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	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	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

All Methods Static Methods Instance Methods Concrete Methods
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.
`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

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

- 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"
  - 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)
```

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 Detail

NexusImporter

NexusImporter

NexusImporter

NexusImporter

Method Detail

findNextBlock

getNextBlockName

iterator

parseTaxaBlock

parseCharactersBlock

parseDataBlock

parseTreesBlock

parseDistancesBlock

importAlignments

importSequences

hasTree

importNextTree

importTrees

startReadingTrees

importDistanceMatrices

findEndBlock

makeIntoAllowableIdentifier