org.forester.io.parsers.phyloxml
Class PhyloXmlHandler

java.lang.Object
  org.xml.sax.helpers.DefaultHandler
      org.forester.io.parsers.phyloxml.PhyloXmlHandler

All Implemented Interfaces:

org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler

public final class PhyloXmlHandler
extends org.xml.sax.helpers.DefaultHandler

Method Summary

static boolean	attributeEqualsValue(XmlElement element, java.lang.String attributeName, java.lang.String attributeValue)
void	characters(char[] chars, int start_index, int end_index)
void	endElement(java.lang.String namespace_uri, java.lang.String local_name, java.lang.String qualified_name)
static java.lang.String	getAtttributeValue(XmlElement element, java.lang.String attributeName)
static java.util.Map<java.lang.String,Sequence>	getSequenceMapByIdForPhylogeny(Phylogeny ph)
void	startDocument()
void	startElement(java.lang.String namespace_uri, java.lang.String local_name, java.lang.String qualified_name, org.xml.sax.Attributes attributes)

Methods inherited from class org.xml.sax.helpers.DefaultHandler

endDocument, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

characters

public void characters(char[] chars,
                       int start_index,
                       int end_index)

Specified by:

characters in interface org.xml.sax.ContentHandler

Overrides:

characters in class org.xml.sax.helpers.DefaultHandler

endElement

public void endElement(java.lang.String namespace_uri,
                       java.lang.String local_name,
                       java.lang.String qualified_name)
                throws org.xml.sax.SAXException

Specified by:

endElement in interface org.xml.sax.ContentHandler

Overrides:

endElement in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException

startDocument

public void startDocument()
                   throws org.xml.sax.SAXException

Specified by:

startDocument in interface org.xml.sax.ContentHandler

Overrides:

startDocument in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException

startElement

public void startElement(java.lang.String namespace_uri,
                         java.lang.String local_name,
                         java.lang.String qualified_name,
                         org.xml.sax.Attributes attributes)
                  throws org.xml.sax.SAXException

Specified by:

startElement in interface org.xml.sax.ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException

attributeEqualsValue

public static boolean attributeEqualsValue(XmlElement element,
                                           java.lang.String attributeName,
                                           java.lang.String attributeValue)

getAtttributeValue

public static java.lang.String getAtttributeValue(XmlElement element,
                                                  java.lang.String attributeName)

getSequenceMapByIdForPhylogeny

public static java.util.Map<java.lang.String,Sequence> getSequenceMapByIdForPhylogeny(Phylogeny ph)