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uk.ac.ebi.kraken.interfaces.uniprot
Interface UniProtEntry

All Superinterfaces:
Serializable
public interface UniProtEntry
extends Serializable

This is the Interface to the contents of a UniProt entry. It holds all the data of the UniProt flat files. Implementations of this data structure are returned and processed by all Kraken tools working with UniProt data.

Method Summary
 List<Citation> getCitations()
           
 List<Citation> getCitations(CitationTypeEnum type)
           
 Collection<Comment> getComments()
           
<T extends Comment>
List<T>
getComments(CommentType type)
           
 Collection<DatabaseCrossReference> getDatabaseCrossReferences()
          Returns the list of DatabaseCrossReferences annotated in the UniProtEntry.
<T extends DatabaseCrossReference>
List<T>
getDatabaseCrossReferences(DatabaseType type)
           
 Description getDescription()
          Deprecated. see getProteinDescription()
 EntryAudit getEntryAudit()
          Returns the Entry Audit Information.
 Evidence getEvidence(EvidenceId id)
          Numerous elements in the model could contain lists of evidenceId the evidence ids correspond to a item of evidence listed in the getEvidences()

This method is a convenience method to allow users to quickly access the relavent evidence information.
 List<Evidence> getEvidences()
          Returns the list of Evidences annotated in the UniProtEntry.
 List<Feature> getFeatures()
           
<T extends Feature>
Collection<T>
getFeatures(FeatureType type)
           
 List<Gene> getGenes()
          Returns the Genes in which this protein is encoded.
 List<Go> getGoTerms()
           
 InternalSection getInternalSection()
           
 List<Keyword> getKeywords()
          Returns the list of Keywords annotated in the UniProtEntry.
 List<NcbiTaxonomyId> getNcbiTaxonomyIds()
           
 List<Organelle> getOrganelles()
           
 Organism getOrganism()
          Returns the Organisms in which this protein is found.
 List<OrganismHost> getOrganismHosts()
          Returns the list of organism hosts.
 List<Organism> getOrganisms()
          Deprecated. 
 PrimaryUniProtAccession getPrimaryUniProtAccession()
          Returns the Primary UniProtAccessions of the UniProtEntry.
 ProteinDescription getProteinDescription()
           
 ProteinExistence getProteinExistence()
           
 List<SecondaryUniProtAccession> getSecondaryUniProtAccessions()
          Returns the list of UniProtAccessions of the UniProtEntry.
 Sequence getSequence()
          Returns the Sequence annotation in the UniProtEntry.
 String getSplicedSequence(String isoformName)
          Returns the actual sequence of the isoform that is passed in as a parameter.
 List<NcbiTaxon> getTaxonomy()
          Returns the taxonomy annotated in the UniProtEntry.
 UniProtEntryType getType()
          Returns the type of the UniProtEntry which is UniProtEntryType.SWISSPROT if the entry is annotated as STANDARD in the ID line and UniProtEntryType.TREMBL if it is annotated PRELIMINARY.
 UniParcEntry getUniParcEntry()
          Deprecated. 
 UniProtId getUniProtId()
          Returns the UniProtId of the UniProtEntry.
 boolean hasCitations()
           
 void setCitations(List<Citation> citation)
           
 void setComments(Collection<Comment> comments)
           
 void setDatabaseCrossReferences(List<DatabaseCrossReference> DatabaseCrossReferences)
          Sets the DatabaseCrossReference annotation of the UniProtEntry to a given list of DatabaseCrossReference values.
 void setDescription(Description description)
          Deprecated. see setProteinDescription()
 void setEntryAudit(EntryAudit entryAudit)
           
 void setEvidences(List<Evidence> evidences)
          Sets the Evidence annotation of the UniProtEntry to a given list of Evidences.
 void setFeatures(Collection<Feature> features)
           
 void setFeatures(List<Feature> features)
           
 void setGenes(List<Gene> genes)
          Sets the Genes in which this protein is encoded.
 void setInternalSection(InternalSection internalSection)
           
 void setKeywords(List<Keyword> keywords)
          Sets the Keyword annotation of the UniProtEntry to a given list of Keyword values.
 void setNcbiTaxonomyIds(List<NcbiTaxonomyId> id)
           
 void setOrganelles(List<Organelle> organelles)
           
