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

G

G_BASE_COLOR - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
G_HIGHLIGHT_COLOR - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
generateComplexVariantView(String, ExperimentBean, ExperimentBean, boolean, boolean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Generates images required for the complex variant view.
generateComplexVariantView(ChromRenderBean, ChromRenderBean, boolean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Generates images required for the complex variant view.
generateComplexVariantView(String, ExperimentBean, ExperimentBean, boolean, boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
generateComplexVariantView(ChromRenderBean, ChromRenderBean, boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
generateFillForColor(Color) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
generateFullChrom(String, ExperimentBean, boolean, boolean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Generates a full chromatogram image.
generateFullChrom(String, ExperimentBean, boolean, boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
generateVariantViewSet(String, ExperimentBean, ExperimentBean, boolean, boolean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Generates images required for the simple variant view.
generateVariantViewSet(String, ExperimentBean, ExperimentBean, boolean, boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
generateVariantViewSingle(String, ExperimentBean, boolean, boolean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService
Generates an image as used in the simple variant view.
generateVariantViewSingle(String, ExperimentBean, boolean, boolean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.ChromatogramServiceImpl
 
GERM_SUB - Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType
Germline substitution variant type.
getAmpLength() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the length of the amplimer.
getAmplimer() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Returns the currently set amplimer as a string.
getAmplimer(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Returns the currently set amplimer as a formatted string with width as defined by lineSize.
getAmplimerConfig() - Static method in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
Gets a map of AmplimerBeans accessible by amplimer name.
getAmplimerData() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean
Get the AmplimerBean assosiated with this TraceGroupBean.
getAmplimerGroup(List, AmplimerBean) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.FileLocatorService
Constructs a TraceGroupBean for the specified amplimer.
getAmplimerGroup(List, AmplimerBean) - Method in class uk.ac.sanger.cgp.standalonecsa.services.FileLocatorServiceImpl
 
getAmplimerName() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the amplimer name.
getAmplimerName() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Gets the amplimer name
getAmplimerPos() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the position in the file name, once split on the delimiter, that represents the amplimer name.
getAmplimerReadingFrameRegion(String, String) - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.AlignmentService
Maps the amplimer (querySeq) to the CDS (targetSeq).
getAmplimerReadingFrameRegion(String, String) - Method in class uk.ac.sanger.cgp.standalonecsa.services.AlignmentServiceImpl
 
getAmplimerReversed() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Indicated if the amplimer need to be reverse complimented to match the CDS sequence.
getAmplimerSeq() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getAntisenseIdentifier() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the character indicating an antisense/reverse sequencing file.
getBestAntisenseWildtype() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean
Get the best antisense/reverse wildtype ExperimentBean.
getBestSenseWildtype() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean
Get the best sense/forward wildtype ExperimentBean.
getCds() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the CdsBean object assigned to this amplimer.
getCdsSeq(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean
Gets the CDS DNA sequence formatted to the width provided.
getCdsSeq() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean
Gets the unformatted CDS DNA sequence.
getCdsStart() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the position of the cds that the amplimer starts to match (indexed from 1).
getCdsStartIndex() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the position of the cds that the amplimer starts to match (indexed from 0).
getChromatogram() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getChromatogram(ExperimentBean) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.FileHandler
 
getClasspathProperties(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.PropertyUtils
For a given location this method will load the file into a properties object
getCodingStart() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the start of the coding portion of the amplimer (indexed from 1).
getCodingStartIndex() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the start of the coding portion of the amplimer (indexed from 0).
getCodingStop() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the stop of the coding portion of the amplimer (indexed from 1).
getCodingStopIndex() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the stop of the coding portion of the amplimer (indexed from 0).
getComplimentExp() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
The ExperimentBean of any compliment experiment, requires correct use of ExperimentBean.runNumber for experiment pairing.
getComplimentFileName() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
The file name of any compliment experiment, requires correct use of ExperimentBean.runNumber for experiment pairing.
getCompResult() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get the result of a comparison.
getCoords(int) - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults
gets the coordinates of a specific hit.
getCoordsList() - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults
Retrieves the Coordinates list object.
getCsaSelectionScore() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get ExperimentBean.csaSelectionScore.
getCsaSelectionScorePrim() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get ExperimentBean.csaSelectionScore as a primitive int.
getCsaTrace() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get the CsaTrace object.
getDelimiter() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the character that has been used to divide filename components e.g.
getDirectionPos() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the position in the file name, once split on the delimiter, that represents the sequencing direction.
getDnaName() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get the DNA/sample name.
getDnaNamePos() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the position in the file name, once split on the delimiter, that represents the DNA/sample name.
getError() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get any CsaError that may have been handled during analysis.
getException() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get any exception that may have been handled on the creation of a CsaError.
getFeatureColor() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FeatureBean
 
