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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.services.AlignmentServiceImpl
public class AlignmentServiceImpl
An implementation of basic alignment tools for aligning an amplimer (query) to a CDS (target)
Field Summary | |
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protected static org.apache.commons.logging.Log |
log
The logging instance (log4j). |
Constructor Summary | |
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AlignmentServiceImpl()
Creates a new instance of AlignmentServiceImpl |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected static final org.apache.commons.logging.Log log
Constructor Detail |
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public AlignmentServiceImpl()
Method Detail |
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public int[] getAmplimerReadingFrameRegion(java.lang.String targetSeq, java.lang.String querySeq)
AlignmentService
int[]
of size 3:
(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.
getAmplimerReadingFrameRegion
in interface AlignmentService
targetSeq
- the longer of the two sequences e.g. the CDSquerySeq
- the shorter of the two sequences e.g. the amplimer
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