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. 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

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 enum

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

Description

NexusImporter(Reader reader)

NexusImporter(Reader reader, boolean compactTrees)

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

NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)

NexusImporter(Reader reader, long expectedLength)
Method Summary

Modifier and Type

Method

Description

void

findEndBlock()

Read ahead to the end of the current block.

NexusImporter.NexusBlock

findNextBlock()

Read ahead to the next block in the input.

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.

List<Alignment>

importAlignments()

Import all alignments in the input from the current position.

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.

List<Sequence>

importSequences()

Import all sequences in the input from the current position

List<Tree>

importTrees()

Import all trees in the file from the current position.

Iterator<Tree>

iterator()

static String

makeIntoAllowableIdentifier(String identifier)

List<Sequence>

parseCharactersBlock(List<Taxon> taxonList)

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

List<Sequence>

parseDataBlock(List<Taxon> taxonList)

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

DistanceMatrix

parseDistancesBlock(List<Taxon> taxonList)

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

List<Taxon>

parseTaxaBlock()

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

List<Tree>

parseTreesBlock(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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- NexusImporter
  
  public NexusImporter(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(Reader reader)
- NexusImporter
  
  public NexusImporter(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(Reader reader, boolean compactTrees)
  
  Deprecated.
  Use NexusImporter(Reader reader, boolean compactTrees, long expectedInputLength)
  
  Parameters:
  
  reader -
  
  compactTrees -
Method Details
- findNextBlock
  
  public NexusImporter.NexusBlock findNextBlock() throws 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:
  
  IOException
- getNextBlockName
  
  public String getNextBlockName()
  
  Returns:
  
  the name of the next block which will be read. eg "TREES"
- iterator
  
  public Iterator<Tree> iterator()
  
  Specified by:
  
  iterator in interface Iterable<Tree>
  
  Returns:
  
  an Iterator over the trees in the nexus input.
- parseTaxaBlock
  
  public List<Taxon> parseTaxaBlock() throws ImportException, IOException
  
  Parse the next 'TAXA' block encountered in the input.
  
  Throws:
  
  ImportException
  
  IOException
- parseCharactersBlock
  
  public List<Sequence> parseCharactersBlock(List<Taxon> taxonList) throws ImportException, IOException
  
  Parse the next 'CHARACTERS' block encountered in the input.
  
  Throws:
  
  ImportException
  
  IOException
- parseDataBlock
  
  public List<Sequence> parseDataBlock(List<Taxon> taxonList) throws ImportException, IOException
  
  Parse the next 'DATA' block encountered in the input.
  
  Throws:
  
  ImportException
  
  IOException
- parseTreesBlock
  
  public List<Tree> parseTreesBlock(List<Taxon> taxonList) throws ImportException, IOException
  
  Parse the next 'TREES' block encountered in the input.
  
  Throws:
  
  ImportException
  
  IOException
- parseDistancesBlock
  
  public DistanceMatrix parseDistancesBlock(List<Taxon> taxonList) throws ImportException, IOException
  
  Parse the next 'DISTANCES' block encountered in the input.
  
  Throws:
  
  ImportException
  
  IOException
- importAlignments
  
  public List<Alignment> importAlignments() throws IOException, ImportException
  
  Import all alignments in the input from the current position.
  
  Specified by:
  
  importAlignments in interface AlignmentImporter
  
  Throws:
  
  IOException
  
  ImportException
- importSequences
  
  public List<Sequence> importSequences() throws IOException, ImportException
  
  Import all sequences in the input from the current position
  
  Specified by:
  
  importSequences in interface SequenceImporter
  
  Throws:
  
  IOException
  
  ImportException
- hasTree
  
  public boolean hasTree() throws 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:
  
  IOException
  
  ImportException
- importNextTree
  
  public Tree importNextTree() throws 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:
  
  IOException
  
  ImportException
- importTrees
  
  public List<Tree> importTrees() throws 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:
  
  IOException
  
  ImportException
- startReadingTrees
  
  public boolean startReadingTrees() throws 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:
  
  IOException
  
  ImportException
- importDistanceMatrices
  
  public List<DistanceMatrix> importDistanceMatrices() throws IOException, ImportException
  
  Import all distance matrices from all DISTANCES blocks in the input form the current position.
  
  Specified by:
  
  importDistanceMatrices in interface DistanceMatrixImporter
  
  Throws:
  
  IOException
  
  ImportException
- findEndBlock
  
  public void findEndBlock() throws IOException
  
  Read ahead to the end of the current block.
  
  Throws:
  
  IOException
- makeIntoAllowableIdentifier
  
  public static String makeIntoAllowableIdentifier(String identifier)

Class NexusImporter

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Details

NexusImporter

NexusImporter

NexusImporter

NexusImporter

Method Details

findNextBlock

getNextBlockName

iterator

parseTaxaBlock

parseCharactersBlock

parseDataBlock

parseTreesBlock

parseDistancesBlock

importAlignments

importSequences

hasTree

importNextTree

importTrees

startReadingTrees

importDistanceMatrices

findEndBlock

makeIntoAllowableIdentifier