_\bo_\bt_\be_\bi_\bn_\bR_\be_\bf_\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n formatLocation creates an EMBL/Genbank style representation of a\n Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in\n interface org.biojava.bio.seq.io._\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n formatLocation creates a String representation of a Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bS_\bt_\br_\bi_\bn_\bg_\bB_\bu_\bf_\bf_\be_\br_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in\n class org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n formatLocation creates a String representation of a Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in class\n- org.biojava.bio.seq.io._\bE_\bm_\bb_\bl_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n+ org.biojava.bio.seq.io._\bP_\br_\bo_\bt_\be_\bi_\bn_\bR_\be_\bf_\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Formats the location of a feature.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in interface\n org.biojava.bio.seq.io._\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n Formats the location of a feature.\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in class\n org.biojava.bio.seq.io._\bS_\bw_\bi_\bs_\bs_\bp_\br_\bo_\bt_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n Deprecated.\n Creates a string representation of the location of a feature\n _\bf_\bo_\br_\bm_\ba_\bt_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b(_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bS_\bt_\br_\ba_\bn_\bd_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\b._\bS_\bt_\br_\ba_\bn_\bd_\b) - Method in class\n- org.biojava.bio.seq.io._\bE_\bm_\bb_\bl_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n+ org.biojava.bio.seq.io._\bP_\br_\bo_\bt_\be_\bi_\bn_\bR_\be_\bf_\bS_\be_\bq_\bF_\bi_\bl_\be_\bF_\bo_\br_\bm_\be_\br\n formatLocation creates an EMBL/Genbank style representation of a\n Location.\n _\bf_\bo_\br_\bm_\ba_\bt_\bO_\bu_\bt_\bp_\bu_\bt_\b(_\b) - Method in class org.biojava.bio.alignment._\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bP_\ba_\bi_\br\n \u00a0\n _\bf_\bo_\br_\bm_\ba_\bt_\bO_\bu_\bt_\bp_\bu_\bt_\b(_\bi_\bn_\bt_\b) - Method in class org.biojava.bio.alignment._\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bP_\ba_\bi_\br\n This method provides a BLAST-like formated alignment from the given\n Strings, in which the sequence coordinates and the information \"Query\" or\n@@ -12482,21 +12482,21 @@\n org.biojava.utils.bytecode._\bG_\be_\bn_\be_\br_\ba_\bt_\be_\bd_\bC_\bo_\bd_\be_\bM_\be_\bt_\bh_\bo_\bd\n \u00a0\n _\bg_\be_\bt_\bC_\bo_\bn_\bt_\ba_\bi_\bn_\bs_\bT_\be_\br_\bm_\b(_\b) - Static method in class\n org.biojavax.bio.seq._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bF_\be_\ba_\bt_\bu_\br_\be_\bR_\be_\bl_\ba_\bt_\bi_\bo_\bn_\bs_\bh_\bi_\bp\n Gets the default CONTAINS term used for defining the relationship between\n features.\n _\bg_\be_\bt_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Return the content handler.\n _\bg_\be_\bt_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n correct this later\n _\bg_\be_\bt_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bS_\bt_\br_\be_\ba_\bm_\b(_\bI_\bn_\bp_\bu_\bt_\bS_\bo_\bu_\br_\bc_\be_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Create a stream from an an InputSource, picking the correct stream\n according to order of precedance.\n _\bg_\be_\bt_\bC_\bo_\bn_\bt_\be_\bx_\bt_\b(_\b) - Method in class\n org.biojava.bio.seq.projection._\bP_\br_\bo_\bj_\be_\bc_\bt_\be_\bd_\bF_\be_\ba_\bt_\bu_\br_\be_\bH_\bo_\bl_\bd_\be_\br\n \u00a0\n _\bg_\be_\bt_\bC_\bo_\bn_\bt_\be_\bx_\bt_\b(_\b) - Method in class org.biojava.stats.svm._\bT_\br_\ba_\bi_\bn_\bi_\bn_\bg_\bE_\bv_\be_\bn_\bt\n \u00a0\n@@ -13265,15 +13265,15 @@\n getDownstreamEndType returns the double-stranded end type produced by the\n primary (intra-site or downstream) cut.\n _\bg_\be_\bt_\bD_\bP_\b(_\b) - Method in class org.biojava.bio.dp._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\bT_\br_\ba_\bi_\bn_\be_\br\n \u00a0\n _\bg_\be_\bt_\bD_\bP_\b(_\b) - Method in interface org.biojava.bio.dp._\bT_\br_\ba_\bi_\bn_\bi_\bn_\bg_\bA_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm\n \u00a0\n _\bg_\be_\bt_\bD_\bT_\bD_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bg_\be_\bt_\bD_\bT_\bD_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bg_\be_\bt_\bE_\b(_\b) - Method in class org.biojava.bio.proteomics._\bS_\bt_\br_\bu_\bc_\bt_\bu_\br_\be_\bT_\bo_\bo_\bl_\bs\n \u00a0\n _\bg_\be_\bt_\bE_\bc_\bN_\bu_\bm_\bb_\be_\br_\b(_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn_\b) - Method in class\n@@ -13417,15 +13417,15 @@\n _\bg_\be_\bt_\bE_\bn_\bd_\bO_\bf_\bR_\be_\bc_\bo_\br_\bd_\b(_\b) - Method in class\n org.biojava.bio.program.tagvalue._\bL_\bi_\bn_\be_\bS_\bp_\bl_\bi_\bt_\bP_\ba_\br_\bs_\be_\br\n Get the current string indicating that a record has ended.