info.bioinfweb.treegraph.document.io.phyloxml
Class PhyloXMLReader

java.lang.Object
  info.bioinfweb.treegraph.document.io.AbstractDocumentReader
      info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader

All Implemented Interfaces:

DocumentReader, PhyloXMLConstants

public class PhyloXMLReader
extends AbstractDocumentReader
implements PhyloXMLConstants

Since:

2.0.35

Author:

Ben Stöver

Field Summary

private java.util.Vector<java.lang.String>	names
private java.util.Vector<Tree>	phylogenies
private javax.xml.stream.XMLEventReader	reader

Fields inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader

document

Fields inherited from interface info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLConstants

ATTR_BRANCH_LENGTH, ATTR_BRANCH_LENGTH_UNIT, ATTR_ROOTED, ATTR_TYPE, BRANCH_WIDT_DATA_NAME, DEFAULT_CONFIDENCE_NAME, DEFAULT_TREE_NAME, ID_PREFIX, NAMESPACE_URI, TAG_ACCESSION, TAG_AUTHORITY, TAG_BRANCH_LENGTH, TAG_CLADE, TAG_CODE, TAG_COLOR_BLUE, TAG_COLOR_GREEN, TAG_COLOR_RED, TAG_COMMON_NAME, TAG_CONFIDENCE, TAG_DATE, TAG_DESCRIPTION, TAG_DISTRIBUTION, TAG_LINE_COLOR, TAG_LINE_WIDTH, TAG_LOCATION, TAG_MAX, TAG_MIN, TAG_NAME, TAG_PHYLOGENY, TAG_RANK, TAG_ROOT, TAG_SCIENTIFIC_NAME, TAG_SEQUENCE, TAG_SYMBOL, TAG_SYNONYM, TAG_TAXONOMY, TAG_VALUE

Constructor Summary

PhyloXMLReader()

Method Summary

Document	read(java.io.InputStream stream, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
private java.awt.Color	readColor()
private void	readDate(Node node)
private void	readDistribution(Node node)
private void	readDocument(javax.xml.stream.events.StartElement rootElement)
private void	readPhylogeny(javax.xml.stream.events.StartElement rootElement)
private void	readSequence(javax.xml.stream.events.StartElement rootElement, Node node)
private Node	readSubtree(javax.xml.stream.events.StartElement rootElement, Node parent)
private void	readTaxonomy(Node node)
private void	storeHiddenData(HiddenDataMap map, java.lang.String keyPrefix, javax.xml.stream.events.StartElement element)

Methods inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader

read, read, read, read, read

Methods inherited from class java.lang.Object

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

Field Detail

reader

private javax.xml.stream.XMLEventReader reader

names

private java.util.Vector<java.lang.String> names

phylogenies

private java.util.Vector<Tree> phylogenies

Constructor Detail

PhyloXMLReader

public PhyloXMLReader()

Method Detail

readColor

private java.awt.Color readColor()
                          throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

storeHiddenData

private void storeHiddenData(HiddenDataMap map,
                             java.lang.String keyPrefix,
                             javax.xml.stream.events.StartElement element)
                      throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readTaxonomy

private void readTaxonomy(Node node)
                   throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readSequence

private void readSequence(javax.xml.stream.events.StartElement rootElement,
                          Node node)
                   throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readDistribution

private void readDistribution(Node node)
                       throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readDate

private void readDate(Node node)
               throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readSubtree

private Node readSubtree(javax.xml.stream.events.StartElement rootElement,
                         Node parent)
                  throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readPhylogeny

private void readPhylogeny(javax.xml.stream.events.StartElement rootElement)
                    throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

readDocument

private void readDocument(javax.xml.stream.events.StartElement rootElement)
                   throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

read

public Document read(java.io.InputStream stream,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws java.lang.Exception

Specified by:

read in interface DocumentReader

Throws:

java.lang.Exception