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R

reconfigure() - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
REF_SUB - Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType
Reference substitution variant type.
RENDER_AMPLIMER - Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.FeatureType
FeatureType to indicate amplimer sequence drawing
renderAmplimer(AmplimerBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Generates the amplimer html page.
renderAmplimer(AmplimerBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
renderChromatogram(ChromRenderBean, boolean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Generates a simple variant or full trace image.
renderChromatogram(ChromRenderBean, boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
renderIndex(Map, String) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Generates the index html page.
renderIndex(Map, String) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
renderTraceInfo(TraceGroupBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Generates variant trace html page.
renderTraceInfo(TraceGroupBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
renderTraceSummary(TraceGroupBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Generates the variant trace summary html page.
renderTraceSummary(TraceGroupBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
renderVariantTraceResults(TraceGroupBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Generate the called variant html pages.
renderVariantTraceResults(TraceGroupBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
renderWildtypePanel(TraceGroupBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Generates wildtype trace html page.
renderWildtypePanel(TraceGroupBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
resetPreviousRendered() - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Resets the set of files that have been previously rendered and written to a file.
resetPreviousRendered() - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
resetService() - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ViewService
Resets the chromatogram service.
resetService() - Method in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
revCompDna(String) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.AnalysisService
Performs reverse compliment translation of a DNA string.
revCompDna(String) - Method in class uk.ac.sanger.cgp.standalonecsa.services.AnalysisServiceImpl
 
runJabawat(String, String, JabawatResults, int) - Static method in class uk.ac.sanger.cgp.standalonecsa.jabawat.Jabawat
Runs the core of the JaBaWAT alignment program using two strings representing the sequences.

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