\n _\bg_\be_\bt_\bE_\bn_\bd_\bO_\bf_\bR_\be_\bc_\bo_\br_\bd_\b(_\b) - Method in class\n org.biojava.bio.program.tagvalue._\bR_\be_\bg_\be_\bx_\bP_\ba_\br_\bs_\be_\br\n Get the explicit end-of-record string.\n _\bg_\be_\bt_\bE_\bn_\bt_\bi_\bt_\by_\bR_\be_\bs_\bo_\bl_\bv_\be_\br_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bg_\be_\bt_\bE_\bn_\bt_\bi_\bt_\by_\bR_\be_\bs_\bo_\bl_\bv_\be_\br_\b(_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n This class has an EntityResolver that resolves the public ID specifying\n the NCBI DTDs to resource files within the BioJava libraries.\n _\bg_\be_\bt_\bE_\bn_\bt_\br_\by_\bB_\by_\bN_\ba_\bm_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in interface\n org.biojava.utils.candy._\bC_\ba_\bn_\bd_\by_\bV_\bo_\bc_\ba_\bb_\bu_\bl_\ba_\br_\by\n@@ -13448,15 +13448,15 @@\n org.biojavax.bio.phylo.io.nexus._\bC_\bh_\ba_\br_\ba_\bc_\bt_\be_\br_\bs_\bB_\bl_\bo_\bc_\bk\n \u00a0\n _\bg_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class org.biojava.bio.program.gff._\bG_\bF_\bF_\bP_\ba_\br_\bs_\be_\br\n Find the error handler used by this parser.\n _\bg_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class org.biojava.bio.program.gff3._\bG_\bF_\bF_\b3_\bP_\ba_\br_\bs_\be_\br\n Find the error handler used by this parser.\n _\bg_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bg_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bg_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\b) - Method in class org.biojava.utils.process._\bE_\bx_\bt_\be_\br_\bn_\ba_\bl_\bP_\br_\bo_\bc_\be_\bs_\bs\n Gets the output error handler which is responsible for the standard error\n output of the external process.\n@@ -13533,15 +13533,15 @@\n _\bg_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\b) - Method in class org.biojavax.bio.seq._\bE_\bm_\bp_\bt_\by_\bR_\bi_\bc_\bh_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n Retrieves the feature this location is associated with.\n _\bg_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\b) - Method in interface org.biojavax.bio.seq._\bR_\bi_\bc_\bh_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n Retrieves the feature this location is associated with.\n _\bg_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\b) - Method in class org.biojavax.bio.seq._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n Retrieves the feature this location is associated with.\n _\bg_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bg_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bg_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\bD_\be_\bs_\bc_\bT_\be_\br_\bm_\b(_\b) - Static method in class\n org.biojavax.bio.seq._\bR_\bi_\bc_\bh_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b._\bT_\be_\br_\bm_\bs\n Getter for the FeatureDesc term\n@@ -15517,21 +15517,21 @@\n Getter for property namespace.\n _\bg_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\b(_\b) - Method in class org.biojavax.bio._\bS_\bi_\bm_\bp_\bl_\be_\bB_\bi_\bo_\bE_\bn_\bt_\br_\by\n Returns the namespace of this bioentry.\n _\bg_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bI_\bd_\b(_\b) - Method in class\n org.biojava.utils.lsid._\bL_\bi_\bf_\be_\bS_\bc_\bi_\be_\bn_\bc_\be_\bI_\bd_\be_\bn_\bt_\bi_\bf_\bi_\be_\br\n Return the namespace id for this identifier within the authority.\n _\bg_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bP_\br_\be_\bf_\bi_\bx_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Describe getNamespacePrefix method here.\n _\bg_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bP_\br_\be_\bf_\bi_\bx_\be_\bs_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Support SAX2 configuration of namespace support of parser.\n _\bg_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bs_\b(_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Support SAX2 configuration of namespace support of parser.\n _\bg_\be_\bt_\bN_\ba_\bm_\be_\bT_\bo_\bS_\by_\bm_\bb_\bo_\bl_\b(_\b) - Method in class org.biojava.bio.seq.io._\bN_\ba_\bm_\be_\bT_\bo_\bk_\be_\bn_\bi_\bz_\ba_\bt_\bi_\bo_\bn\n \u00a0\n _\bg_\be_\bt_\bN_\bC_\bB_\bI_\bT_\ba_\bx_\bI_\bD_\b(_\b) - Method in interface org.biojavax.bio.taxa._\bN_\bC_\bB_\bI_\bT_\ba_\bx_\bo_\bn\n Gets the NCBI taxon ID.\n _\bg_\be_\bt_\bN_\bC_\bB_\bI_\bT_\ba_\bx_\bI_\bD_\b(_\b) - Method in class org.biojavax.bio.taxa._\bS_\bi_\bm_\bp_\bl_\be_\bN_\bC_\bB_\bI_\bT_\ba_\bx_\bo_\bn\n Gets the NCBI taxon ID.\n@@ -16348,15 +16348,15 @@\n _\bg_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class org.biojava.bio._\bO_\bv_\be_\br_\bl_\ba_\by_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn\n \u00a0\n _\bg_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class org.biojavax._\bE_\bm_\bp_\bt_\by_\bR_\bi_\bc_\bh_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn\n Retrieve the value of a property by key.