info.bioinfweb.libralign.model.io

Class AlignmentDataReader

java.lang.Object

info.bioinfweb.libralign.model.io.AlignmentDataReader

public class AlignmentDataReader
extends java.lang.Object

Reads the contents of AlignmentModels and DataModels from a stream of JPhyloIO events.

Since:

0.4.0

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.io

Constructor Summary

Constructors

Constructor and Description
AlignmentDataReader(java.io.File file) Creates a new instance of this class.
AlignmentDataReader(java.io.File file, AlignmentModelFactory<?> alignmentModelFactory) Creates a new instance of this class.
AlignmentDataReader(java.io.InputStream stream) Creates a new instance of this class.
AlignmentDataReader(java.io.InputStream stream, AlignmentModelFactory<?> alignmentModelFactory) Creates a new instance of this class.
AlignmentDataReader(info.bioinfweb.jphyloio.JPhyloIOEventReader eventReader, AlignmentModelFactory<?> alignmentModelFactory) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
boolean	addDataModelReader(DataModelEventReader<?> reader) Adds the specified data model reader to this instance, if it is not already present.
AlignmentModelEventReader	getAlignmentModelReader() Returns the alignment event reader used create to and read alignment model instances
protected info.bioinfweb.jphyloio.events.JPhyloIOEvent	processNextEvent()
void	readAll() Processes all events from the underlying JPhyloIO event stream.
boolean	removeDataModelReader(DataModelEventReader<?> reader) Removes the specified data model reader from this instance.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentDataReader

public AlignmentDataReader(info.bioinfweb.jphyloio.JPhyloIOEventReader eventReader,
                           AlignmentModelFactory<?> alignmentModelFactory)

Creates a new instance of this class.

A new instance must be created for each stream of JPhyloIO events that shall be processed.

Parameters:

eventReader - the reader providing JPhyloIO events

alignmentModelFactory - the factory to create alignment model instances during reading

Throws:

java.lang.NullPointerException - if eventReader or alignmentModelReader are null

AlignmentDataReader

public AlignmentDataReader(java.io.File file,
                           AlignmentModelFactory<?> alignmentModelFactory)
                    throws java.lang.Exception

Creates a new instance of this class.

The format of the specified files is guessed using JPhyloIOReaderWriterFactory.guessReader(File, ReadWriteParameterMap).

Parameters:

file - the file to be loaded

alignmentModelFactory - the factory to create alignment model instances during reading

Throws:

java.lang.NullPointerException - if file or alignmentModelReader are null

java.lang.Exception - if an exception is thrown by JPhyloIOReaderWriterFactory.guessReader(File, ReadWriteParameterMap) while guessing the format of file

AlignmentDataReader

public AlignmentDataReader(java.io.InputStream stream,
                           AlignmentModelFactory<?> alignmentModelFactory)
                    throws java.lang.Exception

Creates a new instance of this class.

The format of the specified files is guessed using JPhyloIOReaderWriterFactory.guessReader(InputStream, ReadWriteParameterMap).

Parameters:

stream - the input stream providing the data to be loaded

alignmentModelFactory - the factory to create alignment model instances during reading

Throws:

java.lang.NullPointerException - if stream or alignmentModelReader are null

java.lang.Exception - if an exception is thrown by JPhyloIOReaderWriterFactory.guessReader(InputStream, ReadWriteParameterMap) while guessing the format of stream

AlignmentDataReader

public AlignmentDataReader(java.io.File file)
                    throws java.lang.Exception

Creates a new instance of this class.

The format of the specified files is guessed using JPhyloIOReaderWriterFactory.guessReader(File, ReadWriteParameterMap) and an instance of BioPolymerCharAlignmentModelFactory will be used to create new model instances for the loaded data.

Parameters:

file - the file to be loaded

Throws:

java.lang.NullPointerException - if file is null

java.lang.Exception - if an exception is thrown by JPhyloIOReaderWriterFactory.guessReader(File, ReadWriteParameterMap) while guessing the format of file

AlignmentDataReader

public AlignmentDataReader(java.io.InputStream stream)
                    throws java.lang.Exception

Creates a new instance of this class.

The format of the specified files is guessed using JPhyloIOReaderWriterFactory.guessReader(InputStream, ReadWriteParameterMap) and an instance of BioPolymerCharAlignmentModelFactory will be used to create new model instances for the loaded data.

Parameters:

stream - the input stream providing the data to be loaded

Throws:

java.lang.NullPointerException - if stream is null

java.lang.Exception - if an exception is thrown by JPhyloIOReaderWriterFactory.guessReader(InputStream, ReadWriteParameterMap) while guessing the format of stream

Method Detail

getAlignmentModelReader

public AlignmentModelEventReader getAlignmentModelReader()

Returns the alignment event reader used create to and read alignment model instances

Returns:

the alignment model reader using the factory that was passed to the constructor

addDataModelReader

public boolean addDataModelReader(DataModelEventReader<?> reader)

Adds the specified data model reader to this instance, if it is not already present. All JPhyloIO events processed from now on will be forwarded to that reader.

It is recommended to add all readers before the first method that processed events (e.g. #readUnitlNextAlignmentModel()) is called. If new readers are added in between, its up to the application developer to make sure that these reader still work properly without knowledge of the events that were already consumed.

Parameters:

reader - the reader to be added

Returns:

true if the new reader was added, false if the specified reader was already present

Throws:

java.lang.IllegalArgumentException - if the specified reader does not reference this instance by DataModelEventReader.getMainReader()

removeDataModelReader

public boolean removeDataModelReader(DataModelEventReader<?> reader)

Removes the specified data model reader from this instance.

Parameters:

reader - the reader to be removed

Returns:

true if the specified reader was removed, false if that reader was not contained in this instance

processNextEvent

protected info.bioinfweb.jphyloio.events.JPhyloIOEvent processNextEvent()
                                                                 throws java.lang.Exception

Throws:

java.lang.Exception

readAll

public void readAll()
             throws java.lang.Exception

Processes all events from the underlying JPhyloIO event stream. The resulting models can be accessed by AlignmentModelEventReader.getCompletedModels() or by the according data model readers, if specified before calling this method.

Throws:

java.lang.Exception - if an exception was thrown by JPhyloIOEventReader.next().