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

S

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.

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