\n _\bg_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class org.biojavax._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn\n Deprecated.\u00a0\n _\bg_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bg_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bg_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n org.biojava.bio._\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn_\bT_\by_\bp_\be_\b._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt\n \u00a0\n@@ -18646,15 +18646,15 @@\n _\bg_\be_\bt_\bU_\bR_\bI_\b(_\b) - Method in interface org.biojava.bio.seq._\bF_\be_\ba_\bt_\bu_\br_\be_\bT_\by_\bp_\be_\bs_\b._\bT_\by_\bp_\be\n Get the URI for this type.\n _\bg_\be_\bt_\bU_\bR_\bI_\b(_\b) - Method in interface org.biojavax._\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be\n If the namespace has a URI, this will return it.\n _\bg_\be_\bt_\bU_\bR_\bI_\b(_\b) - Method in class org.biojavax._\bS_\bi_\bm_\bp_\bl_\be_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be\n If the namespace has a URI, this will return it.\n _\bg_\be_\bt_\bU_\bR_\bI_\bF_\br_\bo_\bm_\bP_\br_\be_\bf_\bi_\bx_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Gets the URI for a namespace prefix, given that prefix, or null if the\n prefix is not recognised.\n _\bg_\be_\bt_\bU_\bR_\bL_\b(_\b) - Method in class org.biojava.bio.gui.sequence._\bI_\bm_\ba_\bg_\be_\bM_\ba_\bp_\b._\bH_\bo_\bt_\bS_\bp_\bo_\bt\n getURL returns the hotspot URL.\n _\bg_\be_\bt_\bU_\bR_\bN_\b(_\b) - Method in class org.biojava.bio.seq.impl._\bD_\bu_\bm_\bm_\by_\bS_\be_\bq_\bu_\be_\bn_\bc_\be\n \u00a0\n _\bg_\be_\bt_\bU_\bR_\bN_\b(_\b) - Method in class org.biojava.bio.seq.impl._\bS_\bi_\bm_\bp_\bl_\be_\bG_\ba_\bp_\bp_\be_\bd_\bS_\be_\bq_\bu_\be_\bn_\bc_\be\n@@ -21003,15 +21003,15 @@\n org.biojava.bio.seq._\bF_\be_\ba_\bt_\bu_\br_\be_\bT_\by_\bp_\be_\bs\n Work out if one type is a sub-type of another.\n _\bi_\bs_\bs_\bu_\be - Variable in class org.biojava.bibliography._\bB_\bi_\bb_\bl_\bi_\bo_\bJ_\bo_\bu_\br_\bn_\ba_\bl_\bA_\br_\bt_\bi_\bc_\bl_\be\n The issue of the journal.\n _\bi_\bs_\bs_\bu_\be_\bS_\bu_\bp_\bp_\bl_\be_\bm_\be_\bn_\bt - Variable in class\n org.biojava.bibliography._\bB_\bi_\bb_\bl_\bi_\bo_\bJ_\bo_\bu_\br_\bn_\ba_\bl_\bA_\br_\bt_\bi_\bc_\bl_\be\n Suplement.\n- _\bi_\bS_\bt_\ba_\bt_\be - Variable in class org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ _\bi_\bS_\bt_\ba_\bt_\be - Variable in class org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bi_\bs_\bT_\ba_\bx_\bo_\bn_\bH_\bi_\bd_\bd_\be_\bn_\b(_\b) - Method in interface org.biojavax.bio.taxa._\bN_\bC_\bB_\bI_\bT_\ba_\bx_\bo_\bn\n used in getNameHierarchy() to determine whether this taxonomy level is\n displayed\n _\bi_\bs_\bT_\ba_\bx_\bo_\bn_\bH_\bi_\bd_\bd_\be_\bn_\b(_\b) - Method in class org.biojavax.bio.taxa._\bS_\bi_\bm_\bp_\bl_\be_\bN_\bC_\bB_\bI_\bT_\ba_\bx_\bo_\bn\n Returns the taxonomy hierarchy of this taxon entry in the form: most\n specific; less specific; ...; least specific.\n@@ -23589,22 +23589,23 @@\n _\bO_\bf_\bf_\bs_\be_\bt_\bR_\bu_\bl_\be_\br_\bR_\be_\bn_\bd_\be_\br_\be_\br_\b(_\bi_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Constructor for class\n org.biojava.bio.gui.sequence._\bO_\bf_\bf_\bs_\be_\bt_\bR_\bu_\bl_\be_\br_\bR_\be_\bn_\bd_\be_\br_\be_\br\n \u00a0\n _\bO_\bF_\bF_\bS_\bE_\bT_\bS - Static variable in interface\n org.biojava.bio.chromatogram._\bC_\bh_\br_\bo_\bm_\ba_\bt_\bo_\bg_\br_\ba_\bm\n The sequence label for the trace offsets of the called bases.\n _\bo_\bF_\bu_\bl_\bl_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bP_\br_\be_\bf_\bi_\bx - Variable in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n- _\bo_\bH_\ba_\bn_\bd_\bl_\be_\br - Variable in class org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ _\bo_\bH_\ba_\bn_\bd_\bl_\be_\br - Variable in class\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bO_\bm_\bo_\bn_\bo - Static variable in class org.biojava.bio.proteomics._\bM_\ba_\bs_\bs_\bC_\ba_\bl_\bc\n Constant value of Oxygen monoisotopic mass\n _\bo_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bP_\br_\be_\bf_\bi_\bx - Variable in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bo_\bn_\be_\b(_\b) - Static method in class org.biojavax.ga.util._\bG_\bA_\bT_\bo_\bo_\bl_\bs\n \u00a0\n _\bO_\bN_\bE - Static variable in class org.biojava.bio._\bC_\ba_\br_\bd_\bi_\bn_\ba_\bl_\bi_\bt_\by_\bC_\bo_\bn_\bs_\bt_\br_\ba_\bi_\bn_\bt\n The property should have exactly one value.\n _\bO_\bN_\bE_\b__\bO_\bR_\b__\bM_\bO_\bR_\bE - Static variable in class org.biojava.bio._\bC_\ba_\br_\bd_\bi_\bn_\ba_\bl_\bi_\bt_\by_\bC_\bo_\bn_\bs_\bt_\br_\ba_\bi_\bn_\bt\n The property should have one or more values.