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Packages that use CsaError | |
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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 |
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Methods in uk.ac.sanger.cgp.standalonecsa.beans that return CsaError | |
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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 | |
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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 |
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Fields in uk.ac.sanger.cgp.standalonecsa.enums declared as CsaError | |
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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. |
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