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INCLUSIVE_BOUNDRY
- Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.
FeatureType
FeatureType to indicate a feature where the range between the provided positions should be shaded
init(RuntimeServices)
- Method in class uk.ac.sanger.cgp.standalonecsa.services.
VelocityLogImpl
Required to initialise object.
INS
- Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.
Constants.VariantType
Insertion variant type
installPath
- Static variable in class uk.ac.sanger.cgp.standalonecsa.gui.
SetupBase
The path to which installation is occurring.
IO
- Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.
CsaError
Use when catching and handling file access problems.
isBest()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
Applies to wildtype traces only, indicates if this is the current best wildtype experiment based on
ExperimentBean.csaSelectionScore
.
isCompared()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
Indicates if the experiment has been used in a comparison.
isComplimentPresent()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
Indicates that a compliment experiment is avilable, requires correct use of
ExperimentBean.runNumber
for experiment pairing.
isFlagAssessed()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
True when flagging has been attempted on this experiment.
isOthersPresent()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
Indicates when non-substitution variants are available.
isSense()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
True when this experiment was sequenced in the sense direction (with respect to the amplimer sequence).
isSenseTranslated()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
CdsBean
Indicates that the CDS DNA sequence translated best in the provided orientation.
isSubsPresent()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
Indicates when substitution variants are available.
isWildtype()
- Method in class uk.ac.sanger.cgp.standalonecsa.beans.
ExperimentBean
True when a wildtype experiment.
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