org.biojavax.bio.phylo.io.nexus
Class TaxaBlock

java.lang.Object
  extended by org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
      extended by org.biojavax.bio.phylo.io.nexus.TaxaBlock
All Implemented Interfaces:
NexusBlock, NexusObject

public class TaxaBlock
extends NexusBlock.Abstract

Represents Nexus taxa blocks.

Since:
1.6
Author:
Richard Holland, Tobias Thierer, Jim Balhoff

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlock
NexusBlock.Abstract
 
Field Summary
static java.lang.String TAXA_BLOCK
          A constant representing the name of Taxa blocks.
 
Constructor Summary
TaxaBlock()
          Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name.
 
Method Summary
 void addComment(NexusComment comment)
          Adds a comment.
 void addTaxLabel(java.lang.String taxLabel)
          Add a TAXLABEL.
 boolean containsTaxLabel(java.lang.String taxLabel)
          Checks to see if we contain the given TAXLABEL.
 java.util.List getComments()
          Returns all comments.
 int getDimensionsNTax()
          Get the NTAX value.
 java.util.List getTaxLabels()
          Get the TAXLABEL values added so far.
 void removeComment(NexusComment comment)
          Removes a comment.
 void removeTaxLabel(java.lang.String taxLabel)
          Removes the given TAXLABEL.
 void setDimensionsNTax(int dimensionsNTax)
          Set the NTAX value.
protected  void writeBlockContents(java.io.Writer writer)
          Implement this to write out block contents, not including the BEGIN and END tags.
 
Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
getBlockName, writeObject, writeToken
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

TAXA_BLOCK

public static final java.lang.String TAXA_BLOCK
A constant representing the name of Taxa blocks.

See Also:
Constant Field Values
Constructor Detail

TaxaBlock

public TaxaBlock()
Delegates to NexusBlock.Abstract constructor using TaxaBlock.TAXA_BLOCK as the name.

Method Detail

setDimensionsNTax

public void setDimensionsNTax(int dimensionsNTax)
Set the NTAX value.

Parameters:
dimensionsNTax - the NTAX value.

getDimensionsNTax

public int getDimensionsNTax()
Get the NTAX value.

Returns:
the NTAX value.

addTaxLabel

public void addTaxLabel(java.lang.String taxLabel)
                 throws ParseException
Add a TAXLABEL. If it already exists, or is a number that refers to an index position that already exists, an exception is thrown.

Parameters:
taxLabel - the label to add.
Throws:
ParseException - if the label cannot be added.

removeTaxLabel

public void removeTaxLabel(java.lang.String taxLabel)
Removes the given TAXLABEL.

Parameters:
taxLabel - the label to remove.

containsTaxLabel

public boolean containsTaxLabel(java.lang.String taxLabel)
Checks to see if we contain the given TAXLABEL.

Parameters:
taxLabel - the label to check for.
Returns:
true if we already contain it.

getTaxLabels

public java.util.List getTaxLabels()
Get the TAXLABEL values added so far.

Returns:
this labels so far.

addComment

public void addComment(NexusComment comment)
Adds a comment.

Parameters:
comment - the comment to add.

removeComment

public void removeComment(NexusComment comment)
Removes a comment.

Parameters:
comment - the comment to remove.

getComments

public java.util.List getComments()
Returns all comments.

Returns:
all the selected comments.

writeBlockContents

protected void writeBlockContents(java.io.Writer writer)
                           throws java.io.IOException
Description copied from class: NexusBlock.Abstract
Implement this to write out block contents, not including the BEGIN and END tags.

Specified by:
writeBlockContents in class NexusBlock.Abstract
Parameters:
writer - the writer to write to.
Throws:
java.io.IOException - if writing failed.