info.bioinfweb.libralign.model.io

Class IOTools

java.lang.Object

info.bioinfweb.libralign.model.io.IOTools

public class IOTools
extends java.lang.Object

Collection of convenience methods for reading and writing contents of AlignmentModels to file formats supported by JPhyloIO.

Since:

0.6.0

Author:

Ben Stöver

See Also:

AlignmentDataReader, AlignmentModelDataAdapter

Module:

info.bioinfweb.libralign.io

Constructor Summary

Constructors

Constructor and Description
IOTools()

Method Summary

Modifier and Type	Method and Description
static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter	createDocumentAdapter(AlignmentModel<T> model) Creates a document data adapter that allows to write the contents of model to a file using e.g.
static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter	createDocumentAdapter(AlignmentModel<T> model, java.lang.String alignmentLabel) Creates a document data adapter that allows to write the contents of model to a file using e.g.
static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter	createDocumentAdapter(AlignmentModel<T> model, java.lang.String alignmentLabel, boolean linkOTUs) Creates a document data adapter that allows to write the contents of model to a file using e.g.
static java.util.List<AlignmentModel<?>>	readAlignments(java.io.File file) Reads a set of alignments from a file into a list of alignment model instances.
static java.util.List<AlignmentModel<?>>	readAlignments(java.io.File file, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Reads a set of alignments from a file into a list of alignment model instances.
static <T> void	writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.File file, java.lang.String format) Writes the contents of an alignment model to a file in the specified format.
static <T> void	writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.File file, java.lang.String format, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Writes the contents of an alignment model to a file in the specified format.
static <T> void	writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.OutputStream stream, java.lang.String format) Writes the contents of an alignment model to a file in the specified format.
static <T> void	writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.OutputStream stream, java.lang.String format, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Writes the contents of an alignment model to a file in the specified format.
static <T> void	writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.Writer writer, java.lang.String format) Writes the contents of an alignment model to a file in the specified format.
static <T> void	writeSingleAlignment(AlignmentModel<T> model, java.lang.String alignmentLabel, java.io.Writer writer, java.lang.String format, info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Writes the contents of an alignment model to a file in the specified format.

Methods inherited from class java.lang.Object

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

Constructor Detail

IOTools

public IOTools()

Method Detail

readAlignments

public static java.util.List<AlignmentModel<?>> readAlignments(java.io.File file,
                                                               info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
                                                        throws java.lang.Exception

Reads a set of alignments from a file into a list of alignment model instances.

This is a convenience method that uses AlignmentDataReader and BioPolymerCharAlignmentModelFactory internally.

Parameters:

file - the file to read the alignment(s) from

parameters - the writer parameters for the JPhyloIO writer that is used internally

Returns:

a list if read alignments (May have the length 0, if no alignment was present in the specified file.)

Throws:

java.lang.Exception - if an exception occurs while reading the file (See AlignmentDataReader.readAll() and the documentation of its constructor for details on exceptions that could occur.)

readAlignments

public static java.util.List<AlignmentModel<?>> readAlignments(java.io.File file)
                                                        throws java.lang.Exception

Reads a set of alignments from a file into a list of alignment model instances.

This is a convenience method that uses AlignmentDataReader and BioPolymerCharAlignmentModelFactory internally. It uses an empty parameter list for the JPhyloIO writer. Use readAlignments(File, ReadWriteParameterMap) instead, if you want to specify parameters.

Parameters:

file - the file to read the alignment(s) from

Returns:

a list if read alignments (May have the length 0, if no alignment was present in the specified file.)

Throws:

java.lang.Exception - if an exception occurs while reading the file (See AlignmentDataReader.readAll() and the documentation of its constructor for details on exceptions that could occur.)

createDocumentAdapter

public static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter createDocumentAdapter(AlignmentModel<T> model,
                                                                                                                          java.lang.String alignmentLabel,
                                                                                                                          boolean linkOTUs)

Creates a document data adapter that allows to write the contents of model to a file using e.g. JPhyloIOEventWriter.writeDocument(info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter, File, ReadWriteParameterMap).

The result is a list based document data adapter that allows to add additional adapter instances for e.g. alignments, OTU lists or trees.

This is a convenience method. Application code may also create instances of ListBasedDocumentDataAdapter and AlignmentModelDataAdapter directly.

Parameters:

model - the alignment model providing the content to be written

alignmentLabel - the label of the alignment to be written (Maybe null.)

linkOTUs - Specify true here, if each sequence shall link an OTU or false otherwise. (If true is specified, a respective OTU list adapter must be added to the returned document adapter. See #getLinkedOTUID(int) for details on how OTU IDs are generated.)

Returns:

the document data adapter providing access to the contents of model

See Also:

AlignmentModelDataAdapter

createDocumentAdapter

public static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter createDocumentAdapter(AlignmentModel<T> model,
                                                                                                                          java.lang.String alignmentLabel)

Creates a document data adapter that allows to write the contents of model to a file using e.g. JPhyloIOEventWriter.writeDocument(info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter, File, ReadWriteParameterMap).

The result is a list based document data adapter that allows to add additional adapter instances for e.g. alignments, OTU lists or trees. The contained matrix adapter does not link any OTUs to sequences. Use createDocumentAdapter(AlignmentModel, String, boolean) instead if you model OTUs.

This is a convenience method. Application code may also create instances of ListBasedDocumentDataAdapter and AlignmentModelDataAdapter directly.

Parameters:

model - the alignment model providing the content to be written

alignmentLabel - the label of the alignment to be written (Maybe null.)

