rapgreen

Class TreeFilter

java.lang.Object

rapgreen.TreeFilter

public class TreeFilter
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	clean Support threshold
static java.util.Vector	idList List of taxids to remove
static java.util.Hashtable	idTable Table of taxids to remove
static boolean	ignoreCode
static java.lang.String	key
static boolean	newick
static boolean	newick2NHX
static java.io.File	outputFile Output cluster file
static boolean	replaceId
static java.io.File	speciesFile Input species tree file
static java.io.File	treeFile Input tree file

Constructor Summary

Constructors

Constructor and Description
TreeFilter()

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

treeFile

public static java.io.File treeFile

Input tree file

speciesFile

public static java.io.File speciesFile

Input species tree file

outputFile

public static java.io.File outputFile

Output cluster file

idList

public static java.util.Vector idList

List of taxids to remove

idTable

public static java.util.Hashtable idTable

Table of taxids to remove

clean

public static boolean clean

Support threshold

newick

public static boolean newick

newick2NHX

public static boolean newick2NHX

replaceId

public static boolean replaceId

ignoreCode

public static boolean ignoreCode

key

public static java.lang.String key

Constructor Detail

TreeFilter

public TreeFilter()

Method Detail

main

public static void main(java.lang.String[] args)