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

java.lang.Object
  extended by uk.ac.sanger.cgp.standalonecsa.enums.CsaError

public class CsaError
extends java.lang.Object

This class converts handled exceptions into meaningful messages. It should not be used for exceptions that will be thrown.

Author:
Original: kr2, $Author: kr2 $

Field Summary
static CsaError BAD_AB1_BASE_CALL
          Use when catching and handling a BioError with root cause of IllegalSymbolException.
static CsaError BAD_COMMENT_BLOCK
          Use when catching and handling an BadCommentException from autoCSA caused by missing DYEP.
static CsaError BAD_TRACE
          Bad trace is a standard exception thrown by autoCSA, usually due to insufficient peaks.
static CsaError CHROMATOGRAM_FORMAT
          Use when catching and handling unknown chromatogram objects (via BioJava).
static 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 FAILED_MOB_CORR
          This can be thrown by autoCSA when the mobility correction step fails, currently only applies to 'ab1' files.
static CsaError IO
          Use when catching and handling file access problems.
static CsaError OUTSIDE_OF_COVERAGE
          The region of the amplimer or image being worked on is outside of the coverage.
static CsaError UNKNOWN_CHROMATOGRAM
          Use when catching and handling files that do not appear to be ab1 or scf.
static CsaError UNKNOWN_SCAN_START
          Use when indicating that a start scan position in the trace cannot be identified.
static CsaError UNKNOWN_SCAN_STOP
          Use when indicating that a stop scan position in the trace cannot be identified.
static CsaError UNSUPPORTED_CHROM_FORMAT
          Use when catching and handling an UnsupportedChromatogramFormatException from BioJava.
 
Method Summary
 java.lang.String toString()
          Get a string representation of the object.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

IO

public static final CsaError IO
Use when catching and handling file access problems.


CHROMATOGRAM_FORMAT

public static final CsaError CHROMATOGRAM_FORMAT
Use when catching and handling unknown chromatogram objects (via BioJava).


UNKNOWN_CHROMATOGRAM

public static final CsaError UNKNOWN_CHROMATOGRAM
Use when catching and handling files that do not appear to be ab1 or scf.


CSA_CHECKED_RUNTIME

public static final CsaError CSA_CHECKED_RUNTIME
This is here to handle a specific problem seen in autoCSA on Linux under a specific version of Java. Basically the evaluation of the condition in the loop was not being executed for some unknown reason. Hopefully this will never be seen as it has not occurred since 2005.


BAD_TRACE

public static final CsaError BAD_TRACE
Bad trace is a standard exception thrown by autoCSA, usually due to insufficient peaks.


FAILED_MOB_CORR

public static final CsaError FAILED_MOB_CORR
This can be thrown by autoCSA when the mobility correction step fails, currently only applies to 'ab1' files.


OUTSIDE_OF_COVERAGE

public static final CsaError OUTSIDE_OF_COVERAGE
The region of the amplimer or image being worked on is outside of the coverage.


UNSUPPORTED_CHROM_FORMAT

public static final CsaError UNSUPPORTED_CHROM_FORMAT
Use when catching and handling an UnsupportedChromatogramFormatException from BioJava.


BAD_COMMENT_BLOCK

public static final CsaError BAD_COMMENT_BLOCK
Use when catching and handling an BadCommentException from autoCSA caused by missing DYEP.


BAD_AB1_BASE_CALL

public static final CsaError BAD_AB1_BASE_CALL
Use when catching and handling a BioError with root cause of IllegalSymbolException.


UNKNOWN_SCAN_START

public static final CsaError UNKNOWN_SCAN_START
Use when indicating that a start scan position in the trace cannot be identified.


UNKNOWN_SCAN_STOP

public static final CsaError UNKNOWN_SCAN_STOP
Use when indicating that a stop scan position in the trace cannot be identified.

Method Detail

toString

public java.lang.String toString()
Get a string representation of the object.

Overrides:
toString in class java.lang.Object
Returns:
a string representation of the object