Uses of Class
uk.ac.sanger.cgp.standalonecsa.enums.CsaError

Packages that use CsaError
uk.ac.sanger.cgp.standalonecsa.beans The beans used by Standalone AutoCSA. 
uk.ac.sanger.cgp.standalonecsa.enums The immutable objects used in Standalone AutoCSA. 
 

Uses of CsaError in uk.ac.sanger.cgp.standalonecsa.beans
 

Methods in uk.ac.sanger.cgp.standalonecsa.beans that return CsaError
 CsaError ExperimentBean.getError()
          Get any CsaError that may have been handled during analysis.
 

Methods in uk.ac.sanger.cgp.standalonecsa.beans with parameters of type CsaError
 void ExperimentBean.setError(CsaError error)
          Set any CsaError that may have been handled during analysis.
 void ExperimentBean.setError(CsaError error, java.lang.Throwable exception)
          Set any CsaError that may have been handled during analysis, along with any associated exception.
 

Uses of CsaError in uk.ac.sanger.cgp.standalonecsa.enums
 

Fields in uk.ac.sanger.cgp.standalonecsa.enums declared as CsaError
static CsaError CsaError.BAD_AB1_BASE_CALL
          Use when catching and handling a BioError with root cause of IllegalSymbolException.
static CsaError CsaError.BAD_COMMENT_BLOCK
          Use when catching and handling an BadCommentException from autoCSA caused by missing DYEP.
static CsaError CsaError.BAD_TRACE
          Bad trace is a standard exception thrown by autoCSA, usually due to insufficient peaks.
static CsaError CsaError.CHROMATOGRAM_FORMAT
          Use when catching and handling unknown chromatogram objects (via BioJava).
static CsaError CsaError.CSA_CHECKED_RUNTIME
          This is here to handle a specific problem seen in autoCSA on Linux under a specific version of Java.
static CsaError CsaError.FAILED_MOB_CORR
          This can be thrown by autoCSA when the mobility correction step fails, currently only applies to 'ab1' files.
static CsaError CsaError.IO
          Use when catching and handling file access problems.
static CsaError CsaError.OUTSIDE_OF_COVERAGE
          The region of the amplimer or image being worked on is outside of the coverage.
static CsaError CsaError.UNKNOWN_CHROMATOGRAM
          Use when catching and handling files that do not appear to be ab1 or scf.
static CsaError CsaError.UNKNOWN_REASON
          Use when an unexpected exception is thrown
static CsaError CsaError.UNKNOWN_SCAN_START
          Use when indicating that a start scan position in the trace cannot be identified.
static CsaError CsaError.UNKNOWN_SCAN_STOP
          Use when indicating that a stop scan position in the trace cannot be identified.
static CsaError CsaError.UNSUPPORTED_CHROM_FORMAT
          Use when catching and handling an UnsupportedChromatogramFormatException from BioJava.