uk.ac.sanger.cgp.standalonecsa.services
Class AlignmentServiceImpl

java.lang.Object
  uk.ac.sanger.cgp.standalonecsa.services.AlignmentServiceImpl

All Implemented Interfaces:

AlignmentService

public class AlignmentServiceImpl
extends java.lang.Object
implements AlignmentService

An implementation of basic alignment tools for aligning an amplimer (query) to a CDS (target)

Author:

Original: kr2, $Author: kr2 $

Field Summary

protected static org.apache.commons.logging.Log

log The logging instance (log4j).

Constructor Summary

AlignmentServiceImpl()
Creates a new instance of AlignmentServiceImpl

Method Summary

int[]

getAmplimerReadingFrameRegion(java.lang.String targetSeq, java.lang.String querySeq) Maps the amplimer (querySeq) to the CDS (targetSeq).

Methods inherited from class java.lang.Object

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

Field Detail

log

protected static final org.apache.commons.logging.Log log

The logging instance (log4j).

Constructor Detail

AlignmentServiceImpl

public AlignmentServiceImpl()

Creates a new instance of AlignmentServiceImpl

Method Detail

getAmplimerReadingFrameRegion

public int[] getAmplimerReadingFrameRegion(java.lang.String targetSeq,
                                           java.lang.String querySeq)

Maps the amplimer (querySeq) to the CDS (targetSeq). This method returns an int[] of size 3:
[0] - Coding start in query sequence
[1] - Coding stop in query sequence
[2] - Start of coding match on target sequence

All mappings are indexed from 1. If (int[] == null) no match was found. All alignments should be performed with both the forward and reverse complimented version of the query sequence looking for the longest match in the results.

Specified by:

getAmplimerReadingFrameRegion in interface AlignmentService

Parameters:

targetSeq - the longer of the two sequences e.g. the CDS

querySeq - the shorter of the two sequences e.g. the amplimer

Returns:

the mapping results {queryStart, queryStop, startOnTarget}