org.biojavax.bio.phylo.io.nexus
Interface CharactersBlockListener

All Superinterfaces:
NexusBlockListener
All Known Subinterfaces:
DataBlockListener
All Known Implementing Classes:
CharactersBlockBuilder, DataBlockBuilder

public interface CharactersBlockListener
extends NexusBlockListener

Listens to events that represent Nexus characters blocks.

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

Method Summary
 void addCharLabel(java.lang.String charLabel)
           
 void addCharState(java.lang.String charState)
           
 void addCharStateKeyword(java.lang.String charState, java.lang.String keyword)
           
 void addEquate(java.lang.String symbol, java.util.List symbols)
           
 void addItem(java.lang.String item)
           
 void addMatrixEntry(java.lang.String taxa)
           
 void addState(java.lang.String state)
           
 void addStateLabel(java.lang.String state, java.lang.String label)
           
 void addSymbol(java.lang.String symbol)
           
 void addTaxLabel(java.lang.String taxLabel)
          Add a TAXLABEL.
 void appendMatrixData(java.lang.String taxa, java.lang.Object data)
           
 void setCharStateLabel(java.lang.String charState, java.lang.String label)
           
 void setDataType(java.lang.String dataType)
           
 void setDimensionsNChar(int dimensionsNChar)
          Set the NCHAR value.
 void setDimensionsNTax(int dimensionsNTax)
          Set the NTAX value.
 void setEliminateEnd(int eliminateEnd)
           
 void setEliminateStart(int eliminateStart)
           
 void setGap(java.lang.String gap)
           
 void setInterleaved(boolean interleaved)
           
 void setLabels(boolean labels)
           
 void setMatchChar(java.lang.String matchChar)
           
 void setMissing(java.lang.String missing)
           
 void setRespectCase(boolean respectCase)
           
 void setStatesFormat(java.lang.String statesFormat)
           
 void setTokens(boolean tokens)
           
 void setTransposed(boolean transposed)
           
 
Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener
beginComment, commentText, endBlock, endComment, endTokenGroup, startBlock
 

Method Detail

setDimensionsNTax

void setDimensionsNTax(int dimensionsNTax)
Set the NTAX value.

Parameters:
dimensionsNTax - the NTAX value.

setDimensionsNChar

void setDimensionsNChar(int dimensionsNChar)
Set the NCHAR value.

Parameters:
dimensionsNChar - the NCHAR value.

setDataType

void setDataType(java.lang.String dataType)

setRespectCase

void setRespectCase(boolean respectCase)

setMissing

void setMissing(java.lang.String missing)

setGap

void setGap(java.lang.String gap)

addSymbol

void addSymbol(java.lang.String symbol)

addEquate

void addEquate(java.lang.String symbol,
               java.util.List symbols)

setMatchChar

void setMatchChar(java.lang.String matchChar)

setLabels

void setLabels(boolean labels)

setTransposed

void setTransposed(boolean transposed)

setInterleaved

void setInterleaved(boolean interleaved)

addItem

void addItem(java.lang.String item)

setStatesFormat

void setStatesFormat(java.lang.String statesFormat)

setTokens

void setTokens(boolean tokens)

setEliminateStart

void setEliminateStart(int eliminateStart)

setEliminateEnd

void setEliminateEnd(int eliminateEnd)

addTaxLabel

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.

addCharState

void addCharState(java.lang.String charState)

setCharStateLabel

void setCharStateLabel(java.lang.String charState,
                       java.lang.String label)

addCharStateKeyword

void addCharStateKeyword(java.lang.String charState,
                         java.lang.String keyword)

addCharLabel

void addCharLabel(java.lang.String charLabel)

addState

void addState(java.lang.String state)

addStateLabel

void addStateLabel(java.lang.String state,
                   java.lang.String label)

addMatrixEntry

void addMatrixEntry(java.lang.String taxa)

appendMatrixData

void appendMatrixData(java.lang.String taxa,
                      java.lang.Object data)