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F

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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