 void setOrganism(Organism organism)
          Sets the Organisms in which this protein is found.
 void setOrganismHosts(List<OrganismHost> hosts)
          Sets the list of organism hosts.
 void setOrganisms(List<Organism> organisms)
          Deprecated. 
 void setPrimaryUniProtAccession(PrimaryUniProtAccession uniProtAccession)
           
 void setProteinDescription(ProteinDescription description)
           
 void setProteinExistence(ProteinExistence proteinExistence)
           
 void setSecondaryUniProtAccessions(List<SecondaryUniProtAccession> uniProtAccessions)
          Sets the UniProtAccessions of the UniProtEntry to a given list of UniProtAccession values.
 void setSequence(Sequence sequence)
          Sets the Sequence annotation in the UniProtEntry to a given value.
 void setTaxonomy(List<NcbiTaxon> taxonomy)
          Sets the taxonomy annotation of the UniProtEntry to a given list of Keyword values.
 void setType(UniProtEntryType type)
          Sets the type of the UniProtEntry which is UniProtEntryType.SWISSPROT if the entry is annotated as STANDARD in the ID line and UniProtEntryType.TREMBL if it is annotated PRELIMINARY.
 void setUniParcEntry(UniParcEntry uniParcEntry)
          Deprecated. 
 void setUniProtId(String uniProtIdStr)
           
 void setUniProtId(UniProtId uniProtId)
          Sets the UniProtId of the UniProtEntry to a given value.
 

Method Detail

getSplicedSequence

String getSplicedSequence(String isoformName)
Returns the actual sequence of the isoform that is passed in as a parameter. 

 CC   -!- ALTERNATIVE PRODUCTS:
 CC       Event=Alternative splicing; Named isoforms=6;
 CC       Name=1;
 CC         IsoId=Q9NQ94-1; Sequence=Displayed;
 CC       Name=2;
 CC         IsoId=Q9NQ94-2; Sequence=VSP_051929;
 CC         Note=Major isoform found in 66-78% of cDNA clones;
 CC       Name=3;
 CC         IsoId=Q9NQ94-3; Sequence=VSP_051926, VSP_051929;
 CC       Name=4;
 CC         IsoId=Q9NQ94-4; Sequence=VSP_051927, VSP_051929;
 CC         Note=Does not exhibit APOBEC1 complementation activity. Ref.4
 CC         sequence is in conflict in positions: 33:I->T. No experimental
 CC         confirmation available;
 CC       Name=5;
 CC         IsoId=Q9NQ94-5; Sequence=VSP_051925;
 CC         Note=Does not exhibit APOBEC1 complementation activity;
 CC       Name=6;
 CC         IsoId=Q9NQ94-6; Sequence=VSP_051928;
 CC         Note=Minor isoform found in 2-3% of cDNA clones;
 ...

therefore passing in "6" into this function will return the sequence assocated with VSP_051928

Parameters:
isoformName -
Returns:
the Sequenced of the named isoform or "" if name does not match

getEvidence

Evidence getEvidence(EvidenceId id)
Numerous elements in the model could contain lists of evidenceId the evidence ids correspond to a item of evidence listed in the getEvidences()

This method is a convenience method to allow users to quickly access the relavent evidence information.

Parameters:
id -
Returns:
the evidence matching the given id

getOrganismHosts

List<OrganismHost> getOrganismHosts()
Returns the list of organism hosts. This data item is optional and appears only in viral entries. It indicates the host organism(s) that are susceptible to be infected by a virus.

This value can be found in the OH line of the flat file on the marked position. 
 OC   Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae;
 OC   Hepatovirus.
 OX   NCBI_TaxID=31707;
 OH   NCBI_TaxID=9481; Callithrix.
 OH   NCBI_TaxID=9536; Cercopithecus hamlyni (Owl-faced monkey) (Hamlyn's monkey).
 OH   NCBI_TaxID=9539; Macaca (macaques).
 OH   NCBI_TaxID=9598; Pan troglodytes (Chimpanzee).
 RN   [1]
 ...

Returns:
The list of organism hosts.

setOrganismHosts

void setOrganismHosts(List<OrganismHost> hosts)
Sets the list of organism hosts. This data item is optional and appears only in viral entries. It indicates the host organism(s) that are susceptible to be infected by a virus.

