info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus

Class SetsBlock

java.lang.Object

org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlock

All Implemented Interfaces:

org.biojavax.bio.phylo.io.nexus.NexusBlock, org.biojavax.bio.phylo.io.nexus.NexusObject

public class SetsBlock
extends org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

Represents a part of the contents of a SETS block of a Nexus file. (Only CharSet commands are stored.)

Author:

Ben Stöver

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlock

org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	SETS_BLOCK

Constructor Summary

Constructors

Constructor and Description
SetsBlock()

Method Summary

Modifier and Type	Method and Description
void	addCharSet(java.lang.String name) Adds a new character set with the specified name, if not already present.
void	addCharSetInterval(java.lang.String name, int start, int end) Adds the specified interval to the specified character set.
CharSet	getCharSet(java.lang.String name)
java.util.Collection<CharSet>	values()
protected void	writeBlockContents(java.io.Writer writer) The implementation of this method is empty since it is not used in HIR-Finder.

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

SETS_BLOCK

public static final java.lang.String SETS_BLOCK

See Also:

Constant Field Values

Constructor Detail

SetsBlock

public SetsBlock()

Method Detail

addCharSet

public void addCharSet(java.lang.String name)

Adds a new character set with the specified name, if not already present.

Parameters:

name -

addCharSetInterval

public void addCharSetInterval(java.lang.String name,
                               int start,
                               int end)

Adds the specified interval to the specified character set.

Parameters:

name -

start -

end -

Throws:

java.lang.IllegalArgumentException - if there is no character set with the specified name present.

getCharSet

public CharSet getCharSet(java.lang.String name)

values

public java.util.Collection<CharSet> values()

writeBlockContents

protected void writeBlockContents(java.io.Writer writer)
                           throws java.io.IOException

The implementation of this method is empty since it is not used in HIR-Finder.

Specified by:

writeBlockContents in class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract

Throws:

java.io.IOException

See Also:

NexusBlock.Abstract.writeBlockContents(java.io.Writer)