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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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