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

    java.lang.Object
      org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
          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 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(String taxLabel)` Add a TAXLABEL.
`boolean` `containsTaxLabel(String taxLabel)` Checks to see if we contain the given TAXLABEL.
`List` `getComments()` Returns all comments.
`int` `getDimensionsNTax()` Get the NTAX value.
`List` `getTaxLabels()` Get the TAXLABEL values added so far.
`void` `removeComment(NexusComment comment)` Removes a comment.
`void` `removeTaxLabel(String taxLabel)` Removes the given TAXLABEL.
`void` `setDimensionsNTax(int dimensionsNTax)` Set the NTAX value.
`protected void` `writeBlockContents(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 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(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(String taxLabel)

  Removes the given TAXLABEL.

  Parameters:
    `taxLabel` - the label to remove.

### containsTaxLabel

    public boolean containsTaxLabel(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 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 List getComments()

  Returns all comments.

  Returns:
    all the selected comments.

### writeBlockContents

    protected void writeBlockContents(Writer writer)
                               throws 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:
    `IOException` - if writing failed.