Package utility

Class Constants

java.lang.Object
utility.Constants
public final class Constants extends Object
A utility class that holds constant values used throughout the project.

This class provides a centralized location for defining constants, ensuring consistency and reducing the risk of hardcoding values in multiple places. The constants include symbols, sequence types, and other project-specific values. All fields are declared as static final to indicate that they are constants and cannot be modified.

  • Field Details

    • EMPTY

      public static final String EMPTY
      Empty string constant.
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    • COLON

      public static final String COLON
      Colon string constant.
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    • SEMICOLON

      public static final String SEMICOLON
      Semicolon string constant.
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    • COMMA

      public static final String COMMA
      Comma string constant.
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    • TAB

      public static final String TAB
      Tabulator string constant.
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    • DOT

      public static final String DOT
      Dot string constant.
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    • EQUAL

      public static final String EQUAL
      Equals sign string constant.
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    • SIGN

      public static final String SIGN
      Number sign string constant.
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    • PIPE

      public static final String PIPE
      Pipe string constant.
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    • anyNucleotide

      public static final String anyNucleotide
      Represents the nucleotide used to denote any base in a sequence.

      This constant is used in scenarios where a specific nucleotide cannot be determined and is represented by the character 'N'.

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    • stopCodon

      public static final String stopCodon
      Represents the stop codon in a sequence.

      This constant is used to denote the stop codon, which is represented by the character '*'. The stop codon signals the termination of translation in a nucleotide sequence.

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    • lowCoverageCallPrefix

      public static final String lowCoverageCallPrefix
      Prefix used to indicate low coverage variant calls.

      This constant is used to mark variant calls with insufficient read depth, represented by the prefix 'x'.

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    • lowFrequencyCallPrefix

      public static final String lowFrequencyCallPrefix
      Prefix used to indicate low frequency variant calls.

      This constant is used to mark variant calls with low allele frequency, represented by the prefix 'f'.

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    • gapString

      public static final String gapString
      String representation of a gap in a sequence.
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    • gapChar

      public static final char gapChar
      Character representation of a gap in a sequence.
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    • synonymous

      public static final String synonymous
      Represents the term used for synonymous Feature.Alleles that are not actually stored.
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    • $Attributable_frequencyReference

      public static final String $Attributable_frequencyReference
      Key used to represent the reference frequency of an attributable entity.

      This constant is used as a key in data structures to store or retrieve the reference frequency associated with a feature or sample.

      For features, this corresponds to the proportion of samples that are not associated with any variant on the feature locus. For samples, this corresponds to the proportion of features for which the sample is not associated with any variant.

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    • $Attributable_frequencyDisrupted

      public static final String $Attributable_frequencyDisrupted
      Key used to represent the disrupted frequency of an attributable entity.

      This constant is used as a key in data structures to store or retrieve the reference frequency associated with a feature or sample and is only used if proteoform information is processed.

      For features, this corresponds to the proportion of proteoforms that are associated with an start_lost or stop_gained SO effect. For samples, this corresponds to the proportion of coding features for which the sample is associated with a proteoform that is itself associated with an start_lost or stop_gained SO effect.

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    • $Contig_length

      public static final String $Contig_length
      Key used to represent the length of a contig.
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    • $Feature_children

      public static final String $Feature_children
      Key used to represent the children of a feature.
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    • $Feature_numberOfAlleles

      public static final String $Feature_numberOfAlleles
      Key used to represent the number of alleles of a feature.

      This constant is used as a key in data structures to store or retrieve the number of alleles associated with a specific feature.

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    • $Feature_numberOfProteoforms

      public static final String $Feature_numberOfProteoforms
      Key used to represent the number of proteoforms of a feature.

      This constant is used as a key in data structures to store or retrieve the number of proteoforms associated with a specific feature.

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    • $SequenceType_effects

      public static final String $SequenceType_effects
      Key used to represent the effects of a SequenceType.

      This constant is used as a key in

      • Feature.Allele data structures to store or retrieve the effects associated with a specific allele, i.e., all distinct snpeff_effect values of VariantInformation instances associated with the object.
      • Feature.Proteoform data structures to store or retrieve the effects derived in the constructor of the class.
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    • $SequenceType_clusterLabel

      public static final String $SequenceType_clusterLabel
      Key used to represent the cluster label of a sequence type.
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    • $SequenceType_clusterIndex

      public static final String $SequenceType_clusterIndex
      Key used to represent the cluster index of a sequence type.
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    • $SequenceType_clusterOutlierScore

      public static final String $SequenceType_clusterOutlierScore
      Key used to represent the outlier score of a sequence type.
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    • $SequenceType_sequenceLengthVariation

      public static final String $SequenceType_sequenceLengthVariation
      Key used to represent the net shift in sequence length of a sequence type.

      This constant is used as a key in data structures to store or retrieve the net shift value associated with a specific sequence type. The net shift typically represents the cumulative effect of insertions and deletions on the sequence length.

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    • $SequenceType_frequency

      public static final String $SequenceType_frequency
      Key used to represent the frequency of a sequence type.

      This constant is used as a key in data structures to store or retrieve the frequency value associated with a specific sequence type. The frequency represents the proportion of samples that exhibit the specified sequence type.

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    • $Allele_proteoform

      public static final String $Allele_proteoform
      Key used to represent the proteoform of an allele.
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    • $Sample_numberOfCalls

      public static final String $Sample_numberOfCalls
      Key used to represent the number of calls in a sample.
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    • $Sample_numberOfFiltered

      public static final String $Sample_numberOfFiltered
      Key used to represent the number of filtered calls in a sample.
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    • $Sample_numberOfSubstitutions

      public static final String $Sample_numberOfSubstitutions
      Key used to represent the number of substitutions in a sample.
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    • $Sample_numberOfIndels

      public static final String $Sample_numberOfIndels
      Key used to represent the number of insertions in a sample.
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    • $Sample_meanCoverage

      public static final String $Sample_meanCoverage
      Key used to represent the mean coverage of a sample wrt. all calls.
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    • $Sample_meanQuality

      public static final String $Sample_meanQuality
      Key used to represent the mean coverage of a sample wrt. all calls.
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    • $VariantInformation_frequency

      public static final String $VariantInformation_frequency
      Key used to represent the frequency of a variant in the stored samples.
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    • lineSeparator

      public static final String lineSeparator
      The system-dependent line separator string.

    • baseSymbols

      public static final String baseSymbols
      The base symbols of the IUPAC nucleotide and amino acid code.
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    • snpEffAttributeKeyPrefix

      public static final String snpEffAttributeKeyPrefix
      Prefix for SnpEff attribute keys.
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    • snpEffKeys

      public static final ArrayList<String> snpEffKeys
      SnpEff annotation field names.

  • Constructor Details

    • Constants

      public Constants()