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java.lang.Objectuk.ac.sanger.cgp.standalonecsa.services.AnalysisServiceImpl
public class AnalysisServiceImpl
Handles the actual processing of a unit of work.
Expected path would be:
- Analyse variant and wildtype traces
- Select best normal traces
- Perform comparisons
- Pad coordinates to full amplimer
- Invert coordinates and reverse compliment sequence for reverse/antisense results
- Flag variants (if indicated in standaloneCsa.properties)
- Remove variants outside of Region Of Interest (if indicated in standaloneCsa.properties)
- Divide variants into categories for view types and annotate
Full analysis, comparison, flagging and annotation would involve the use of the following two methods:
- analyseTraceGroup(TraceGroupBean tgb)
- compareTraceGroup(TraceGroupBean tgb)
Field Summary | |
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protected static org.apache.commons.logging.Log |
log
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Constructor Summary | |
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AnalysisServiceImpl()
Creates a new instance of FileLocatorServiceImpl |
Method Summary | |
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void |
analyseTraceGroup(TraceGroupBean tgb)
Performs trace analysis over all experiments in the TraceGroupBean. |
void |
annotateVar(uk.ac.sanger.cgp.autocsa.beans.Mutation var,
AmplimerBean amplimer)
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void |
cdsTranslation(CdsBean cds)
Completes the setup of the CdsBean. |
void |
compareTraceGroup(TraceGroupBean tgb)
Performs comparisons over all valid experiments in the TraceGroupBean. |
java.lang.String |
revCompDna(java.lang.String dnaSeq)
Performs reverse compliment translation of a DNA string. |
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 AnalysisServiceImpl()
Method Detail |
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public void analyseTraceGroup(TraceGroupBean tgb)
AnalysisService
analyseTraceGroup
in interface AnalysisService
tgb
- the trace group to be analysedpublic void compareTraceGroup(TraceGroupBean tgb)
AnalysisService
Constants.Zygosity.HETEROZYGOUS_TO_CHANGE
to
Constants.Zygosity.HETEROZYGOUS
compareTraceGroup
in interface AnalysisService
tgb
- the trace group to perform comparisons onpublic void annotateVar(uk.ac.sanger.cgp.autocsa.beans.Mutation var, AmplimerBean amplimer)
annotateVar
in interface AnalysisService
public void cdsTranslation(CdsBean cds)
AnalysisService
cdsTranslation
in interface AnalysisService
cds
- the CdsBean to have protein translation performedpublic java.lang.String revCompDna(java.lang.String dnaSeq)
AnalysisService
revCompDna
in interface AnalysisService
dnaSeq
- the DNA sequence to be reverse complimented
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