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(String, ExperimentBean, ExperimentBean, boolean, 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

Maps the amplimer (querySeq) to the CDS (targetSeq).

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.

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(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.

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.

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.

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

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.

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.