|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
See:
Description
Packages | |
---|---|
uk.ac.sanger.cgp.standalonecsa.beans | The beans used by Standalone AutoCSA. |
uk.ac.sanger.cgp.standalonecsa.control | The controlling main methods used in the application. |
uk.ac.sanger.cgp.standalonecsa.enums | The immutable objects used in Standalone AutoCSA. |
uk.ac.sanger.cgp.standalonecsa.exceptions | The exception classes used in Standalone AutoCSA. |
uk.ac.sanger.cgp.standalonecsa.gui | The interactive setup GUI used in the Standalone AutoCSA application. |
uk.ac.sanger.cgp.standalonecsa.interfaces | The service interface classes used in Standalone AutoCSA. |
uk.ac.sanger.cgp.standalonecsa.jabawat | The core of the alignment system used in Standalone AutoCSA. |
uk.ac.sanger.cgp.standalonecsa.services | The implementations of the services used in Standalone AutoCSA. |
uk.ac.sanger.cgp.standalonecsa.util | The utility classes used in Standalone AutoCSA. |
Description of how Standalone AutoCSA can be integrated into a pipeline.
If you wish to use this package as part of your pipeline, but with more control of the processing, the following methods do the actual work and must be run in the following order:
FileLocatorService.getAmplimerGroup(List files, AmplimerBean amplimer)
, or by constructing in a way suitable for your system.AnalysisService.analyseTraceGroup(TraceGroupBean tgb)
AnalysisService.compareTraceGroup(TraceGroupBean tgb)
ChromatogramService.generateFullChrom(String imageLoc, ExperimentBean expBean, boolean writeImage, boolean drawBaseChar)
ChromatogramService.generateVariantViewSet(String imageLoc, ExperimentBean expBean, ExperimentBean normExp, boolean drawBaseChar, boolean writeToFile)
ChromatogramService.generateVariantViewSingle(String pathRoot, ExperimentBean expBean, boolean writeToFile, boolean drawBaseChar)
ChromatogramService.generateComplexVariantView(String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile)
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |