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info.bioinfweb.treegraph.document.io.newick
Class NewickReader

java.lang.Object
  info.bioinfweb.treegraph.document.io.AbstractDocumentReader
      info.bioinfweb.treegraph.document.io.TextStreamReader
          info.bioinfweb.treegraph.document.io.newick.NewickReader

All Implemented Interfaces:

DocumentReader

public class NewickReader
extends TextStreamReader
implements DocumentReader

Reads text files consisting only of Newick strings.

Author:

Ben Stöver

Nested Class Summary

private static class

NewickReader.Status

Field Summary

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

document, loadLogger

Constructor Summary

NewickReader()
Contructs an instance of NewickReader.

Method Summary

Document	read(File file, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternals) If you want to implement file specific functionalities you should override this method.
Document	read(InputStream stream, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternals)
private String[]	splitDocument(String content)
private String	terminateNewick(String newick)

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

Methods inherited from interface info.bioinfweb.treegraph.document.io.DocumentReader

read, read, read, read

Constructor Detail

NewickReader

public NewickReader()

Contructs an instance of NewickReader.

Method Detail

terminateNewick

private String terminateNewick(String newick)

splitDocument

private String[] splitDocument(String content)

read

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

Specified by:

read in interface DocumentReader

Throws:

Exception

read

public Document read(File file,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter,
                     TreeSelector selector,
                     boolean translateInternals)
              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)