\n@@ -25049,21 +25050,21 @@\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class org.biojava.bio.program.tagvalue._\bR_\be_\bg_\be_\bx_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in interface\n org.biojava.bio.program.tagvalue._\bT_\ba_\bg_\bV_\ba_\bl_\bu_\be_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bP_\ba_\br_\bs_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bP_\ba_\br_\bs_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Parse the specified readable.\n _\bp_\ba_\br_\bs_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Full implementation of interface method.\n _\bp_\ba_\br_\bs_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class org.biojava.bio.program.sax._\bP_\bd_\bb_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bp_\ba_\br_\bs_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class org.biojava.naming._\bO_\bb_\bd_\ba_\bU_\br_\bi_\bP_\ba_\br_\bs_\be_\br\n@@ -25612,15 +25613,15 @@\n \u00a0\n _\bp_\br_\be_\bC_\bh_\ba_\bn_\bg_\be_\b(_\bC_\bh_\ba_\bn_\bg_\be_\bE_\bv_\be_\bn_\bt_\b) - Method in class\n org.biojava.utils._\bC_\bh_\ba_\bn_\bg_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b._\bL_\bo_\bg_\bg_\bi_\bn_\bg_\bL_\bi_\bs_\bt_\be_\bn_\be_\br\n \u00a0\n _\bp_\br_\be_\bC_\bh_\ba_\bn_\bg_\be_\b(_\bC_\bh_\ba_\bn_\bg_\be_\bE_\bv_\be_\bn_\bt_\b) - Method in interface org.biojava.utils._\bC_\bh_\ba_\bn_\bg_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br\n Called before a change takes place.\n _\bp_\br_\be_\bf_\bi_\bx_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Given an unprefixed element name, returns a new element name with a\n namespace prefix\n _\bp_\br_\be_\bs_\bs_\b(_\b) - Method in class\n org.biojava.bio.dp.twohead._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\bM_\ba_\bt_\br_\bi_\bx_\bP_\ba_\bi_\br_\bD_\bP_\bC_\bu_\br_\bs_\bo_\br\n \u00a0\n _\bp_\br_\be_\bs_\bs_\b(_\b) - Method in class org.biojava.bio.dp.twohead._\bL_\bi_\bg_\bh_\bt_\bP_\ba_\bi_\br_\bD_\bP_\bC_\bu_\br_\bs_\bo_\br\n Returns the minimal context of the DP matrix necessary to compute the\n@@ -26551,27 +26552,26 @@\n Reads an alignment in FASTA format.\n _\br_\be_\ba_\bd_\b(_\bB_\bu_\bf_\bf_\be_\br_\be_\bd_\bR_\be_\ba_\bd_\be_\br_\b) - Method in class\n org.biojava.bio.seq.io._\bM_\bS_\bF_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bF_\bo_\br_\bm_\ba_\bt\n Reads an MSF Alignment File\n _\br_\be_\ba_\bd_\b(_\bB_\bu_\bf_\bf_\be_\br_\be_\bd_\bR_\be_\ba_\bd_\be_\br_\b,_\b _\bT_\ba_\bg_\bV_\ba_\bl_\bu_\be_\bP_\ba_\br_\bs_\be_\br_\b,_\b _\bT_\ba_\bg_\bV_\ba_\bl_\bu_\be_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n org.biojava.bio.program.tagvalue._\bP_\ba_\br_\bs_\be_\br\n \u00a0\n- _\br_\be_\ba_\bd_\b(_\bF_\bi_\bl_\be_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ _\br_\be_\ba_\bd_\b(_\bF_\bi_\bl_\be_\b) - Method in class org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\br_\be_\ba_\bd_\b(_\bF_\bi_\bl_\be_\b) - Method in interface org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Read zero or more FASTQ formatted sequences from the specified file.\n _\br_\be_\ba_\bd_\b(_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\br_\be_\ba_\bd_\b(_\bI_\bn_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Read zero or more FASTQ formatted sequences from the specified input\n stream.\n- _\br_\be_\ba_\bd_\b(_\bU_\bR_\bL_\b) - Method in class org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ _\br_\be_\ba_\bd_\b(_\bU_\bR_\bL_\b) - Method in class org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\br_\be_\ba_\bd_\b(_\bU_\bR_\bL_\b) - Method in interface org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Read zero or more FASTQ formatted sequences from the specified url.\n _\br_\be_\ba_\bd_\ba_\bb_\bl_\be_\bF_\bi_\bl_\be_\bN_\ba_\bm_\be_\bs - Static variable in class\n org.biojavax.bio.seq.io._\bE_\bM_\bB_\bL_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\br_\be_\ba_\bd_\ba_\bb_\bl_\be_\bF_\bi_\bl_\be_\bs - Static variable in class org.biojavax.bio.seq.io._\bF_\ba_\bs_\bt_\ba_\bF_\bo_\br_\bm_\ba_\bt\n@@ -30130,15 +30130,15 @@\n _\bs_\be_\bt_\bC_\bo_\bn_\bs_\bt_\br_\ba_\bi_\bn_\bt_\bs_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b,_\b _\bP_\br_\bo_\bp_\be_\br_\bt_\by_\bC_\bo_\bn_\bs_\bt_\br_\ba_\bi_\bn_\bt_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b) - Method in class\n org.biojava.bio._\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn_\bT_\by_\bp_\be_\b._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt\n \u00a0\n _\bs_\be_\bt_\bC_\bo_\bn_\bs_\bt_\br_\ba_\bi_\bn_\bt_\bs_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b,_\b _\bP_\br_\bo_\bp_\be_\br_\bt_\by_\bC_\bo_\bn_\bs_\bt_\br_\ba_\bi_\bn_\bt_\b,_\b _\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn_\b) - Method in interface\n org.biojava.bio._\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn_\bT_\by_\bp_\be\n Set the constraints associated with a property.