getFeatures() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getFeatureStart() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FeatureBean
 
getFeatureStop() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FeatureBean
 
getFeatureType() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FeatureBean
 
getFileExtension() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the file extension for the input sequencing files.
getFileNoPath() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Returns the name of the file linked to this experiment with no path.
getFileNoPathOrExtension() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Gets the filename with no path or extension.
getFileProperties() - Static method in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
Creates a FileProcessingInfoBean based on standaloneCsa.properties.
getGroupType() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.VariantGroup
Get the VariantType of this group
getHits() - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults
Retrieves the number of hits from the object.
getHorizScale() - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
getKey() - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults
Gets the name of the sequence.
getMapsToCds() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
The name of the CDS that this amplimer should map to.
getName() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean
Get the name of this CDS.
getOutcome() - Method in class uk.ac.sanger.cgp.standalonecsa.jabawat.JabawatResults
Retrieves the direction of the query.
getPerBaseScans() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getProperties() - Static method in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
Get the properties object for standaloneCsa.properties.
getProperties(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.PropertyUtils
 
getProperty(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
Gets the value of the specified property from standaloneCsa.properties.
getProteinSeq(int) - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean
Get the protein sequence of the provided CDS formatted to the specified width in characters.
getProteinSeq() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean
Get the unformatted protein sequence of the provided CDS.
getRenderedHeight() - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
getRenderedWidth() - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
getRoi() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the current region of interest.
getRoiStart() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the current start position of the ROI on the amplimer.
getRoiStop() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Gets the current stop position of the ROI on the amplimer.
getRunNumber() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get run of this experiment, used to pair sense and antisense experiments when multiple sequence traces are provided.
getRunPos() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the position in the file name, once split on the delimiter, that represents the run position.
getSampleTypePos() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the position in the file name, once split on the delimiter, that represents the sample type.
getSenseIdentifier() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the character indicating a sense/forward sequencing file.
getStartRenderAtBase() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getStartScan() - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
getStopRenderAtBase() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getStopScan() - Method in class uk.ac.sanger.cgp.standalonecsa.util.SimpleChromGraphic
 
getStrandPreFlaggingCountStatus() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Flagging parameter, here for convenience.
getTraceCoverageStart() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getTraceCoverageStop() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ChromRenderBean
 
getTraceDetails() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get the TraceDetails object
getTraceFiles() - Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.FileLocatorService
Gets a list of possible trace filenames.
getTraceFiles() - Method in class uk.ac.sanger.cgp.standalonecsa.services.FileLocatorServiceImpl
 
getTraceStatus() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Textual description of the experiment status.
getUniqueNameForFile() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Returns a unique name for a result.
getUniqueNameForVariant() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Returns a unique name for a variant see ExperimentBean.setVariantToRender(Mutation variantToRender).
getVarDetailsList() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.VariantGroup
Get the list of MutationDetails objects.
getVariantGroups() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get the map of different classes of variant.
getVariantList() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.VariantGroup
Get the list of Mutation objects.
getVariantToRender() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.ExperimentBean
Get the current variant being rendered.
getVariantTraces() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean
Get the set of variant traces.
getWildtypeIdentifier() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.FileProcessingInfoBean
Get the text that indicates a wildtype sample/DNA.
getWildtypeTraces() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.TraceGroupBean
Get the set of wildtype traces.

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