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I

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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