\n _\bs_\be_\bt_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Allow an application to register a content event handler.\n _\bs_\be_\bt_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br\n sets the ContentHandler for this object\n _\bs_\be_\bt_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bC_\bo_\bn_\bt_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n this sets the ContentHandler that receives SAX events from the internal\n@@ -30566,15 +30566,15 @@\n _\bs_\be_\bt_\bD_\bo_\bu_\bb_\bl_\be_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.symbol._\bS_\bi_\bm_\bp_\bl_\be_\bS_\by_\bm_\bb_\bo_\bl_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\bT_\ba_\bb_\bl_\be\n \u00a0\n _\bs_\be_\bt_\bD_\bo_\bu_\bb_\bl_\be_\bV_\ba_\bl_\bu_\be_\b(_\bd_\bo_\bu_\bb_\bl_\be_\b) - Method in class\n org.biojava.utils.stax._\bD_\bo_\bu_\bb_\bl_\be_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\bB_\ba_\bs_\be\n Override this method to do something useful with the double we collect.\n _\bs_\be_\bt_\bD_\bT_\bD_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bD_\bT_\bD_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bs_\be_\bt_\bD_\bT_\bD_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bD_\bT_\bD_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bs_\be_\bt_\bE_\bl_\be_\bm_\be_\bn_\bt_\bI_\bd_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bM_\ba_\bt_\bc_\bh_\bR_\be_\bg_\bi_\bo_\bn\n \u00a0\n@@ -30645,15 +30645,15 @@\n _\bs_\be_\bt_\bE_\bn_\bd_\bO_\bf_\bR_\be_\bc_\bo_\br_\bd_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.tagvalue._\bL_\bi_\bn_\be_\bS_\bp_\bl_\bi_\bt_\bP_\ba_\br_\bs_\be_\br\n Set the string indicating that a record has ended.\n _\bs_\be_\bt_\bE_\bn_\bd_\bO_\bf_\bR_\be_\bc_\bo_\br_\bd_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.tagvalue._\bR_\be_\bg_\be_\bx_\bP_\ba_\br_\bs_\be_\br\n Set the explicit end-of-record string.\n _\bs_\be_\bt_\bE_\bn_\bt_\bi_\bt_\by_\bR_\be_\bs_\bo_\bl_\bv_\be_\br_\b(_\bE_\bn_\bt_\bi_\bt_\by_\bR_\be_\bs_\bo_\bl_\bv_\be_\br_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bs_\be_\bt_\bE_\bn_\bt_\bi_\bt_\by_\bR_\be_\bs_\bo_\bl_\bv_\be_\br_\b(_\bE_\bn_\bt_\bi_\bt_\by_\bR_\be_\bs_\bo_\bl_\bv_\be_\br_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n This class has an EntityResolver that resolves the public ID specifying\n the NCBI DTDs to resource files within the BioJava libraries.\n _\bs_\be_\bt_\bE_\bn_\bv_\bi_\br_\bo_\bn_\bm_\be_\bn_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\bi_\be_\bs_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b[_\b]_\b) - Method in class\n org.biojava.utils.process._\bE_\bx_\bt_\be_\br_\bn_\ba_\bl_\bP_\br_\bo_\bc_\be_\bs_\bs\n@@ -30670,15 +30670,15 @@\n org.biojava.bio.program.gff3._\bG_\bF_\bF_\b3_\bP_\ba_\br_\bs_\be_\br\n Set the error handler used by this parser.\n _\bs_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.utils.process._\bE_\bx_\bt_\be_\br_\bn_\ba_\bl_\bP_\br_\bo_\bc_\be_\bs_\bs\n Sets the output error handler which is responsible for the standard error\n output of the external process.\n _\bs_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bs_\be_\bt_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bE_\br_\br_\bo_\br_\bH_\ba_\bn_\bd_\bl_\be_\br_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bs_\be_\bt_\bE_\bv_\be_\bn_\bt_\bs_\b(_\bL_\bi_\bs_\bt_\b) - Method in class\n org.biojavax.bio.seq.io._\bU_\bn_\bi_\bP_\br_\bo_\bt_\bC_\bo_\bm_\bm_\be_\bn_\bt_\bP_\ba_\br_\bs_\be_\br\n Setter for property events.\n@@ -30699,15 +30699,15 @@\n _\bs_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.gff._\bG_\bF_\bF_\bR_\be_\bc_\bo_\br_\bd_\bF_\bi_\bl_\bt_\be_\br_\b._\bF_\be_\ba_\bt_\bu_\br_\be_\bF_\bi_\bl_\bt_\be_\br\n Set the feature to feature.\n _\bs_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.program.gff._\bS_\bi_\bm_\bp_\bl_\be_\bG_\bF_\bF_\bR_\be_\bc_\bo_\br_\bd\n Set the feature type to type.\n _\bs_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bb_\bo_\bo_\bl_\be_\ba_\bn_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Handles support for ReasoningDomain and Namespace-prefixes\n _\bs_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bb_\bo_\bo_\bl_\be_\ba_\bn_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n by default, we set the parser to non-validating.\n _\bs_\be_\bt_\bF_\be_\ba_\bt_\bu_\br_\be_\b(_\bR_\bi_\bc_\bh_\bF_\be_\ba_\bt_\bu_\br_\be_\b) - Method in class\n org.biojavax.bio.seq._\bC_\bo_\bm_\bp_\bo_\bu_\bn_\bd_\bR_\bi_\bc_\bh_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n Sets the feature this location is associated with.\n@@ -31428,15 +31428,15 @@\n Call back method so the event emitter can tell the listener the namespace\n of the record being read.