info.bioinfweb.treegraph.document.io
Class AbstractDocumentReader

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

All Implemented Interfaces:

DocumentReader

Direct Known Subclasses:

PhyloXMLReader, TextStreamReader, TGFReader, XTGReader

public abstract class AbstractDocumentReader
extends java.lang.Object
implements DocumentReader

Field Summary

protected Document

document

Constructor Summary

AbstractDocumentReader()

Method Summary

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

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

Field Detail

document

protected Document document

Constructor Detail

AbstractDocumentReader

public AbstractDocumentReader()

Method Detail

read

public Document read(java.io.File file)
              throws java.lang.Exception

Specified by:

read in interface DocumentReader

Throws:

java.lang.Exception

read

public Document read(java.io.File file,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter)
              throws java.lang.Exception

Specified by:

read in interface DocumentReader

Throws:

java.lang.Exception

read

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

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

Throws:

java.lang.Exception

See Also:

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

read

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

Specified by:

read in interface DocumentReader

Throws:

java.lang.Exception

read

public Document read(java.io.InputStream stream)
              throws java.lang.Exception

Specified by:

read in interface DocumentReader

Throws:

java.lang.Exception