A B C D E F G H I J L M O P R S T U V W

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

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