\n _\bs_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\b(_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\b) - Method in class\n org.biojavax.bio.seq.io._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bB_\bu_\bi_\bl_\bd_\be_\br\n Call back method so the event emitter can tell the listener the namespace\n of the record being read.\n _\bs_\be_\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bP_\br_\be_\bf_\bi_\bx_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bs_\be_\bt_\bN_\be_\bg_\bS_\bh_\ba_\bp_\be_\b(_\bS_\bh_\ba_\bp_\be_\b) - Method in class\n org.biojava.stats.svm.tools._\bC_\bl_\ba_\bs_\bs_\bi_\bf_\bi_\be_\br_\bE_\bx_\ba_\bm_\bp_\bl_\be_\b._\bP_\bo_\bi_\bn_\bt_\bC_\bl_\ba_\bs_\bs_\bi_\bf_\bi_\be_\br\n Set the Shape to represent the negative points.\n _\bs_\be_\bt_\bN_\be_\bs_\bt_\be_\bd_\bK_\be_\br_\bn_\be_\bl_\b(_\bS_\bV_\bM_\bK_\be_\br_\bn_\be_\bl_\b) - Method in class\n org.biojava.stats.svm._\bC_\ba_\bc_\bh_\bi_\bn_\bg_\bK_\be_\br_\bn_\be_\bl\n \u00a0\n@@ -31732,15 +31732,15 @@\n _\bs_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n org.biojavax._\bE_\bm_\bp_\bt_\by_\bR_\bi_\bc_\bh_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn\n Set the value of a property.\n _\bs_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bO_\bb_\bj_\be_\bc_\bt_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n org.biojavax._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bA_\bn_\bn_\bo_\bt_\ba_\bt_\bi_\bo_\bn\n Deprecated.\u00a0\n _\bs_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Do-nothing implementation of interface method\n _\bs_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bO_\bb_\bj_\be_\bc_\bt_\b) - Method in class\n org.biojava.bio.program.sax.blastxml._\bB_\bl_\ba_\bs_\bt_\bX_\bM_\bL_\bP_\ba_\br_\bs_\be_\br_\bF_\ba_\bc_\ba_\bd_\be\n \u00a0\n _\bs_\be_\bt_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bS_\bt_\bA_\bX_\bP_\br_\bo_\bp_\be_\br_\bt_\by_\bH_\ba_\bn_\bd_\bl_\be_\br\n \u00a0\n@@ -34317,15 +34317,15 @@\n _\bs_\bt_\ba_\br_\bt_\bE_\bl_\be_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bA_\bt_\bt_\br_\bi_\bb_\bu_\bt_\be_\bs_\b,_\b _\bD_\be_\bl_\be_\bg_\ba_\bt_\bi_\bo_\bn_\bM_\ba_\bn_\ba_\bg_\be_\br_\b) - Method\n in class org.biojava.utils.stax._\bS_\bt_\br_\bi_\bn_\bg_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\bB_\ba_\bs_\be\n \u00a0\n _\bs_\bt_\ba_\br_\bt_\bE_\bl_\be_\bm_\be_\bn_\bt_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bA_\bt_\bt_\br_\bi_\bb_\bu_\bt_\be_\bs_\b) - Method in class\n org.biojava.bio.program.xml._\bB_\ba_\bs_\be_\bX_\bM_\bL_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bs_\bt_\ba_\br_\bt_\bE_\bl_\be_\bm_\be_\bn_\bt_\b(_\bQ_\bN_\ba_\bm_\be_\b,_\b _\bA_\bt_\bt_\br_\bi_\bb_\bu_\bt_\be_\bs_\b) - Method in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n Utility method to centralize sending of a SAX startElement message to\n document handler\n _\bs_\bt_\ba_\br_\bt_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bA_\bt_\bt_\br_\bi_\bb_\bu_\bt_\be_\bs_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bB_\bi_\bo_\bS_\be_\bq_\bH_\ba_\bn_\bd_\bl_\be_\br\n \u00a0\n _\bs_\bt_\ba_\br_\bt_\bE_\bl_\be_\bm_\be_\bn_\bt_\bH_\ba_\bn_\bd_\bl_\be_\br_\b(_\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bS_\bt_\br_\bi_\bn_\bg_\b,_\b _\bA_\bt_\bt_\br_\bi_\bb_\bu_\bt_\be_\bs_\b) - Method in class\n org.biojava.bio.seq.io.agave._\bA_\bG_\bA_\bV_\bE_\bB_\bi_\bo_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bH_\ba_\bn_\bd_\bl_\be_\br\n@@ -35003,15 +35003,15 @@\n org.biojava.bio.seq._\bF_\be_\ba_\bt_\bu_\br_\be_\bF_\bi_\bl_\bt_\be_\br_\b._\bS_\bt_\br_\ba_\bn_\bd_\bF_\bi_\bl_\bt_\be_\br\n Build a new filter that matches all features of a given strand.\n _\bS_\bt_\br_\ba_\bn_\bd_\bP_\ba_\br_\bs_\be_\br - Class in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bb_\bi_\bo_\b._\bs_\be_\bq\n Process strings and return strand objects.\n _\bS_\bt_\br_\ba_\bn_\bd_\bP_\ba_\br_\bs_\be_\br_\b(_\b) - Constructor for class org.biojava.bio.seq._\bS_\bt_\br_\ba_\bn_\bd_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bs_\bt_\br_\be_\ba_\bm_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bS_\bt_\br_\be_\ba_\bm_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\ba_\bn_\bg_\be_\br_\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n \u00a0\n _\bs_\bt_\br_\be_\ba_\bm_\b(_\bR_\be_\ba_\bd_\ba_\bb_\bl_\be_\b,_\b _\bS_\bt_\br_\be_\ba_\bm_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bR_\be_\ba_\bd_\be_\br\n Stream the specified readable.\n _\bS_\bt_\br_\be_\ba_\bm_\bL_\bi_\bs_\bt_\be_\bn_\be_\br - Interface in _\bo_\br_\bg_\b._\bb_\bi_\bo_\bj_\ba_\bv_\ba_\b._\bb_\bi_\bo_\b._\bp_\br_\bo_\bg_\br_\ba_\bm_\b._\bf_\ba_\bs_\bt_\bq\n Event based parser callback.