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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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