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). |
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 CDSquerySeq
- the shorter of the two sequences e.g. the amplimer
- Returns:
- the mapping results {queryStart, queryStop, startOnTarget}