\n _\bs_\bt_\br_\be_\ba_\bm_\bN_\be_\bx_\bt_\b(_\bS_\be_\bq_\bI_\bO_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Method in class\n@@ -36025,18 +36025,18 @@\n _\bT_\bI_\bT_\bL_\bE_\b__\bT_\bA_\bG - Static variable in class org.biojavax.bio.seq.io._\bI_\bN_\bS_\bD_\bs_\be_\bq_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\bT_\bI_\bT_\bL_\bE_\b__\bT_\bA_\bG - Static variable in class org.biojavax.bio.seq.io._\bU_\bn_\bi_\bP_\br_\bo_\bt_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\bT_\bI_\bT_\bL_\bE_\b__\bT_\bA_\bG - Static variable in class org.biojavax.bio.seq.io._\bU_\bn_\bi_\bP_\br_\bo_\bt_\bX_\bM_\bL_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bP_\br_\be_\bf_\bi_\bx_\be_\bs - Variable in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bt_\bN_\ba_\bm_\be_\bs_\bp_\ba_\bc_\be_\bs - Variable in class\n- org.biojava.bio.program.sax._\bB_\bl_\ba_\bs_\bt_\bL_\bi_\bk_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n+ org.biojava.bio.program.sax._\bF_\ba_\bs_\bt_\ba_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\bS_\bA_\bX_\bP_\ba_\br_\bs_\be_\br\n \u00a0\n _\bt_\bo - Variable in class org.biojava.bio.dp._\bT_\br_\ba_\bi_\bn_\be_\br_\bT_\br_\ba_\bn_\bs_\bi_\bt_\bi_\bo_\bn\n \u00a0\n _\bt_\bo - Variable in class org.biojava.bio.dp._\bT_\br_\ba_\bn_\bs_\bi_\bt_\bi_\bo_\bn\n \u00a0\n _\bT_\bO_\b__\bA_\b__\bL_\bE_\bA_\bF - Static variable in class org.biojava.bio.symbol._\bU_\bk_\bk_\bo_\bn_\be_\bn_\bS_\bu_\bf_\bf_\bi_\bx_\bT_\br_\be_\be\n \u00a0\n@@ -36755,15 +36755,15 @@\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in interface org.biojavax.bio.seq._\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn\n Takes this position and returns a copy translated by 'distance' bases.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in class org.biojavax.bio.seq._\bS_\bi_\bm_\bp_\bl_\be_\bP_\bo_\bs_\bi_\bt_\bi_\bo_\bn\n Takes this position and returns a copy translated by 'distance' bases.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bi_\bn_\bt_\b) - Method in class org.biojavax.bio.seq._\bS_\bi_\bm_\bp_\bl_\be_\bR_\bi_\bc_\bh_\bL_\bo_\bc_\ba_\bt_\bi_\bo_\bn\n Create a location that is a translation of this location.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in class\n- org.biojava.bio.symbol._\bS_\bi_\bm_\bp_\bl_\be_\bG_\be_\bn_\be_\bt_\bi_\bc_\bC_\bo_\bd_\be_\bT_\ba_\bb_\bl_\be\n+ org.biojava.bio.symbol._\bA_\bb_\bs_\bt_\br_\ba_\bc_\bt_\bM_\ba_\bn_\by_\bT_\bo_\bO_\bn_\be_\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n \u00a0\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\b) - Method in interface\n org.biojava.bio.symbol._\bT_\br_\ba_\bn_\bs_\bl_\ba_\bt_\bi_\bo_\bn_\bT_\ba_\bb_\bl_\be\n Translate a single symbol from source alphabet to the target alphabet.\n _\bt_\br_\ba_\bn_\bs_\bl_\ba_\bt_\be_\b(_\bS_\by_\bm_\bb_\bo_\bl_\bL_\bi_\bs_\bt_\b) - Static method in class\n org.biojava.bio.seq._\bG_\be_\bn_\be_\bt_\bi_\bc_\bC_\bo_\bd_\be_\bs\n Translate RNA into protein (with termination symbols).\n@@ -37680,40 +37680,40 @@\n width.\n _\bW_\bO_\bR_\bM_\b__\bN_\bU_\bC_\bL_\bE_\bA_\bR - Static variable in class org.biojava.bio.symbol._\bC_\bo_\bd_\bo_\bn_\bP_\br_\be_\bf_\bT_\bo_\bo_\bl_\bs\n Caenorhabditis elegans codon preferences\n _\bW_\br_\ba_\bp_\bp_\be_\br_\b(_\bS_\be_\ba_\br_\bc_\bh_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b) - Constructor for class\n org.biojava.bio.program.ssaha._\bS_\be_\ba_\br_\bc_\bh_\bL_\bi_\bs_\bt_\be_\bn_\be_\br_\b._\bW_\br_\ba_\bp_\bp_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified file.\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bF_\bi_\bl_\be_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified file.\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bI_\bt_\be_\br_\ba_\bb_\bl_\be_\b<_\bF_\ba_\bs_\bt_\bq_\b>_\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified output\n stream.\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.seq.io._\bF_\ba_\bs_\bt_\ba_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bF_\bo_\br_\bm_\ba_\bt\n Writes out the alignment to an FASTA file.\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b,_\b _\bi_\bn_\bt_\b) - Method in class\n org.biojava.bio.seq.io._\bM_\bS_\bF_\bA_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\bF_\bo_\br_\bm_\ba_\bt\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in class\n- org.biojava.bio.program.fastq._\bI_\bl_\bl_\bu_\bm_\bi_\bn_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n+ org.biojava.bio.program.fastq._\bS_\bo_\bl_\be_\bx_\ba_\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n \u00a0\n _\bw_\br_\bi_\bt_\be_\b(_\bO_\bu_\bt_\bp_\bu_\bt_\bS_\bt_\br_\be_\ba_\bm_\b,_\b _\bF_\ba_\bs_\bt_\bq_\b._\b._\b._\b) - Method in interface\n org.biojava.bio.program.fastq._\bF_\ba_\bs_\bt_\bq_\bW_\br_\bi_\bt_\be_\br\n Write the specified FASTQ formatted sequences to the specified output\n stream.