phylosort
Class PhyloSort

java.lang.Object
  phylosort.PhyloSort

public class PhyloSort
extends java.lang.Object

Phylogenetic trees sorting tool

Version:

$Revision: 1.14 $

Author:

Ahmed Moustafa

Constructor Summary

PhyloSort()

Method Summary

static java.util.List<java.util.List<java.lang.String>>	loadGroups(java.lang.String filename) Loads groups of taxa from a text file
static int	sort(java.lang.String infolder, java.lang.String outfolder, java.util.List<java.util.List<java.lang.String>> query) Sorts trees from an input folder to an output folder based on a set of query taxa

Methods inherited from class java.lang.Object

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

Constructor Detail

PhyloSort

public PhyloSort()

Method Detail

loadGroups

public static java.util.List<java.util.List<java.lang.String>> loadGroups(java.lang.String filename)
                                                                   throws java.lang.Exception

Loads groups of taxa from a text file

Parameters:

filename - Text file name to load taxa groups from

Returns:

List of lists of groups

Throws:

java.lang.Exception

sort

public static int sort(java.lang.String infolder,
                       java.lang.String outfolder,
                       java.util.List<java.util.List<java.lang.String>> query)
                throws java.lang.Exception

Sorts trees from an input folder to an output folder based on a set of query taxa

Parameters:

infolder - Input folder

outfolder - Output folder

query - Groups of taxa

Returns:

Number of sorted (matching) trees

Throws:

java.lang.Exception