This value can be found in the OH line of the flat file on the marked position. 
 OC   Viruses; ssRNA positive-strand viruses, no DNA stage; Picornaviridae;
 OC   Hepatovirus.
 OX   NCBI_TaxID=31707;
 OH   NCBI_TaxID=9481; Callithrix.
 OH   NCBI_TaxID=9536; Cercopithecus hamlyni (Owl-faced monkey) (Hamlyn's monkey).
 OH   NCBI_TaxID=9539; Macaca (macaques).
 OH   NCBI_TaxID=9598; Pan troglodytes (Chimpanzee).
 RN   [1]
 ...

Parameters:
hosts - The list of organism hosts.

setType

void setType(UniProtEntryType type)
Sets the type of the UniProtEntry which is UniProtEntryType.SWISSPROT if the entry is annotated as STANDARD in the ID line and UniProtEntryType.TREMBL if it is annotated PRELIMINARY.

This value can be found in the ID line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Parameters:
type - The type of the UniProtEntry.

getType

UniProtEntryType getType()
Returns the type of the UniProtEntry which is UniProtEntryType.SWISSPROT if the entry is annotated as STANDARD in the ID line and UniProtEntryType.TREMBL if it is annotated PRELIMINARY.

This value can be found in the ID line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Returns:
The type of the UniProtEntry.

getUniProtId

UniProtId getUniProtId()
Returns the UniProtId of the UniProtEntry.

This value can be found in the ID line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Returns:
The UniProtId of the UniProtEntry.

setUniProtId

void setUniProtId(UniProtId uniProtId)
Sets the UniProtId of the UniProtEntry to a given value.

This value can be found in the ID line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Parameters:
uniProtId - The UniProtId of the UniProtEntry.

setUniProtId

void setUniProtId(String uniProtIdStr)

getSecondaryUniProtAccessions

List<SecondaryUniProtAccession> getSecondaryUniProtAccessions()
Returns the list of UniProtAccessions of the UniProtEntry.

These values can be found in the AC line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Returns:
All UniProtAccessions of the UniProtEntry.

getPrimaryUniProtAccession

PrimaryUniProtAccession getPrimaryUniProtAccession()
Returns the Primary UniProtAccessions of the UniProtEntry.

This value can be found in first elements in the AC line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Returns:
All UniProtAccessions of the UniProtEntry.

setSecondaryUniProtAccessions

void setSecondaryUniProtAccessions(List<SecondaryUniProtAccession> uniProtAccessions)
Sets the UniProtAccessions of the UniProtEntry to a given list of UniProtAccession values.

This value can be found in the AC line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...
In XML: 
 <entry dataset="Swiss-Prot" created="1986-07-21" modified="2005-02-01">
 <accession>P99999</accession>
 <accession>P00001</accession>
 <accession>Q6NUR2</accession>
 <accession>Q6NX69</accession>
 <accession>Q96BV4</accession>
 <name>CYC_HUMAN</name>
 <protein>
 <name>Cytochrome c</name>
 </protein>
 ...
 </entry>

Parameters:
uniProtAccessions - The UniProtAccessions of the UniProtEntry.

setPrimaryUniProtAccession

void setPrimaryUniProtAccession(PrimaryUniProtAccession uniProtAccession)

getEntryAudit

EntryAudit getEntryAudit()
Returns the Entry Audit Information.

These values can be found in the DT line of the flat file on the marked position. 
 ID   CYC_HUMAN      STANDARD;      PRT;   104 AA.
 AC   P99999; P00001; Q6NUR2; Q6NX69; Q96BV4;
 DT   21-JUL-1986 (Rel. 01, Created)
 DT   21-JUL-1986 (Rel. 01, Last sequence update)
 DT   01-FEB-2005 (Rel. 46, Last annotation update)
 DE   Cytochrome c.
 ...

Returns:
The EntryAudit of the UniProtEntry.

setEntryAudit

void setEntryAudit(EntryAudit entryAudit)

getKeywords

List<Keyword> getKeywords()
Returns the list of Keywords annotated in the UniProtEntry.

