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

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setAmplimer(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

Set the amplimer to the provided string.

setAmplimerData(AmplimerBean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean

Set the AmplimerBean assosiated with this TraceGroupBean.

setAmplimerName(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

Sets the amplimer name.

setAmplimerName(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the amplimerName to the provided string

setAmplimerPos(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the position in the file name, once split on the delimiter, that represents the amplimer name.

setAntisenseIdentifier(char) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the character indicating an antisense/reverse sequencing file.

setBest(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set this experiment as best.

setBestAntisenseWildtype(ExperimentBean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean

Set the best antisense/reverse wildtype ExperimentBean.

setBestSenseWildtype(ExperimentBean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean

Set the best sense/forward wildtype ExperimentBean.

setCdsSeq(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean

Set the CDS DNA sequence to the provided string.

setComplimentExp(ExperimentBean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the ExperimentBean of any compliment experiment, requires correct use of ExperimentBean.runNumber for experiment pairing.

setCompResult(CSAOutput) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the CSAOutput, result of a comparison.

setCsaSelectionScore(Float) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set ExperimentBean.csaSelectionScore.

setCsaTrace(CsaTraceInterface) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the CsaTrace object.

setDelimiter(char) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the character that has been used to divide filename components e.g.

setDirectionPos(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the position in the file name, once split on the delimiter, that represents the direction of sequencing.

setDnaName(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the dna name

setDnaNamePos(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the position in the file name, once split on the delimiter, that represents the DNA/sample name.

setError(CsaError) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set any CsaError that may have been handled during analysis.

setError(CsaError, Throwable) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set any CsaError that may have been handled during analysis, along with any associated exception.

setFileExtension(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the file extension for the input sequencing files.

setFileProperties(FileProcessingInfoBean) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig

Public access for testing classes only, not for general use.

setFlagAssessed(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

True when flagging has been attempted on this experiment.

setHits(int) - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults

Adds the number of hits to the object.

setKey(String) - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults

Adds the name of the query to the object.

setMobilityCorrect(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set to true if mobility correction should be performed, only affects 'scf' files and currently not a valid option.

setOthersPresent(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set indicator for when non-substitution variants are available.

setOutcome(String) - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults

Adds the direction of the query to the object.

setProteinSeq(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean

Set the protein sequence to the provided string.

setRoi(Integer, Integer) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

Sets the region of interest to the provided values.

setRoi(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

String wrapper of AmplimerBean.setRoi(Integer roiStart, Integer roiStop)

setRoi(int[]) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

int[] wrapper of AmplimerBean.setRoi(Integer roiStart, Integer roiStop).

setRoiStart(Integer) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

Sets the roi start position on the amplimer

setRoiStop(Integer) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean

Sets the roi stop position on the amplimer

setRunNumber(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set run of this experiment, used to pair sense and antisense experiments when multiple sequence traces are provided.

setRunNumber(Integer) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set run of this experiment, used to pair sense and antisense experiments when multiple sequence traces are provided.

setRunPos(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the position in the file name, once split on the delimiter, that represents the run number.

setSampleTypePos(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the position in the file name, once split on the delimiter, that represents the type of sample.

setSense(char) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the sequencing direction with respect to the amplimer.

setSenseIdentifier(char) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the character indicating a sense/forward sequencing file.

setSenseTranslated(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean

Sets the senseTranslated boolean to the provided value.

setStrandPreFlaggingCountStatus(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Flagging parameter, here for convenience.

setSubsPresent(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set indicator for when substitution variants are available.

setTraceDetails(TraceDetailsInterface) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the TraceDetails object

setTraceStatus(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set a textual description of the experiment status.

SetupBase - Class in uk.ac.sanger.cgp.standalonecsa.gui

This is the GUI component of StandaloneCSA.

SetupBase(Frame, boolean, String) - Constructor for class uk.ac.sanger.cgp.standalonecsa.gui.SetupBase

Creates new form SetupBase

setupInfo - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils

setupOffsetTransform(Graphics2D) - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic

Developer is resposible for saving the original transform and reinstating

setupSystem() - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils

SetupUtils - Class in uk.ac.sanger.cgp.standalonecsa.util

SetupUtils() - Constructor for class uk.ac.sanger.cgp.standalonecsa.util.SetupUtils

Creates a new instance of FileHandler

setupXoffsetTransform(Graphics2D) - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic

Developer is resposible for saving the original transform and reinstating

setupYoffsetTransform(Graphics2D) - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic

Developer is resposible for saving the original transform and reinstating

setVariantToRender(Mutation) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the variant to be rendered.

setVariantTraces(TreeSet) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean

Set the new set of variant traces.

setWildtype(boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean

Set the wildtype indicator

setWildtypeIdentifier(String) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean

Set the text that indicates a wildtype sample/DNA.

setWildtypeTraces(TreeSet) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean

Set the new set of wildtype traces.

SimpleChromGraphic - Class in uk.ac.sanger.cgp.standalonecsa.util

SimpleChromGraphic() - Constructor for class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic

SimpleChromGraphic(Chromatogram, int, int, int, float) - Constructor for class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic

The supplied height is used to calculate the scaling factor for the image.

SimpleChromGraphic(Chromatogram, int, int, int, float, int, boolean) - Constructor for class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic

SPEC_INDEL - Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType

Speculative insertion/deletion variant type.

StandaloneCsa - Class in uk.ac.sanger.cgp.standalonecsa.control

This is the main driving class for the analysis system and handles the linking together of all components.

StandaloneCsa() - Constructor for class uk.ac.sanger.cgp.standalonecsa.control.StandaloneCsa

Creates a new instance of StandaloneCsa

STATUS_LOC - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig

The location where the status.properties file is expected to be.

STATUS_PROPERTIES - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig

Holds the pre-loaded content from status.properties.

storeCoords(int, int) - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults

Stores the coordinates within the object.

SUB - Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType

Substitution variant type.

SUBSTITUTION_PATH - Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.VariantType

VariantType for the substitution view.