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C

C_BASE_COLOR - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
C_HIGHLIGHT_COLOR - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
CdsBean - Class in uk.ac.sanger.cgp.standalonecsa.beans
A CdsBean holds information regarding the name, dna sequence, protein sequence and coding orientation of the CDS.
CdsBean(String, String) - Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean
Creates a new instance of CdsBean from it's name and DNA sequence.
cdsTranslation(CdsBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.AnalysisService
Completes the setup of the CdsBean.
cdsTranslation(CdsBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.AnalysisServiceImpl
 
CHAR_ONLY - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
checkAndBuildComponent(Properties, String, String, String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
checkForLocation(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
chooseInput(boolean, File, Component) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
chooseInput(boolean, Component) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
CHROMATOGRAM_FORMAT - Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.CsaError
Use when catching and handling unknown chromatogram objects (via BioJava).
ChromatogramService - Interface in uk.ac.sanger.cgp.standalonecsa.interfaces
This interface provides access to all the methods that a view should require for rendering chromatogram graphics.
ChromatogramServiceImpl - Class in uk.ac.sanger.cgp.standalonecsa.services
This class handles rendering of chromatogram graphics.
ChromatogramServiceImpl() - Constructor for class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
Creates a new instance of ChromatogramServiceImpl
ChromRenderBean - Class in uk.ac.sanger.cgp.standalonecsa.beans
 
ChromRenderBean(Chromatogram, int, int, int, int, List, String) - Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
Creates a new instance of ChromRenderBean
compareTo(Object) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
 
compareTraceGroup(TraceGroupBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.AnalysisService
Performs comparisons over all valid experiments in the TraceGroupBean.
compareTraceGroup(TraceGroupBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.AnalysisServiceImpl
 
COMPLEX_INDEL - Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType
Complex insertion/deletion variant type.
CONFIG_LOC - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
The location where the standaloneCsa.properties file is expected to be.
Constants - Class in uk.ac.sanger.cgp.standalonecsa.beans
 
Constants.PreFlagging - Class in uk.ac.sanger.cgp.standalonecsa.beans
Constants used to indicate pre flagging status.
Constants.TraceStatus - Class in uk.ac.sanger.cgp.standalonecsa.beans
Constants used to indicate trace status.
Constants.VariantType - Class in uk.ac.sanger.cgp.standalonecsa.beans
Constants used to indicate variant type.
Constants.Zygosity - Class in uk.ac.sanger.cgp.standalonecsa.beans
Constants used to indicate zygosity
createCsaAnalysisPropFile(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
createDefaultResources() - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
createDefaultResources(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
createMobCorrFiles(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
 
createOutputDirs(File, boolean) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.FileHandler
 
cs - Variable in class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
 
CSA_ANALYSIS_LOC - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
The location where the csa_analysis.properties file is expected to be.
CSA_CHECKED_RUNTIME - Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.CsaError
This is here to handle a specific problem seen in autoCSA on Linux under a specific version of Java.
CsaConfig - Class in uk.ac.sanger.cgp.standalonecsa.util
This class handles access to configuration property files.
CsaConfig() - Constructor for class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
Creates a new instance of CsaConfig
CsaError - Class in uk.ac.sanger.cgp.standalonecsa.enums
This class converts handled exceptions into meaningful messages.
CsaRenderException - Exception in uk.ac.sanger.cgp.standalonecsa.exceptions
Used to throw exceptions specific to the rendering of the results.
CsaRenderException() - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRenderException
Creates a new instance of CsaRenderException without detail message.
CsaRenderException(String) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRenderException
Constructs an instance of CsaRenderException with specified detail message.
CsaRenderException(Throwable) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRenderException
Constructs an instance of CsaRenderException with specified causing exception.
CsaRenderException(String, Throwable) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRenderException
Constructs an instance of CsaRenderException with specified detail message and specified causing exception.
CsaRuntimeAlignmentException - Exception in uk.ac.sanger.cgp.standalonecsa.exceptions
Used to throw exceptions arising from alignment problems.
CsaRuntimeAlignmentException() - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeAlignmentException
Creates a new instance of CsaRuntimeAlignmentException without detail message.
CsaRuntimeAlignmentException(String) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeAlignmentException
Constructs an instance of CsaRuntimeAlignmentException with specified detail message.
CsaRuntimeAlignmentException(Throwable) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeAlignmentException
Constructs an instance of CsaRuntimeAlignmentException with specified causing exception.
CsaRuntimeAlignmentException(String, Throwable) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeAlignmentException
Constructs an instance of CsaRuntimeAlignmentException with specified detail message and specified causing exception.
CsaRuntimeException - Exception in uk.ac.sanger.cgp.standalonecsa.exceptions
Used for any exception arising from erroneous input data or files that has not been handled in a more appropriate manner.
CsaRuntimeException() - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeException
Creates a new instance of CsaRuntimeException without detail message.
CsaRuntimeException(String) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeException
Constructs an instance of CsaRuntimeException with specified detail message.
CsaRuntimeException(Throwable) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeException
Constructs an instance of CsaRuntimeException with specified causing exception.
CsaRuntimeException(String, Throwable) - Constructor for exception uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeException
Constructs an instance of CsaRuntimeException with specified detail message and specified causing exception.
csvExists() - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.FileLocatorService
Gets the location of the results.csv if it exists.
csvExists() - Method in class uk.ac.sanger.cgp.standalonecsa.services.FileLocatorServiceImpl
 

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