Returns:

the document data adapter providing access to the contents of model

See Also:

AlignmentModelDataAdapter

createDocumentAdapter

public static <T> info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter createDocumentAdapter(AlignmentModel<T> model)

Creates a document data adapter that allows to write the contents of model to a file using e.g. JPhyloIOEventWriter.writeDocument(info.bioinfweb.jphyloio.dataadapters.DocumentDataAdapter, File, ReadWriteParameterMap).

The result is a list based document data adapter that allows to add additional adapter instances for e.g. alignments, OTU lists or trees. The contained matrix adapter does not specify a name for the alignment or link any OTUs to sequences. Use createDocumentAdapter(AlignmentModel, String, boolean) instead if you want to specify.

This is a convenience method. Application code may also create instances of ListBasedDocumentDataAdapter and AlignmentModelDataAdapter directly.

Parameters:

model - the alignment model providing the content to be written

Returns:

the document data adapter providing access to the contents of model

See Also:

AlignmentModelDataAdapter

writeSingleAlignment

public static <T> void writeSingleAlignment(AlignmentModel<T> model,
                                            java.lang.String alignmentLabel,
                                            java.io.Writer writer,
                                            java.lang.String format)
                                     throws java.io.IOException

Writes the contents of an alignment model to a file in the specified format.

Note that this method is a convenience method, which cannot be used if more than one alignment should be written to a single file or if additional data or metadata should be included.

Parameters:

model - the alignment model providing the content to be written

writer - the writer to write the output to (Note that application code is responsible for closing the writer. This method does not close it.)

format - the format of the output (Any format constant defined in JPhyloIOFormatIDs can be passed here.)

Throws:

java.io.IOException - if the underlying JPhyloIO writer thrown an exception during writing to the writer

writeSingleAlignment

public static <T> void writeSingleAlignment(AlignmentModel<T> model,
                                            java.lang.String alignmentLabel,
                                            java.io.Writer writer,
                                            java.lang.String format,
                                            info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
                                     throws java.io.IOException

Writes the contents of an alignment model to a file in the specified format.

Note that this method is a convenience method, which cannot be used if more than one alignment should be written to a single file or if additional data or metadata should be included.

Parameters:

model - the alignment model providing the content to be written

writer - the writer to write the output to (Note that application code is responsible for closing the writer. This method does not close it.)

format - the format of the output (Any format constant defined in JPhyloIOFormatIDs can be passed here.)

parameters - the reader parameters for the JPhyloIO reader that is used internally

Throws:

java.io.IOException - if the underlying JPhyloIO writer thrown an exception during writing to the writer

writeSingleAlignment

public static <T> void writeSingleAlignment(AlignmentModel<T> model,
                                            java.lang.String alignmentLabel,
                                            java.io.OutputStream stream,
                                            java.lang.String format)
                                     throws java.io.IOException

Writes the contents of an alignment model to a file in the specified format.

Note that this method is a convenience method, which cannot be used if more than one alignment should be written to a single file or if additional data or metadata should be included.

Parameters:

model - the alignment model providing the content to be written

stream - the output stream to write the output to (Note that application code is responsible for closing the stream. This method does not close it.)

format - the format of the output (Any format constant defined in JPhyloIOFormatIDs can be passed here.)

Throws:

java.io.IOException - if the underlying JPhyloIO writer thrown an exception during writing to the stream

writeSingleAlignment

public static <T> void writeSingleAlignment(AlignmentModel<T> model,
                                            java.lang.String alignmentLabel,
                                            java.io.OutputStream stream,
                                            java.lang.String format,
                                            info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
                                     throws java.io.IOException

Writes the contents of an alignment model to a file in the specified format.

Note that this method is a convenience method, which cannot be used if more than one alignment should be written to a single file or if additional data or metadata should be included.

Parameters:

model - the alignment model providing the content to be written

stream - the output stream to write the output to (Note that application code is responsible for closing the stream. This method does not close it.)

format - the format of the output (Any format constant defined in JPhyloIOFormatIDs can be passed here.)

parameters - the reader parameters for the JPhyloIO reader that is used internally

Throws:

java.io.IOException - if the underlying JPhyloIO writer thrown an exception during writing to the stream

writeSingleAlignment

public static <T> void writeSingleAlignment(AlignmentModel<T> model,
                                            java.lang.String alignmentLabel,
                                            java.io.File file,
                                            java.lang.String format)
                                     throws java.io.IOException

Writes the contents of an alignment model to a file in the specified format.

Note that this method is a convenience method, which cannot be used if more than one alignment should be written to a single file or if additional data or metadata should be included.

Parameters:

model - the alignment model providing the content to be written

alignmentLabel - the label of the alignment to be written (Maybe null.)

file - the file to write the output to

format - the format of the output (Any format constant defined in JPhyloIOFormatIDs can be passed here.)

Throws:

java.io.IOException - if the underlying JPhyloIO writer thrown an exception during writing to the file

writeSingleAlignment

public static <T> void writeSingleAlignment(AlignmentModel<T> model,
                                            java.lang.String alignmentLabel,
                                            java.io.File file,
                                            java.lang.String format,
                                            info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
                                     throws java.io.IOException

Writes the contents of an alignment model to a file in the specified format.

Note that this method is a convenience method, which cannot be used if more than one alignment should be written to a single file or if additional data or metadata should be included.

Parameters:

model - the alignment model providing the content to be written

file - the file to write the output to

format - the format of the output (Any format constant defined in JPhyloIOFormatIDs can be passed here.)

parameters - the reader parameters for the JPhyloIO reader that is used internally

Throws:

java.io.IOException - if the underlying JPhyloIO writer thrown an exception during writing to the file