phenote.dataadapter.nexus
Class NEXUSAdapter

java.lang.Object
  phenote.dataadapter.AbstractFileAdapter
      phenote.dataadapter.nexus.NEXUSAdapter

All Implemented Interfaces:

DataAdapterI

public class NEXUSAdapter
extends AbstractFileAdapter

Writes Phenote characters to a NEXUS file. Phenote characters are grouped into NEXUS characters via shared "attribute" heritage within PATO. The exporter supports only up to 36 values for any particular attribute, due to various limitations of other widely used NEXUS implementations (e.g. Mesquite & MacClade). There is currently no support for reading of NEXUS files.

Constructor Summary

NEXUSAdapter()

Method Summary

void	commit(CharacterListI charList)
void	commit(CharacterListI charList, java.io.File f)
void	commit(CharacterListI charList, java.io.Writer writer)
java.util.List<java.lang.String>	getExtensions()
void	load()
CharacterListI	load(java.io.File f)
void	setAdapterValue(java.lang.String adapterValue) Set value to use for loading or writeback, for a file adapter this would be the file name - is there a better name for this method? For now just doing String - which may be sufficient - may need an AdapterValue/DataInput object if this gets more involved - but that may not be necasary - certianly string ok for now rename setFilename???

Methods inherited from class phenote.dataadapter.AbstractFileAdapter

getDescription, hasExtension, setDescription, setExtensions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NEXUSAdapter

public NEXUSAdapter()

Method Detail

commit

public void commit(CharacterListI charList)

commit

public void commit(CharacterListI charList,
                   java.io.File f)

commit

public void commit(CharacterListI charList,
                   java.io.Writer writer)

getExtensions

public java.util.List<java.lang.String> getExtensions()

Specified by:

getExtensions in interface DataAdapterI

Overrides:

getExtensions in class AbstractFileAdapter

load

public void load()

load

public CharacterListI load(java.io.File f)

setAdapterValue

public void setAdapterValue(java.lang.String adapterValue)

Description copied from class: AbstractFileAdapter

Set value to use for loading or writeback, for a file adapter this would be the file name - is there a better name for this method? For now just doing String - which may be sufficient - may need an AdapterValue/DataInput object if this gets more involved - but that may not be necasary - certianly string ok for now rename setFilename???

Specified by:

setAdapterValue in interface DataAdapterI

Overrides:

setAdapterValue in class AbstractFileAdapter