BioinfoFieldExtractor
Class GenericSeqConstructor

java.lang.Object
  BioinfoFieldExtractor.GenericSeqConstructor

public class GenericSeqConstructor
extends java.lang.Object

This class provides functionality to extract primitive type from a sample of data values. It takes a consensusSeq object as a parameter and returns a generic seq object. The following are type identified: 0 - constant data field ( The rest are data values ) 1 - long 2 - double 3 - alpha-numeric string 4 - string with any chars including special chars

Author:

Serge Gorbunov

Constructor Summary

GenericSeqConstructor()

Method Summary

GenericSequence	constructGenericSeq(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> alignments) This function constructs a generic message from a consensus message
boolean	verifyLengths(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> seqs) Verifies that all sequences are the same length

Methods inherited from class java.lang.Object

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

Constructor Detail

GenericSeqConstructor

public GenericSeqConstructor()

Method Detail

constructGenericSeq

public GenericSequence constructGenericSeq(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> alignments)

This function constructs a generic message from a consensus message

Parameters:

alignments - An array list of similar messages aligned using global alignment algorithms

Returns:

A generic message object corresponding to the consensus sequence

verifyLengths

public boolean verifyLengths(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> seqs)

Verifies that all sequences are the same length