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FAIL
- Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.
Constants.PreFlagging
Fail pre flagging status
FAILED_MOB_CORR
- Static variable in class uk.ac.sanger.cgp.standalonecsa.beans.
Constants.TraceStatus
Failed to mobility correct trace status.
FAILED_MOB_CORR
- Static variable in class uk.ac.sanger.cgp.standalonecsa.enums.
CsaError
This can be thrown by autoCSA when the mobility correction step fails, currently only applies to 'ab1' files.
FeatureBean
- Class in
uk.ac.sanger.cgp.standalonecsa.beans
FeatureBean(int, int, FeatureType)
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
FeatureBean
Creates a new instance of FeatureBean
FeatureBean(int, int, FeatureType, Color)
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
FeatureBean
Creates a new instance of FeatureBean
FeatureType
- Class in
uk.ac.sanger.cgp.standalonecsa.enums
Used to encapsulate different types of VariantType, currently used for the display pathways.
fileComponentBean
- Static variable in class uk.ac.sanger.cgp.standalonecsa.util.
FileHandler
fileDisplayForGui(String, String, String)
- Static method in class uk.ac.sanger.cgp.standalonecsa.util.
SetupUtils
FileHandler
- Class in
uk.ac.sanger.cgp.standalonecsa.util
FileHandler()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.util.
FileHandler
Creates a new instance of FileHandler
FileLocatorService
- Interface in
uk.ac.sanger.cgp.standalonecsa.interfaces
This interface handles file searching and construction of data objects from filenames.
FileLocatorServiceImpl
- Class in
uk.ac.sanger.cgp.standalonecsa.services
FileLocatorServiceImpl()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.services.
FileLocatorServiceImpl
Creates a new instance of FileLocatorServiceImpl
FileProcessingInfoBean
- Class in
uk.ac.sanger.cgp.standalonecsa.beans
Object to hold all information related to file name construction and processing loaded from standaloneCsa.properties.
FileProcessingInfoBean()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.beans.
FileProcessingInfoBean
Creates a new empty instance of FileProcessingInfoBean.
findFiles(Map, File)
- Static method in class uk.ac.sanger.cgp.standalonecsa.services.
FileLocatorServiceImpl
Self recursing method for finding files in a directory structure.
findOutput()
- Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.
FileLocatorService
Collates information required to construct an index page.
findOutput()
- Method in class uk.ac.sanger.cgp.standalonecsa.services.
FileLocatorServiceImpl
FlaggingService
- Interface in
uk.ac.sanger.cgp.standalonecsa.interfaces
This interface is intended to handle all flagging related calls.
FlaggingServiceImpl
- Class in
uk.ac.sanger.cgp.standalonecsa.services
This class handles all things flagging related.
FlaggingServiceImpl()
- Constructor for class uk.ac.sanger.cgp.standalonecsa.services.
FlaggingServiceImpl
flagTraceGroup(TraceGroupBean)
- Method in interface uk.ac.sanger.cgp.standalonecsa.interfaces.
FlaggingService
Performs variant flagging.
flagTraceGroup(TraceGroupBean)
- Method in class uk.ac.sanger.cgp.standalonecsa.services.
FlaggingServiceImpl
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