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VALID_RESIDUES - Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Static list of valid residues for DNA sequence, including ambiguity codes.
validateResidues(String) - Static method in class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
Validates that the input string only contains DNA residues recognised by AutoCSA.
VARIANT_CALL - Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.FeatureType
FeatureType to indicate variant call features
VariantGroup - Class in uk.ac.sanger.cgp.standalonecsa.beans
Grouping of variants for different displays.
VariantGroup(VariantType) - Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.VariantGroup
Should be constructed using constants for VariantType.
variantsInGroup() - Method in class uk.ac.sanger.cgp.standalonecsa.beans.VariantGroup
Get the number of variants in this group.
VariantType - Class in uk.ac.sanger.cgp.standalonecsa.enums
Used to encapsulate different types of VariantType, currently used for the display pathways.
VELOCITY_PROPERTIES - Static variable in class uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
Holds the pre-loaded content from the file specified under view_config in default.properties.
VelocityLogImpl - Class in uk.ac.sanger.cgp.standalonecsa.services
Allows log messages from the velocity template engine to be sent to the log4j instance.
VelocityLogImpl() - Constructor for class uk.ac.sanger.cgp.standalonecsa.services.VelocityLogImpl
 
ViewService - Interface in uk.ac.sanger.cgp.standalonecsa.interfaces
This interface handles all calls to the VelocityTemplate system when rendering output.
ViewServiceImpl - Class in uk.ac.sanger.cgp.standalonecsa.services
This method handles all things view related.
ViewServiceImpl() - Constructor for class uk.ac.sanger.cgp.standalonecsa.services.ViewServiceImpl
Creates a new instance of FileLocatorServiceImpl

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