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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
 
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, Integer, Integer) - 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

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