BioinfoFieldExtractor
Class MultiSequenceAligner

java.lang.Object
  BioinfoFieldExtractor.MultiSequenceAligner

public class MultiSequenceAligner
extends java.lang.Object

This class provides functionality allowing to align multiple messages using the global alignment techniques.

Author:

Serge Gorbunov

Constructor Summary

MultiSequenceAligner()

Method Summary

java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>	alignMultipleSequences(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> list, java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> gaps, PhylogenTree root)
PhylogenTree	assignTreeAlignments(PhylogenTree root) Assigns the aligned messages sequences to the tree
static java.lang.String	convertArrListToString(java.util.ArrayList<java.lang.Integer> arr)

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiSequenceAligner

public MultiSequenceAligner()

Method Detail

assignTreeAlignments

public PhylogenTree assignTreeAlignments(PhylogenTree root)

Assigns the aligned messages sequences to the tree

Parameters:

root - Root of the phylogenetic tree

alignMultipleSequences

public java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> alignMultipleSequences(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> list,
                                                                                          java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> gaps,
                                                                                          PhylogenTree root)

convertArrListToString

public static java.lang.String convertArrListToString(java.util.ArrayList<java.lang.Integer> arr)