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

java.lang.Object
  extended by info.bioinfweb.treegraph.document.io.AbstractDocumentReader
      extended by info.bioinfweb.treegraph.document.io.phyloxml.PhyloXMLReader
All Implemented Interfaces:
DocumentReader, PhyloXMLConstants
public class PhyloXMLReader
extends AbstractDocumentReader
implements PhyloXMLConstants

Reads a phyloXML document.

Since:
2.0.35
Author:
Ben Stöver

Field Summary
private  Vector<String> names
           
private  Vector<Tree> phylogenies
           
private  XMLEventReader reader
           
 
Fields inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
document, loadLogger
 
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(InputStream stream, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
           
private  Color readColor()
           
private  int readColorValue()
           
private  void readDate(Node node)
           
private  void readDistribution(Node node)
           
private  void readDocument(StartElement rootElement)
           
private  void readPhylogeny(StartElement rootElement)
           
private  void readSequence(StartElement rootElement, Node node)
           
private  Node readSubtree(StartElement rootElement, Node parent)
           
private  void readTaxonomy(Node node)
           
private  void storeHiddenData(HiddenDataMap map, String keyPrefix, StartElement element)
           
 
Methods inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
reachElementEnd, reachElementEnd, 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 XMLEventReader reader

names

private Vector<String> names

phylogenies

private Vector<Tree> phylogenies
Constructor Detail

PhyloXMLReader

public PhyloXMLReader()
Method Detail

readColorValue

private int readColorValue()
                    throws XMLStreamException
Throws:
XMLStreamException

readColor

private Color readColor()
                 throws XMLStreamException
Throws:
XMLStreamException

storeHiddenData

private void storeHiddenData(HiddenDataMap map,
                             String keyPrefix,
                             StartElement element)
                      throws XMLStreamException
Throws:
XMLStreamException

readTaxonomy

private void readTaxonomy(Node node)
                   throws XMLStreamException
Throws:
XMLStreamException

readSequence

private void readSequence(StartElement rootElement,
                          Node node)
                   throws XMLStreamException
Throws:
XMLStreamException

readDistribution

private void readDistribution(Node node)
                       throws XMLStreamException
Throws:
XMLStreamException

readDate

private void readDate(Node node)
               throws XMLStreamException
Throws:
XMLStreamException

readSubtree

private Node readSubtree(StartElement rootElement,
                         Node parent)
                  throws XMLStreamException
Throws:
XMLStreamException

readPhylogeny

private void readPhylogeny(StartElement rootElement)
                    throws XMLStreamException
Throws:
XMLStreamException

readDocument

private void readDocument(StartElement rootElement)
                   throws XMLStreamException
Throws:
XMLStreamException

read

public Document read(InputStream stream,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws Exception
Specified by:
read in interface DocumentReader
Throws:
Exception
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