rapgreen

Class PhylogeneticMapping

java.lang.Object

rapgreen.PhylogeneticMapping

public class PhylogeneticMapping
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	clusterDirectory Input tree files
static java.lang.String	clusterFileName Input cluster file parsed names
static java.util.Hashtable	congruenceTable Congruence statistics
static java.util.Vector	congruenceVector
static java.io.File	generalFile General stats file
static java.util.Hashtable	mappingTable
static java.util.Vector	mappingVector
static int	nb Number of families
static java.io.File	output Output file
static java.lang.String	reference Reference taxon name
static double	support Support threshold
static java.io.File	trashFile Trash file
static java.lang.String	treeDirectory Input tree files
static java.lang.String	treeFileName Input cluster file parsed names
static java.util.Hashtable	unmappingTable
static java.util.Vector	unmappingVector
static boolean	verbose Allow, or not, verbose mod

Constructor Summary

Constructors

Constructor and Description
PhylogeneticMapping()

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args) USAGE: qsub -b y -q arcad.q /usr/local/jdk1.6.0_20/bin/java -mx4096m -cp /home/dufayard/RAP_green rapgreen/PhylogeneticMapping -clusterFiles /home/dufayard/uclust/clusters_0.6/ cluster#.fasta -treeFiles /home/dufayard/uclust/clusters_0.6_rap/ cluster#_genetree.tre -n 37128 -reference SATIVA -output 0.6_allstats.csv -general 0.6_globalstats.txt -trash 0.6_trash.csv

Methods inherited from class java.lang.Object

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

Field Detail

verbose

public static boolean verbose

Allow, or not, verbose mod

treeDirectory

public static java.lang.String treeDirectory

Input tree files

clusterDirectory

public static java.lang.String clusterDirectory

Input tree files

treeFileName

public static java.lang.String treeFileName

Input cluster file parsed names

clusterFileName

public static java.lang.String clusterFileName

Input cluster file parsed names

reference

public static java.lang.String reference

Reference taxon name

nb

public static int nb

Number of families

support

public static double support

Support threshold

output

public static java.io.File output

Output file

generalFile

public static java.io.File generalFile

General stats file

trashFile

public static java.io.File trashFile

Trash file

congruenceTable

public static java.util.Hashtable congruenceTable

Congruence statistics

mappingTable

public static java.util.Hashtable mappingTable

unmappingTable

public static java.util.Hashtable unmappingTable

congruenceVector

public static java.util.Vector congruenceVector

mappingVector

public static java.util.Vector mappingVector

unmappingVector

public static java.util.Vector unmappingVector

Constructor Detail

PhylogeneticMapping

public PhylogeneticMapping()

Method Detail

main

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

USAGE: qsub -b y -q arcad.q /usr/local/jdk1.6.0_20/bin/java -mx4096m -cp /home/dufayard/RAP_green rapgreen/PhylogeneticMapping -clusterFiles /home/dufayard/uclust/clusters_0.6/ cluster#.fasta -treeFiles /home/dufayard/uclust/clusters_0.6_rap/ cluster#_genetree.tre -n 37128 -reference SATIVA -output 0.6_allstats.csv -general 0.6_globalstats.txt -trash 0.6_trash.csv