SequenceAlignmentSAXParser (biojava-legacy 1.9.5 API)

All Methods Instance Methods Concrete Methods  Modifier and Type Method Description void addPrefixMapping​(String poPrefix, String poURI)

Adds a namespace prefix to URI mapping as (key,value) pairs.

protected void changeState​(int piState)

Centralise chaining of iState field to help with debugging.

protected void characters​(char[] ch, int start, int length)

Utility method to centralize the sending of a SAX characters message a document handler.

protected void endElement​(org.biojava.bio.program.sax.QName poQName)

Utility method to centralize the sending of a SAX endElement message a document handler.

ContentHandler getContentHandler()

Return the content handler.

protected BufferedReader getContentStream​(InputSource poSource)

Create a stream from an an InputSource, picking the correct stream according to order of precedance.

DTDHandler getDTDHandler()

Do-nothing implementation of interface method

EntityResolver getEntityResolver()

Do-nothing implementation of interface method

ErrorHandler getErrorHandler()

Do-nothing implementation of interface method

boolean getFeature​(String poName)

Do-nothing implementation of interface method

String getNamespacePrefix()

Describe getNamespacePrefix method here.

boolean getNamespacePrefixes()

Support SAX2 configuration of namespace support of parser.

boolean getNamespaces()

Support SAX2 configuration of namespace support of parser.

Object getProperty​(String name)

Do-nothing implementation of interface method

String getURIFromPrefix​(String poPrefix)

Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.

void parse​(String poSystemId)

Full implementation of interface method.

void parse​(InputSource poSource)

Describe 'parse' method here.

String prefix​(String poElementName)

Given an unprefixed element name, returns a new element name with a namespace prefix

void setContentHandler​(ContentHandler poHandler)

Allow an application to register a content event handler.

void setDTDHandler​(DTDHandler handler)

Do-nothing implementation of interface method

void setEntityResolver​(EntityResolver resolver)

Do-nothing implementation of interface method

void setErrorHandler​(ErrorHandler handler)

Do-nothing implementation of interface method

void setFeature​(String poName, boolean value)

Handles support for ReasoningDomain and Namespace-prefixes

void setNamespacePrefix​(String poPrefix)   void setProperty​(String name, Object value)

Do-nothing implementation of interface method

protected void startElement​(org.biojava.bio.program.sax.QName poQName, Attributes atts)

Utility method to centralize sending of a SAX startElement message to document handler