\n _\bw_\br_\bi_\bt_\be_\b(_\bS_\be_\bq_\bu_\be_\bn_\bc_\be_\b) - Method in class org.biojava.bio.seq.io.agave._\bA_\bg_\ba_\bv_\be_\bW_\br_\bi_\bt_\be_\br\n Writing Sequence.\n"}]}, {"source1": "./usr/share/doc/libbiojava-java/apidocs/member-search-index.js", "source2": "./usr/share/doc/libbiojava-java/apidocs/member-search-index.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\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\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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@@ -14430,40 +14430,40 @@\n \"l\": \"forIndex(int)\"\n }, {\n \"p\": \"org.biojava.bibliography\",\n \"c\": \"BibRef\",\n \"l\": \"format\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n- \"c\": \"EmblFileFormer\",\n+ \"c\": \"ProteinRefSeqFileFormer\",\n \"l\": \"formatLocation(Feature)\",\n \"u\": \"formatLocation(org.biojava.bio.seq.Feature)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SeqFileFormer\",\n \"l\": \"formatLocation(Feature)\",\n \"u\": \"formatLocation(org.biojava.bio.seq.Feature)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SwissprotFileFormer\",\n \"l\": \"formatLocation(Feature)\",\n \"u\": \"formatLocation(org.biojava.bio.seq.Feature)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n- \"c\": \"EmblFileFormer\",\n+ \"c\": \"ProteinRefSeqFileFormer\",\n \"l\": \"formatLocation(Location, StrandedFeature.Strand)\",\n \"u\": \"formatLocation(org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SwissprotFileFormer\",\n \"l\": \"formatLocation(StringBuffer, Location)\",\n \"u\": \"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n- \"c\": \"EmblFileFormer\",\n+ \"c\": \"ProteinRefSeqFileFormer\",\n \"l\": \"formatLocation(StringBuffer, Location, StrandedFeature.Strand)\",\n \"u\": \"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)\"\n }, {\n \"p\": \"org.biojava.bio.seq.io\",\n \"c\": \"SeqFileFormer\",\n \"l\": \"formatLocation(StringBuffer, Location, StrandedFeature.Strand)\",\n \"u\": \"formatLocation(java.lang.StringBuffer,org.biojava.bio.symbol.Location,org.biojava.bio.seq.StrandedFeature.Strand)\"\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\n \"l\": \"getNamespacePrefix()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\n \"l\": \"getNamespacePrefixes()\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\n \"l\": \"oFullNamespacePrefix\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"IlluminaFastqReader\",\n+ \"c\": \"SangerFastqReader\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"IlluminaFastqReader\",\n+ \"c\": \"SangerFastqReader\",\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\": \"IlluminaFastqReader\",\n+ \"c\": \"SangerFastqReader\",\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\": \"IlluminaFastqReader\",\n+ \"c\": \"SangerFastqReader\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"IlluminaFastqReader\",\n+ \"c\": \"SangerFastqReader\",\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\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\n \"l\": \"tNamespacePrefixes\"\n }, {\n \"p\": \"org.biojava.bio.program.sax\",\n- \"c\": \"BlastLikeSAXParser\",\n+ \"c\": \"FastaSequenceSAXParser\",\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\": \"SimpleGeneticCodeTable\",\n+ \"c\": \"AbstractManyToOneTranslationTable\",\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\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\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\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\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\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\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\": \"IlluminaFastqWriter\",\n+ \"c\": \"SolexaFastqWriter\",\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"}]}]}, {"source1": "xz --list", "source2": "xz --list", "unified_diff": "@@ -1,17 +1,17 @@\n Streams: 1\n Blocks: 5\n- Compressed size: 3919.7 KiB (4013816 B)\n+ Compressed size: 3919.8 KiB (4013836 B)\n Uncompressed size: 104.1 MiB (109107200 B)\n Ratio: 0.037\n Check: CRC64\n Stream Padding: 0 B\n Streams:\n Stream Blocks CompOffset UncompOffset CompSize UncompSize Ratio Check Padding\n- 1 5 0 0 4013816 109107200 0.037 CRC64 0\n+ 1 5 0 0 4013836 109107200 0.037 CRC64 0\n Blocks:\n Stream Block CompOffset UncompOffset TotalSize UncompSize Ratio Check\n- 1 1 12 0 1047716 25165824 0.042 CRC64\n- 1 2 1047728 25165824 685436 25165824 0.027 CRC64\n- 1 3 1733164 50331648 976772 25165824 0.039 CRC64\n- 1 4 2709936 75497472 1005668 25165824 0.040 CRC64\n- 1 5 3715604 100663296 298156 8443904 0.035 CRC64\n+ 1 1 12 0 1047736 25165824 0.042 CRC64\n+ 1 2 1047748 25165824 685436 25165824 0.027 CRC64\n+ 1 3 1733184 50331648 976772 25165824 0.039 CRC64\n+ 1 4 2709956 75497472 1005668 25165824 0.040 CRC64\n+ 1 5 3715624 100663296 298156 8443904 0.035 CRC64\n"}]}]}]}