Package util

Class Constants

java.lang.Object

util.Constants

public abstract class Constants
extends Object

Utility class that holds constant values used throughout the application.

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.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Constants.AttributesKeys	A nested utility class that defines keys for various attributes used in the application.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ANY_NUCLEOTIDE	IUPAC symbol for any/unknown nucleotide in a nucleotide sequence.
static final String	BASE_SYMBOLS	Base symbols of the IUPAC nucleotide and amino acid code.
static final String	COLON	Colon string constant.
static final String	COMMA	Comma string constant.
static final String	DOT	Dot string constant.
static final String	EMPTY	Empty string constant.
static final String	EQUAL	Equals sign string constant.
static final String	GAP	String representation of a gap in a sequence.
static final char	GAP_CHAR	Character representation of a gap in a sequence.
static final String	GENOMIC_COORDINATES_PREFIX	Prefix for genomic coordinate notation as per HGVS guidelines.
static final String	GREATER_THAN	Greater than sign string constant.
static final String	LINE_SEPARATOR	System-dependent line separator string.
static final String	PIPE	Pipe symbol string constant.
static final String	REFERENCE	Term used for reference alleles in the context of Alleles.
static final String	SEMICOLON	Semicolon string constant.
static final String	SIGN	Number sign string constant.
static final ArrayList<String>	SNP_EFF_KEYS	SnpEff annotation field names.
static final String	SNP_EFF_PREFIX	Prefix for SnpEff attribute keys.
static final String	SYNONYMOUS	Term used for synonymous proteoforms in the context of Proteoforms.
static final String	TAB	Tabulator string constant.
static final String	TERMINAL_AA	Translated stop codon in an amino acid sequence.
static final String	UNDER_SCORE	Underscore string constant.
static final String	UNDERSCORE	Underscore string constant.

Constructor Summary

Constructors

Constructor	Description
Constants()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

EMPTY

public static final String EMPTY

Empty string constant.

See Also:

• Constant Field Values

COLON

public static final String COLON

Colon string constant.

See Also:

• Constant Field Values

SEMICOLON

public static final String SEMICOLON

Semicolon string constant.

See Also:

• Constant Field Values

COMMA

public static final String COMMA

Comma string constant.

See Also:

• Constant Field Values

TAB

public static final String TAB

Tabulator string constant.

See Also:

• Constant Field Values

DOT

public static final String DOT

Dot string constant.

See Also:

• Constant Field Values

UNDERSCORE

public static final String UNDERSCORE

Underscore string constant.

See Also:

• Constant Field Values

EQUAL

public static final String EQUAL

Equals sign string constant.

See Also:

• Constant Field Values

SIGN

public static final String SIGN

Number sign string constant.

See Also:

• Constant Field Values

UNDER_SCORE

public static final String UNDER_SCORE

Underscore string constant.

See Also:

• Constant Field Values

GREATER_THAN

public static final String GREATER_THAN

Greater than sign string constant.

See Also:

• Constant Field Values

PIPE

public static final String PIPE

Pipe symbol string constant.

See Also:

• Constant Field Values

ANY_NUCLEOTIDE

public static final String ANY_NUCLEOTIDE

IUPAC symbol for any/unknown nucleotide in a nucleotide sequence.

See Also:

• Constant Field Values

TERMINAL_AA

public static final String TERMINAL_AA

Translated stop codon in an amino acid sequence.

See Also:

• Constant Field Values

GAP

public static final String GAP

String representation of a gap in a sequence.

See Also:

• Constant Field Values

GAP_CHAR

public static final char GAP_CHAR

Character representation of a gap in a sequence.

See Also:

• Constant Field Values

GENOMIC_COORDINATES_PREFIX

public static final String GENOMIC_COORDINATES_PREFIX

Prefix for genomic coordinate notation as per HGVS guidelines.

See Also:

• Constant Field Values

REFERENCE

public static final String REFERENCE

Term used for reference alleles in the context of Alleles.

See Also:

• Constant Field Values

SYNONYMOUS

public static final String SYNONYMOUS

Term used for synonymous proteoforms in the context of Proteoforms.

See Also:

• Constant Field Values

BASE_SYMBOLS

public static final String BASE_SYMBOLS

Base symbols of the IUPAC nucleotide and amino acid code.

See Also:

• Constant Field Values

SNP_EFF_PREFIX

public static final String SNP_EFF_PREFIX

Prefix for SnpEff attribute keys.

See Also:

• Constant Field Values

SNP_EFF_KEYS

public static final ArrayList<String> SNP_EFF_KEYS

SnpEff annotation field names.

• 0 = allele
• 1 = effect
• 2 = impact
• 3 = gene_name
• 4 = gene_id
• 5 = feature_type
• 6 = feature_id
• 7 = biotype
• 8 = rank/total
• 9 = hgvs_c
• 10 = hgvs_p
• 11 = cDNA_position
• 12 = cds_position
• 13 = protein_position
• 14 = feature_distance
• 15 = note

LINE_SEPARATOR

public static final String LINE_SEPARATOR

System-dependent line separator string.

Constructor Details

Constants

public Constants()