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

All Known Implementing Classes:

AnalysisServiceImpl

public interface AnalysisService

This interface controls access to analysis implementations.

Author:

Original: kr2, $Author: kr2 $

Method Summary

void	analyseTraceGroup(TraceGroupBean tgb) Performs trace analysis over all experiments in the TraceGroupBean.
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.

Method Detail

analyseTraceGroup

void analyseTraceGroup(TraceGroupBean tgb)

Performs trace analysis over all experiments in the TraceGroupBean. This method is expected to perform the following:
- Analyse the variant experiments via autoCSA
- Analyse the wildtype experiments via autoCSA
- Calculate the best wildtype experiment for each direction

Any changes are written back to the mutable objects in the original object.

Parameters:

tgb - the trace group to be analysed

compareTraceGroup

void compareTraceGroup(TraceGroupBean tgb)

Performs comparisons over all valid experiments in the TraceGroupBean. This method is expected to perform the following:

- Provided a working wildtype experiment is available for the direction of sequencing perform a comparison on the variant experiment (provided experiment is valid).
- Pad any internal data structures to the amplimer size, fill in holes etc.
- Standardise any variants marked as Constants.Zygosity.HETEROZYGOUS_TO_CHANGE to Constants.Zygosity.HETEROZYGOUS
- Convert any reverse coordinates to the forward strand.
- Perform flagging if relevant property is set.
- Remove any variants outside of 'region of interest' if relevent property is set (important if not using flagging).

Any changes are written back to the mutable objects in the original object.

Parameters:

tgb - the trace group to perform comparisons on

cdsTranslation

void cdsTranslation(CdsBean cds)

Completes the setup of the CdsBean. Populates the protein translation of the CDS and marks if the translation required the reverse compliment of the original CDS.

WARNING: this method will only give the best translation as the correct orientation i.e. the translation with the least number of stops.

Parameters:

cds - the CdsBean to have protein translation performed

revCompDna

java.lang.String revCompDna(java.lang.String dnaSeq)

Performs reverse compliment translation of a DNA string.

Parameters:

dnaSeq - the DNA sequence to be reverse complimented

Returns:

the reverse complimented DNA sequence