Package psidev.psi.mi.jami.model

Interface Alias

All Known Implementing Classes:

DefaultAlias, MitabAlias, XmlAlias, XmlAlias, XmlAlias

public interface Alias

Alias is a synonym. It is composed of a name and a type. Ex: alias type = 'gene' and name = 'BRCA2'

Since:

22/11/12

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	AUTHOR_ASSIGNED_NAME	Constant AUTHOR_ASSIGNED_NAME="author assigned name"
static String	AUTHOR_ASSIGNED_NAME_MI	Constant AUTHOR_ASSIGNED_NAME_MI="MI:0345"
static String	COMPLEX_RECOMMENDED_NAME	Constant COMPLEX_RECOMMENDED_NAME="complex recommended name"
static String	COMPLEX_RECOMMENDED_NAME_MI	Constant COMPLEX_RECOMMENDED_NAME_MI="MI:1315"
static String	COMPLEX_SYNONYM	Constant COMPLEX_SYNONYM="complex-synonym"
static String	COMPLEX_SYNONYM_MI	Constant COMPLEX_SYNONYM_MI="MI:0673"
static String	COMPLEX_SYSTEMATIC_NAME	Constant COMPLEX_SYSTEMATIC_NAME="complex systematic name"
static String	COMPLEX_SYSTEMATIC_NAME_MI	Constant COMPLEX_SYSTEMATIC_NAME_MI="MI:1316"
static String	GENE_NAME	Constant GENE_NAME="gene name"
static String	GENE_NAME_MI	Constant GENE_NAME_MI="MI:0301"
static String	GENE_NAME_SYNONYM	Constant GENE_NAME_SYNONYM="gene name synonym"
static String	GENE_NAME_SYNONYM_MI	Constant GENE_NAME_SYNONYM_MI="MI:0302"
static String	ISOFORM_SYNONYM	Constant ISOFORM_SYNONYM="gene name synonym"
static String	ISOFORM_SYNONYM_MI	Constant ISOFORM_SYNONYM_MI="MI:0304"
static String	IUPAC	Constant IUPAC="iupac name"
static String	IUPAC_MI	Constant IUPAC_MI="MI:2007"
static String	LOCUS_NAME	Constant LOCUS_NAME="locus name"
static String	LOCUS_NAME_MI	Constant LOCUS_NAME_MI="MI:0305"
static String	ORF_NAME	Constant ORF_NAME="orf name"
static String	ORF_NAME_MI	Constant ORF_NAME_MI="MI:0306"
static String	SYNONYM	Constant SYNONYM="synonym"
static String	SYNONYM_MI	Constant SYNONYM_MI="MI:1041"

Method Summary

Modifier and Type	Method	Description
String	getName()	Alias name cannot be null.
CvTerm	getType()	The alias type is a controlled vocabulary term.

Field Detail

SYNONYM_MI

static final String SYNONYM_MI

Constant SYNONYM_MI="MI:1041"

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Constant Field Values

SYNONYM

static final String SYNONYM

Constant SYNONYM="synonym"

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Constant Field Values

GENE_NAME_MI

static final String GENE_NAME_MI

Constant GENE_NAME_MI="MI:0301"

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Constant Field Values

GENE_NAME

static final String GENE_NAME

Constant GENE_NAME="gene name"

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Constant Field Values

COMPLEX_SYNONYM

static final String COMPLEX_SYNONYM

Constant COMPLEX_SYNONYM="complex-synonym"

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Constant Field Values

COMPLEX_SYNONYM_MI

static final String COMPLEX_SYNONYM_MI

Constant COMPLEX_SYNONYM_MI="MI:0673"

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Constant Field Values

AUTHOR_ASSIGNED_NAME

static final String AUTHOR_ASSIGNED_NAME

Constant AUTHOR_ASSIGNED_NAME="author assigned name"

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Constant Field Values

AUTHOR_ASSIGNED_NAME_MI

static final String AUTHOR_ASSIGNED_NAME_MI

Constant AUTHOR_ASSIGNED_NAME_MI="MI:0345"

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Constant Field Values

GENE_NAME_SYNONYM

static final String GENE_NAME_SYNONYM

Constant GENE_NAME_SYNONYM="gene name synonym"

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Constant Field Values

GENE_NAME_SYNONYM_MI

static final String GENE_NAME_SYNONYM_MI

Constant GENE_NAME_SYNONYM_MI="MI:0302"

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Constant Field Values

ISOFORM_SYNONYM

static final String ISOFORM_SYNONYM

Constant ISOFORM_SYNONYM="gene name synonym"

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Constant Field Values

ISOFORM_SYNONYM_MI

static final String ISOFORM_SYNONYM_MI

Constant ISOFORM_SYNONYM_MI="MI:0304"

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Constant Field Values

ORF_NAME

static final String ORF_NAME

Constant ORF_NAME="orf name"

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Constant Field Values

ORF_NAME_MI

static final String ORF_NAME_MI

Constant ORF_NAME_MI="MI:0306"

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Constant Field Values

LOCUS_NAME

static final String LOCUS_NAME

Constant LOCUS_NAME="locus name"

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Constant Field Values

LOCUS_NAME_MI

static final String LOCUS_NAME_MI

Constant LOCUS_NAME_MI="MI:0305"

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Constant Field Values

IUPAC_MI

static final String IUPAC_MI

Constant IUPAC_MI="MI:2007"

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Constant Field Values

IUPAC

static final String IUPAC

Constant IUPAC="iupac name"

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Constant Field Values

COMPLEX_RECOMMENDED_NAME

static final String COMPLEX_RECOMMENDED_NAME

Constant COMPLEX_RECOMMENDED_NAME="complex recommended name"

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Constant Field Values

COMPLEX_RECOMMENDED_NAME_MI

static final String COMPLEX_RECOMMENDED_NAME_MI

Constant COMPLEX_RECOMMENDED_NAME_MI="MI:1315"

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Constant Field Values

COMPLEX_SYSTEMATIC_NAME

static final String COMPLEX_SYSTEMATIC_NAME

Constant COMPLEX_SYSTEMATIC_NAME="complex systematic name"

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Constant Field Values

COMPLEX_SYSTEMATIC_NAME_MI

static final String COMPLEX_SYSTEMATIC_NAME_MI

Constant COMPLEX_SYSTEMATIC_NAME_MI="MI:1316"

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Constant Field Values

Method Detail

getType

CvTerm getType()

The alias type is a controlled vocabulary term. The type can be null. Ex : gene name, gene synonym, locus name, ...

Returns:

the type of the current alias

getName

String getName()

Alias name cannot be null. Ex: TP53, BRCA2, ..

Returns:

the alias name.