uk.ac.sanger.cgp.standalonecsa.interfaces
Interface AlignmentService

All Known Implementing Classes:
AlignmentServiceImpl

public interface AlignmentService

This interface controls access to alignment implementations.

Author:
Original: kr2, $Author: kr2 $

Method Summary
 int[] getAmplimerReadingFrameRegion(java.lang.String targetSeq, java.lang.String querySeq)
          Maps the amplimer (querySeq) to the CDS (targetSeq).
 

Method Detail

getAmplimerReadingFrameRegion

int[] getAmplimerReadingFrameRegion(java.lang.String targetSeq,
                                    java.lang.String querySeq)
Maps the amplimer (querySeq) to the CDS (targetSeq). This method is expected to return 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.

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}