jebl.evolution.io

Class NexusImporter

java.lang.Object

jebl.evolution.io.NexusImporter

All Implemented Interfaces:

java.lang.Iterable<Tree>, AlignmentImporter, DistanceMatrixImporter, SequenceImporter, TreeImporter

public class NexusImporter
extends java.lang.Object
implements AlignmentImporter, SequenceImporter, TreeImporter, DistanceMatrixImporter

Class for importing NEXUS file format. This is a good starting point for documentation about the nexus file format: https://www.nescent.org/wg_phyloinformatics/NEXUS_Specification For a quick check if something is probably valid or not, consider this attempt at a nexus grammar (the above page says "Don't treat this as gospel, its just an attempt to get the syntax rules"): http://www.cs.nmsu.edu/~epontell/nexus/nexus_grammar

Version:

$Id: NexusImporter.java 1052 2010-05-10 00:45:35Z richardmoir $

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NexusImporter.MissingBlockException Thrown when a block is missing that is required for importing a particular type of data from the nexus input.
static class	NexusImporter.NexusBlock Represents the block types used in the nexus format

Nested classes/interfaces inherited from interface jebl.evolution.io.DistanceMatrixImporter

DistanceMatrixImporter.Triangle

Constructor Summary

Constructors

Constructor and Description
NexusImporter(java.io.Reader reader)
NexusImporter(java.io.Reader reader, boolean compactTrees) Deprecated. Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)
NexusImporter(java.io.Reader reader, boolean compactTrees, long expectedInputLength)
NexusImporter(java.io.Reader reader, long expectedLength)

Method Summary

Methods

Modifier and Type	Method and Description
void	findEndBlock() Read ahead to the end of the current block.
NexusImporter.NexusBlock	findNextBlock() Read ahead to the next block in the input.
java.lang.String	getNextBlockName()
boolean	hasTree() If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.
java.util.List<Alignment>	importAlignments() Import all alignments in the input from the current position.
java.util.List<DistanceMatrix>	importDistanceMatrices() Import all distance matrices from all DISTANCES blocks in the input form the current position.
Tree	importNextTree() If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.
java.util.List<Sequence>	importSequences() Import all sequences in the input from the current position
java.util.List<Tree>	importTrees() Import all trees in the file from the current position.
java.util.Iterator<Tree>	iterator()
static java.lang.String	makeIntoAllowableIdentifier(java.lang.String identifier)
java.util.List<Sequence>	parseCharactersBlock(java.util.List<Taxon> taxonList) Parse the next 'CHARACTERS' block encountered in the input.
java.util.List<Sequence>	parseDataBlock(java.util.List<Taxon> taxonList) Parse the next 'DATA' block encountered in the input.
DistanceMatrix	parseDistancesBlock(java.util.List<Taxon> taxonList) Parse the next 'DISTANCES' block encountered in the input.
java.util.List<Taxon>	parseTaxaBlock() Parse the next 'TAXA' block encountered in the input.
java.util.List<Tree>	parseTreesBlock(java.util.List<Taxon> taxonList) Parse the next 'TREES' block encountered in the input.
boolean	startReadingTrees() Read nexus blocks until the next TREES block (or the end of the input) is encountered.

Methods inherited from class java.lang.Object

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

Constructor Detail

NexusImporter

public NexusImporter(java.io.Reader reader,
             long expectedLength)

Parameters:

reader -

expectedLength - Expected length of the input in bytes, or 0 if unknown. Used for optimization and tracking progress.

NexusImporter

public NexusImporter(java.io.Reader reader)

NexusImporter

public NexusImporter(java.io.Reader reader,
             boolean compactTrees,
             long expectedInputLength)

Parameters:

reader -

compactTrees - true to import trees as CompactRootedTree, false to use SimpleRootedTree.

expectedInputLength - Expected length of the input in bytes, or 0 if unknown. Used for optimization and tracking progress.

NexusImporter

@Deprecated
public NexusImporter(java.io.Reader reader,
                        boolean compactTrees)

Deprecated. Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)

Parameters:

reader -

compactTrees -

Method Detail

findNextBlock

public NexusImporter.NexusBlock findNextBlock()
                                       throws java.io.IOException

Read ahead to the next block in the input. This should be overridden to provide support for other blocks. Once the block is read in, nextBlock is automatically set to UNKNOWN by findEndBlock.

