Package org.forester.ws.seqdb

Class UniProtEntry

java.lang.Object

org.forester.ws.seqdb.UniProtEntry

All Implemented Interfaces:

SequenceDatabaseEntry

public final class UniProtEntry
extends java.lang.Object
implements SequenceDatabaseEntry

Field Summary

Fields

Modifier and Type	Field	Description
static java.util.regex.Pattern	BindingDB_PATTERN
static java.util.regex.Pattern	CTD_PATTERN
static java.util.regex.Pattern	DrugBank_PATTERN
static java.util.regex.Pattern	GO_PATTERN
static java.util.regex.Pattern	HGNC_PATTERN
static java.util.regex.Pattern	KEGG_PATTERN
static java.util.regex.Pattern	MIM_PATTERN
static java.util.regex.Pattern	NCBI_TAXID_PATTERN
static java.util.regex.Pattern	NextBio_PATTERN
static java.util.regex.Pattern	Orphanet_PATTERN
static java.util.regex.Pattern	PDB_PATTERN
static java.util.regex.Pattern	PharmGKB_PATTERN
static java.util.regex.Pattern	Reactome_PATTERN

Method Summary

Modifier and Type	Method	Description
java.lang.Object	clone()
static SequenceDatabaseEntry	createInstanceFromPlainText(java.util.List<java.lang.String> lines)
java.lang.String	getAccession()
java.util.SortedSet<Annotation>	getAnnotations()
java.lang.String	getChromosome()
java.util.SortedSet<Accession>	getCrossReferences()
java.lang.String	getGeneName()
java.util.SortedSet<GoTerm>	getGoTerms()
java.lang.String	getMap()
MolecularSequence	getMolecularSequence()
java.lang.String	getProvider()
java.lang.String	getSequenceName()
java.lang.String	getSequenceSymbol()
java.lang.String	getTaxonomyIdentifier()
java.lang.String	getTaxonomyScientificName()
boolean	isEmpty()

Methods inherited from class java.lang.Object

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

Field Detail

BindingDB_PATTERN

public static final java.util.regex.Pattern BindingDB_PATTERN

CTD_PATTERN

public static final java.util.regex.Pattern CTD_PATTERN

DrugBank_PATTERN

public static final java.util.regex.Pattern DrugBank_PATTERN

GO_PATTERN

public static final java.util.regex.Pattern GO_PATTERN

KEGG_PATTERN

public static final java.util.regex.Pattern KEGG_PATTERN

MIM_PATTERN

public static final java.util.regex.Pattern MIM_PATTERN

NextBio_PATTERN

public static final java.util.regex.Pattern NextBio_PATTERN

Orphanet_PATTERN

public static final java.util.regex.Pattern Orphanet_PATTERN

PDB_PATTERN

public static final java.util.regex.Pattern PDB_PATTERN

PharmGKB_PATTERN

public static final java.util.regex.Pattern PharmGKB_PATTERN

Reactome_PATTERN

public static final java.util.regex.Pattern Reactome_PATTERN

HGNC_PATTERN

public static final java.util.regex.Pattern HGNC_PATTERN

NCBI_TAXID_PATTERN

public static final java.util.regex.Pattern NCBI_TAXID_PATTERN

Method Detail

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

getAccession

public java.lang.String getAccession()

Specified by:

getAccession in interface SequenceDatabaseEntry

getCrossReferences

public java.util.SortedSet<Accession> getCrossReferences()

Specified by:

getCrossReferences in interface SequenceDatabaseEntry

getGeneName

public java.lang.String getGeneName()

Specified by:

getGeneName in interface SequenceDatabaseEntry

getGoTerms

public java.util.SortedSet<GoTerm> getGoTerms()

Specified by:

getGoTerms in interface SequenceDatabaseEntry

getProvider

public java.lang.String getProvider()

Specified by:

getProvider in interface SequenceDatabaseEntry

getSequenceName

public java.lang.String getSequenceName()

Specified by:

getSequenceName in interface SequenceDatabaseEntry

getSequenceSymbol

public java.lang.String getSequenceSymbol()

Specified by:

getSequenceSymbol in interface SequenceDatabaseEntry

getTaxonomyIdentifier

public java.lang.String getTaxonomyIdentifier()

Specified by:

getTaxonomyIdentifier in interface SequenceDatabaseEntry

getTaxonomyScientificName

public java.lang.String getTaxonomyScientificName()

Specified by:

getTaxonomyScientificName in interface SequenceDatabaseEntry

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface SequenceDatabaseEntry

createInstanceFromPlainText

public static SequenceDatabaseEntry createInstanceFromPlainText(java.util.List<java.lang.String> lines)

getAnnotations

public java.util.SortedSet<Annotation> getAnnotations()

Specified by:

getAnnotations in interface SequenceDatabaseEntry

getMap

public java.lang.String getMap()

Specified by:

getMap in interface SequenceDatabaseEntry

getChromosome

public java.lang.String getChromosome()

Specified by:

getChromosome in interface SequenceDatabaseEntry

getMolecularSequence

public MolecularSequence getMolecularSequence()

Specified by:

getMolecularSequence in interface SequenceDatabaseEntry