PhyloSort

phylosort
Class PhyloSort

java.lang.Object
  extended by 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

PhyloSort

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