public enum AnnotationMessage extends Enum<AnnotationMessage>
Enum Constant and Description |
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ERROR_CHROMOSOME_NOT_FOUND
(E1) Chromosome does not exists in reference genome database.
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ERROR_OUT_OF_CHROMOSOME_RANGE
(E2) The variant's genomic coordinate is greater than chromosome's length.
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ERROR_PROBLEM_DURING_ANNOTATION
(non-standard) There was a problem with the annotation problem, if you see this in the output of the program then
this indicates a bug.
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INFO_COMPOUND_ANNOTATION
(W7) This effect is a result of combining more than one variants (e.g.
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INFO_NON_REFERENCE_ANNOTATION
(W8) An alternative reference sequence was used to calculate this annotation (e.g.
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INFO_REALIGN_3_PRIME
(W6) Variant has been realigned to the most 3prime position within the transcript.
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OTHER_MESSAGE
AnnotationMessage not encoded in enum.
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WARNING_REF_DOES_NOT_MATCH_GENOME
(W1) This means that the "REF" field in the input VCF file does not match the reference genome.
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WARNING_SEQUENCE_NOT_AVAILABLE
(W2) Reference sequence is not available, thus no inference could be performed.
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WARNING_TRANSCRIPT_INCOMPLETE
(W3) A protein coding transcript having a nonmultiple of 3 length.
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WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS
(W4) A protein coding transcript has two or more STOP codons in the middle of the coding sequence (CDS).
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WARNING_TRANSCRIPT_NO_START_CODON
(W5) A protein coding transcript does not have a proper START codon.
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Modifier and Type | Method and Description |
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static AnnotationMessage |
valueOf(String name)
Returns the enum constant of this type with the specified name.
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static AnnotationMessage[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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public static final AnnotationMessage ERROR_CHROMOSOME_NOT_FOUND
public static final AnnotationMessage ERROR_OUT_OF_CHROMOSOME_RANGE
public static final AnnotationMessage WARNING_REF_DOES_NOT_MATCH_GENOME
public static final AnnotationMessage WARNING_SEQUENCE_NOT_AVAILABLE
public static final AnnotationMessage WARNING_TRANSCRIPT_INCOMPLETE
public static final AnnotationMessage WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS
public static final AnnotationMessage WARNING_TRANSCRIPT_NO_START_CODON
public static final AnnotationMessage INFO_REALIGN_3_PRIME
public static final AnnotationMessage INFO_COMPOUND_ANNOTATION
public static final AnnotationMessage INFO_NON_REFERENCE_ANNOTATION
public static final AnnotationMessage ERROR_PROBLEM_DURING_ANNOTATION
public static final AnnotationMessage OTHER_MESSAGE
public static AnnotationMessage[] values()
for (AnnotationMessage c : AnnotationMessage.values()) System.out.println(c);
public static AnnotationMessage valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullCopyright © 2016. All rights reserved.