jebl.evolution.io
Class NexusImporter

java.lang.Object
  jebl.evolution.io.NexusImporter

All Implemented Interfaces:

Iterable<Tree>, AlignmentImporter, DistanceMatrixImporter, SequenceImporter, TreeImporter

public class NexusImporter
extends Object
implements AlignmentImporter, SequenceImporter, TreeImporter, DistanceMatrixImporter

Class for importing NEXUS file format

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

static class	NexusImporter.MissingBlockException
static class	NexusImporter.NexusBlock

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

DistanceMatrixImporter.Triangle

Field Summary

protected ImportHelper

helper

Constructor Summary

NexusImporter(Reader reader)
Constructor

NexusImporter(Reader reader, boolean compactTrees)

Method Summary

void	findEndBlock() Finds the end of the current block.
NexusImporter.NexusBlock	findNextBlock() This function returns an integer to specify what the next block in the file is.
String	getNextBlockName()
boolean	hasTree() return whether another tree is available.
List<Alignment>	importAlignments() importAlignment.
List<DistanceMatrix>	importDistanceMatrices() importDistances.
Tree	importNextTree() import the next tree.
List<Sequence>	importSequences() importSequences.
List<Tree>	importTrees() Import all the trees
Iterator<Tree>	iterator() Returns an iterator over a set of elements of type T.
List<Sequence>	parseCharactersBlock(List<Taxon> taxonList) Parses a 'CHARACTERS' block.
List<Sequence>	parseDataBlock(List<Taxon> taxonList) Parses a 'DATA' block.
DistanceMatrix	parseDistancesBlock(List<Taxon> taxonList)
List<Taxon>	parseTaxaBlock() Parses a 'TAXA' block.
List<Tree>	parseTreesBlock(List<Taxon> taxonList) Parses a 'TREES' block.
boolean	startReadingTrees()

Methods inherited from class java.lang.Object

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

Field Detail

helper

protected final ImportHelper helper

Constructor Detail

NexusImporter

public NexusImporter(Reader reader)

Constructor

NexusImporter

public NexusImporter(Reader reader,
                     boolean compactTrees)

Method Detail

findNextBlock

public NexusImporter.NexusBlock findNextBlock()
                                       throws IOException

This function returns an integer to specify what the next block in the file is. The internal variable nextBlock is also set to this value. This should be overridden to provide support for other blocks. Once the block is read in, nextBlock is automatically set to UNKNOWN_BLOCK by findEndBlock.

Throws:

IOException

getNextBlockName

public String getNextBlockName()

iterator

public Iterator<Tree> iterator()

Returns an iterator over a set of elements of type T.

Specified by:

iterator in interface Iterable<Tree>

Returns:

an Iterator.

parseTaxaBlock

public List<Taxon> parseTaxaBlock()
                           throws ImportException,
                                  IOException

Parses a 'TAXA' block.

Throws:

ImportException

IOException

parseCharactersBlock

public List<Sequence> parseCharactersBlock(List<Taxon> taxonList)
                                    throws ImportException,
                                           IOException

Parses a 'CHARACTERS' block.

Throws:

ImportException

IOException

parseDataBlock

public List<Sequence> parseDataBlock(List<Taxon> taxonList)
                              throws ImportException,
                                     IOException

Parses a 'DATA' block.

Throws:

ImportException

IOException

parseTreesBlock

public List<Tree> parseTreesBlock(List<Taxon> taxonList)
                           throws ImportException,
                                  IOException

Parses a 'TREES' block.

Throws:

ImportException

IOException

parseDistancesBlock

public DistanceMatrix parseDistancesBlock(List<Taxon> taxonList)
                                   throws ImportException,
                                          IOException

Throws:

ImportException

IOException

importAlignments

public List<Alignment> importAlignments()
                                 throws IOException,
                                        ImportException

importAlignment.

Specified by:

importAlignments in interface AlignmentImporter

Throws:

IOException

ImportException

importSequences

public List<Sequence> importSequences()
                               throws IOException,
                                      ImportException

importSequences.

Specified by:

importSequences in interface SequenceImporter

Throws:

IOException

ImportException

hasTree

public boolean hasTree()
                throws IOException,
                       ImportException

return whether another tree is available.

Specified by:

hasTree in interface TreeImporter

Throws:

IOException

ImportException

importNextTree

public Tree importNextTree()
                    throws IOException,
                           ImportException

import the next tree. return the tree or null if no more trees are available

Specified by:

importNextTree in interface TreeImporter

Returns:

the tree

Throws:

IOException

ImportException

importTrees

public List<Tree> importTrees()
                       throws IOException,
                              ImportException

Description copied from interface: TreeImporter

Import all the trees

Specified by:

importTrees in interface TreeImporter

Returns:

the list of trees

Throws:

IOException

ImportException - Any type of tree is fine.

startReadingTrees

public boolean startReadingTrees()
                          throws IOException,
                                 ImportException

Throws:

IOException

ImportException

importDistanceMatrices

public List<DistanceMatrix> importDistanceMatrices()
                                            throws IOException,
                                                   ImportException

importDistances.

Specified by:

importDistanceMatrices in interface DistanceMatrixImporter

Throws:

IOException

ImportException

findEndBlock

public void findEndBlock()
                  throws IOException

Finds the end of the current block.

Throws:

IOException