Returns:

the type of the next block

Throws:

java.io.IOException

getNextBlockName

public java.lang.String getNextBlockName()

Returns:

the name of the next block which will be read. eg "TREES"

See Also:

jebl.evolution.io.NexusImporter.NexusBlock}

iterator

public java.util.Iterator<Tree> iterator()

Specified by:

iterator in interface java.lang.Iterable<Tree>

Returns:

an Iterator over the trees in the nexus input.

parseTaxaBlock

public java.util.List<Taxon> parseTaxaBlock()
                                     throws ImportException,
                                            java.io.IOException

Parse the next 'TAXA' block encountered in the input.

Throws:

ImportException

java.io.IOException

parseCharactersBlock

public java.util.List<Sequence> parseCharactersBlock(java.util.List<Taxon> taxonList)
                                              throws ImportException,
                                                     java.io.IOException

Parse the next 'CHARACTERS' block encountered in the input.

Throws:

ImportException

java.io.IOException

parseDataBlock

public java.util.List<Sequence> parseDataBlock(java.util.List<Taxon> taxonList)
                                        throws ImportException,
                                               java.io.IOException

Parse the next 'DATA' block encountered in the input.

Throws:

ImportException

java.io.IOException

parseTreesBlock

public java.util.List<Tree> parseTreesBlock(java.util.List<Taxon> taxonList)
                                     throws ImportException,
                                            java.io.IOException

Parse the next 'TREES' block encountered in the input.

Throws:

ImportException

java.io.IOException

parseDistancesBlock

public DistanceMatrix parseDistancesBlock(java.util.List<Taxon> taxonList)
                                   throws ImportException,
                                          java.io.IOException

Parse the next 'DISTANCES' block encountered in the input.

Throws:

ImportException

java.io.IOException

importAlignments

public java.util.List<Alignment> importAlignments()
                                           throws java.io.IOException,
                                                  ImportException

Import all alignments in the input from the current position.

Specified by:

importAlignments in interface AlignmentImporter

Throws:

java.io.IOException

ImportException

importSequences

public java.util.List<Sequence> importSequences()
                                         throws java.io.IOException,
                                                ImportException

Import all sequences in the input from the current position

Specified by:

importSequences in interface SequenceImporter

Throws:

java.io.IOException

ImportException

hasTree

public boolean hasTree()
                throws java.io.IOException,
                       ImportException

If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.

Then determine if the current (or next) TREES block contains any more trees. If true then importNextTree will return a non-null value.

Specified by:

hasTree in interface TreeImporter

Returns:

true if another tree is available, false otherwise.

Throws:

java.io.IOException

ImportException

importNextTree

public Tree importNextTree()
                    throws java.io.IOException,
                           ImportException

If not currently reading a TREES block then read ahead to the next TREES block, parsing TRANSLATE and TAXA blocks in the process if necessary.

Then parse the next available tree.

Specified by:

importNextTree in interface TreeImporter

Returns:

the next available tree or null if no more trees are available

Throws:

java.io.IOException

ImportException

importTrees

public java.util.List<Tree> importTrees()
                                 throws java.io.IOException,
                                        ImportException

Import all trees in the file from the current position. Will read ahead to the next TREES block if necessary

Specified by:

importTrees in interface TreeImporter

Returns:

list of trees

Throws:

java.io.IOException

ImportException

startReadingTrees

public boolean startReadingTrees()
                          throws java.io.IOException,
                                 ImportException

Read nexus blocks until the next TREES block (or the end of the input) is encountered.

Returns:

true if a TREES block was found, false otherwise

Throws:

java.io.IOException

ImportException

importDistanceMatrices

public java.util.List<DistanceMatrix> importDistanceMatrices()
                                                      throws java.io.IOException,
                                                             ImportException

Import all distance matrices from all DISTANCES blocks in the input form the current position.

Specified by:

importDistanceMatrices in interface DistanceMatrixImporter

Throws:

java.io.IOException

ImportException

findEndBlock

public void findEndBlock()
                  throws java.io.IOException

Read ahead to the end of the current block.

Throws:

java.io.IOException

makeIntoAllowableIdentifier

public static java.lang.String makeIntoAllowableIdentifier(java.lang.String identifier)