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info.bioinfweb.treegraph.document.io.nexus
Class NexusReader

java.lang.Object
  info.bioinfweb.treegraph.document.io.AbstractDocumentReader
      info.bioinfweb.treegraph.document.io.TextStreamReader
          info.bioinfweb.treegraph.document.io.nexus.NexusReader

All Implemented Interfaces:

DocumentReader

public class NexusReader
extends TextStreamReader

This class reads a tree loads a tree out of a Nexus file. It uses a class that implements info.bioinfweb.treegraph.document.io.nexus.NexusTreeSelector to choose which tree to load, if there are several stored in the Nexus file.

Author:

Ben Stöver

Field Summary

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

document, loadLogger

Constructor Summary

NexusReader()
Constructs an instance of NexusReader.

Method Summary

Document	read(File file, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthAdapter, TreeSelector selector, boolean translateInternalNodes) If you want to implement file specific functionalities you should override this method.
Document	read(InputStream stream, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthAdapter, TreeSelector selector, boolean translateInternalNodes)

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

readStream

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

reachElementEnd, reachElementEnd, read, read, read, read

Methods inherited from class java.lang.Object

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

Constructor Detail

NexusReader

public NexusReader()

Constructs an instance of NexusReader.

Method Detail

read

public Document read(InputStream stream,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws Exception

Throws:

Exception

read

public Document read(File file,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws Exception

Description copied from class: AbstractDocumentReader

If you want to implement file specific functionalities you should override this method. It is called by all other read-methods with a file as parameter.

Specified by:

read in interface DocumentReader

Overrides:

read in class AbstractDocumentReader

Throws:

Exception

See Also:

info.bioinfweb.treegraph.document.io.DocumentReader#read(java.io.File, NodeBranchDataAdapter, int)