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A
A_BASE_COLOR
- Static variable in class uk.ac.sanger.cgp.standalonecsa.util.
SimpleChromGraphic
A_HIGHLIGHT_COLOR
- Static variable in class uk.ac.sanger.cgp.standalonecsa.util.
SimpleChromGraphic
addFeature(FeatureBean)
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ChromRenderBean
addVariant(Mutation, MutationDetails)
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
VariantGroup
Adds Mutation and MutationDetails objects in a controlled manner.
AlignmentService
- Interface in
uk.ac.sanger.cgp.standalonecsa.interfaces
This interface controls access to alignment implementations.
AlignmentServiceImpl
- Class in
uk.ac.sanger.cgp.standalonecsa.services
An implementation of basic alignment tools for aligning an amplimer (query) to a CDS (target)
AlignmentServiceImpl()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.services.
AlignmentServiceImpl
Creates a new instance of AlignmentServiceImpl
ALPHA_NUMERIC
- Static variable in class uk.ac.sanger.cgp.standalonecsa.util.
SetupUtils
AmplimerBean
- Class in
uk.ac.sanger.cgp.standalonecsa.beans
This object handles information pertaining to the amplimer and any associated mappings.
AmplimerBean()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
AmplimerBean
Creates a new instance of AmplimerBean, not for general use.
AmplimerBean(String, String, String, CdsBean)
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
AmplimerBean
Generates a new AmplimerBean using the following parameters
AmplimerBean(String, String, int[])
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
AmplimerBean
Generates a new AmplimerBean using the following parameters
AmplimerBean(String, String, int[], CdsBean)
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
AmplimerBean
Generates a new AmplimerBean using the following parameters
AmplimerBean(String, String, Integer, Integer)
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
AmplimerBean
Generates a new AmplimerBean using the following parameters
AmplimerBean(String, String, Integer, Integer, CdsBean)
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
AmplimerBean
Generates a new AmplimerBean using the following parameters
analyseTraceGroup(TraceGroupBean)
- Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.
AnalysisService
Performs trace analysis over all experiments in the TraceGroupBean.
analyseTraceGroup(TraceGroupBean)
- Method in class uk.ac.sanger.cgp.standalonecsa.services.
AnalysisServiceImpl
AnalysisService
- Interface in
uk.ac.sanger.cgp.standalonecsa.interfaces
This interface controls access to analysis implementations.
AnalysisServiceImpl
- Class in
uk.ac.sanger.cgp.standalonecsa.services
Handles the actual processing of a unit of work.
AnalysisServiceImpl()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.services.
AnalysisServiceImpl
Creates a new instance of FileLocatorServiceImpl
annotateVar(Mutation, AmplimerBean)
- Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.
AnalysisService
annotateVar(Mutation, AmplimerBean)
- Method in class uk.ac.sanger.cgp.standalonecsa.services.
AnalysisServiceImpl
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