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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 Object
implements DocumentReader

Implements basic functionality (especially method delegation) for document readers.

Author:

Ben Stöver

Field Summary

protected Document	document
protected LoadLogger	loadLogger

Constructor Summary

AbstractDocumentReader()

Method Summary

protected void	reachElementEnd(XMLEventReader reader, StartElement element) Delegates to reachElementEnd(XMLEventReader, String) where the name of the specified element is passed as elementDescription.
protected void	reachElementEnd(XMLEventReader reader, String elementDescription) Delegates to XMLUtils.reachElementEnd(XMLEventReader) and adds a warning to the LoadLogger.
Document	read(File file, LoadLogger loadLogger)
Document	read(File file, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter)
Document	read(File file, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes) If you want to implement file specific functionalities you should override this method.
Document	read(InputStream stream, LoadLogger loadLogger)
Document	read(InputStream stream, LoadLogger loadLogger, 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

loadLogger

protected LoadLogger loadLogger

document

protected Document document

Constructor Detail

AbstractDocumentReader

public AbstractDocumentReader()

Method Detail

reachElementEnd

protected void reachElementEnd(XMLEventReader reader,
                               StartElement element)
                        throws XMLStreamException

Delegates to reachElementEnd(XMLEventReader, String) where the name of the specified element is passed as elementDescription.

Parameters:

reader -

element -

Throws:

XMLStreamException

Since:

2.0.42

reachElementEnd

protected void reachElementEnd(XMLEventReader reader,
                               String elementDescription)
                        throws XMLStreamException

Delegates to XMLUtils.reachElementEnd(XMLEventReader) and adds a warning to the LoadLogger.

Parameters:

reader -

elementDescription - a description of the possibly skipped elements (e.g. "Elements under <ScaleBar>)

Throws:

XMLStreamException

Since:

2.0.42

read

public Document read(File file,
                     LoadLogger loadLogger)
              throws Exception

Specified by:

read in interface DocumentReader

Throws:

Exception

read

public Document read(File file,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter)
              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 translateInternalNodes)
              throws 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:

Exception

See Also:

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

read

public Document read(InputStream stream,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter)
              throws Exception

Specified by:

read in interface DocumentReader

Throws:

Exception

read

public Document read(InputStream stream,
                     LoadLogger loadLogger)
              throws Exception

Specified by:

read in interface DocumentReader

Throws:

Exception