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

java.lang.Object
  extended by org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
      extended by org.biojavax.bio.phylo.io.nexus.DistancesBlockBuilder
All Implemented Interfaces:
DistancesBlockListener, NexusBlockBuilder, NexusBlockListener

public class DistancesBlockBuilder
extends NexusBlockBuilder.Abstract
implements DistancesBlockListener

Builds Nexus distances 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.NexusBlockBuilder
NexusBlockBuilder.Abstract
 
Constructor Summary
DistancesBlockBuilder()
           
 
Method Summary
protected  void addComment(NexusComment comment)
          Tell the builder to add the given comment at the current location.
 void addMatrixEntry(java.lang.String taxa)
           
 void addTaxLabel(java.lang.String taxLabel)
          Add a TAXLABEL.
 void appendMatrixData(java.lang.String taxa, java.lang.Object data)
           
 void endBlock()
          Notifies the parser that a block is ending.
 void endTokenGroup()
          Closing a line (semi-colon encountered).
 void setDiagonal(boolean diagonal)
           
 void setDimensionsNChar(int dimensionsNChar)
          Set the NCHAR value.
 void setDimensionsNTax(int dimensionsNTax)
          Set the NTAX value.
 void setInterleaved(boolean interleaved)
           
 void setLabels(boolean labels)
           
 void setMissing(java.lang.String missing)
           
 void setTriangle(java.lang.String triangle)
           
protected  NexusBlock startBlockObject()
          Tell the builder to start a new block object.
 
Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract
beginComment, commentText, endComment, getBlockName, getNexusBlock, startBlock
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
beginComment, commentText, endComment, startBlock
 

Constructor Detail

DistancesBlockBuilder

public DistancesBlockBuilder()
Method Detail

addComment

protected void addComment(NexusComment comment)
Description copied from class: NexusBlockBuilder.Abstract
Tell the builder to add the given comment at the current location.

Specified by:
addComment in class NexusBlockBuilder.Abstract
Parameters:
comment - the comment to add.

startBlockObject

protected NexusBlock startBlockObject()
Description copied from class: NexusBlockBuilder.Abstract
Tell the builder to start a new block object.

Specified by:
startBlockObject in class NexusBlockBuilder.Abstract

endBlock

public void endBlock()
Description copied from interface: NexusBlockListener
Notifies the parser that a block is ending.

Specified by:
endBlock in interface NexusBlockListener

endTokenGroup

public void endTokenGroup()
Description copied from interface: NexusBlockListener
Closing a line (semi-colon encountered). This indicates that anything received after it is on the next logical line of the block.

Specified by:
endTokenGroup in interface NexusBlockListener

addMatrixEntry

public void addMatrixEntry(java.lang.String taxa)
Specified by:
addMatrixEntry in interface DistancesBlockListener

addTaxLabel

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

Specified by:
addTaxLabel in interface DistancesBlockListener
Parameters:
taxLabel - the label to add.
Throws:
ParseException - if the label cannot be added.

appendMatrixData

public void appendMatrixData(java.lang.String taxa,
                             java.lang.Object data)
Specified by:
appendMatrixData in interface DistancesBlockListener

setDimensionsNChar

public void setDimensionsNChar(int dimensionsNChar)
Description copied from interface: DistancesBlockListener
Set the NCHAR value.

Specified by:
setDimensionsNChar in interface DistancesBlockListener
Parameters:
dimensionsNChar - the NCHAR value.

setDimensionsNTax

public void setDimensionsNTax(int dimensionsNTax)
Description copied from interface: DistancesBlockListener
Set the NTAX value.

Specified by:
setDimensionsNTax in interface DistancesBlockListener
Parameters:
dimensionsNTax - the NTAX value.

setInterleaved

public void setInterleaved(boolean interleaved)
Specified by:
setInterleaved in interface DistancesBlockListener

setLabels

public void setLabels(boolean labels)
Specified by:
setLabels in interface DistancesBlockListener

setMissing

public void setMissing(java.lang.String missing)
Specified by:
setMissing in interface DistancesBlockListener

setDiagonal

public void setDiagonal(boolean diagonal)
Specified by:
setDiagonal in interface DistancesBlockListener

setTriangle

public void setTriangle(java.lang.String triangle)
Specified by:
setTriangle in interface DistancesBlockListener