These values can be found in the KW line of the flat file on the marked position. 
 DR   ProDom; PD000375; Cyt_CIAB; 1.
 DR   PROSITE; PS51007; CYTC; 1.
 KW   Acetylation; Apoptosis; Direct protein sequencing; Electron transport;
 KW   Heme; Mitochondrion; Polymorphism; Respiratory chain.
 FT   INIT_MET      0      0
 FT   MOD_RES       1      1       N-acetylglycine.
 ...
In XML: 
 ...
 <dbReference type="PROSITE" id="PS51007" key="69">
 <property type="entry name" value="CYTC"/>
 <property type="match status" value="1"/>
 </dbReference>
 <keyword id="KW-0007">Acetylation</keyword>
 <keyword id="KW-0053">Apoptosis</keyword>
 <keyword id="KW-0903">Direct protein sequencing</keyword>
 <keyword id="KW-0249">Electron transport</keyword>
 <keyword id="KW-0349">Heme</keyword>
 <keyword id="KW-0496">Mitochondrion</keyword>
 <keyword id="KW-0621">Polymorphism</keyword>
 <keyword id="KW-0679">Respiratory chain</keyword>
 <feature type="initiator methionine">
 <location>
 <position position="0"/>
 </location>
 </feature>
 ...

Returns:
The Keyword annotation of the UniProtEntry.

setKeywords

void setKeywords(List<Keyword> keywords)
Sets the Keyword annotation of the UniProtEntry to a given list of Keyword values.

These values can be found in the KW line of the flat file on the marked position. 
 DR   ProDom; PD000375; Cyt_CIAB; 1.
 DR   PROSITE; PS51007; CYTC; 1.
 KW   Acetylation; Apoptosis; Direct protein sequencing; Electron transport;
 KW   Heme; Mitochondrion; Polymorphism; Respiratory chain.
 FT   INIT_MET      0      0
 FT   MOD_RES       1      1       N-acetylglycine.
 ...
In XML: 
 ...
 <dbReference type="PROSITE" id="PS51007" key="69">
 <property type="entry name" value="CYTC"/>
 <property type="match status" value="1"/>
 </dbReference>
 <keyword id="KW-0007">Acetylation</keyword>
 <keyword id="KW-0053">Apoptosis</keyword>
 <keyword id="KW-0903">Direct protein sequencing</keyword>
 <keyword id="KW-0249">Electron transport</keyword>
 <keyword id="KW-0349">Heme</keyword>
 <keyword id="KW-0496">Mitochondrion</keyword>
 <keyword id="KW-0621">Polymorphism</keyword>
 <keyword id="KW-0679">Respiratory chain</keyword>
 <feature type="initiator methionine">
 <location>
 <position position="0"/>
 </location>
 </feature>
 ...

Parameters:
keywords - The Keyword annotation of the UniProtEntry.

getTaxonomy

List<NcbiTaxon> getTaxonomy()
Returns the taxonomy annotated in the UniProtEntry.

These values can be found in the OC line of the flat file on the marked position. 
 ...
 OS   Serratia marcescens.
 OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
 OC   Enterobacteriaceae; Serratia.
 OX   NCBI_TaxID=615;
 ...
In XML: 
 ...
 <organism key="2">
 <name type="scientific">Serratia marcescens</name>
 <dbReference type="NCBI Taxonomy" id="615" key="3"/>
 <lineage>
 <taxon>Bacteria</taxon>
 <taxon>Proteobacteria</taxon>
 <taxon>Gammaproteobacteria</taxon>
 <taxon>Enterobacteriales</taxon>
 <taxon>Enterobacteriaceae</taxon>
 <taxon>Serratia</taxon>
 </lineage>
 </organism>
 ...

Returns:
The Taxonomy of the UniProtEntry.

setTaxonomy

void setTaxonomy(List<NcbiTaxon> taxonomy)
Sets the taxonomy annotation of the UniProtEntry to a given list of Keyword values.

These values can be found in the OC line of the flat file on the marked position. 
 ...
 OS   Serratia marcescens.
 OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
 OC   Enterobacteriaceae; Serratia.
 OX   NCBI_TaxID=615;
 ...
In XML: 
 ...
 <organism key="2">
 <name type="scientific">Serratia marcescens</name>
 <dbReference type="NCBI Taxonomy" id="615" key="3"/>
 <lineage>
 <taxon>Bacteria</taxon>
 <taxon>Proteobacteria</taxon>
 <taxon>Gammaproteobacteria</taxon>
 <taxon>Enterobacteriales</taxon>
 <taxon>Enterobacteriaceae</taxon>
 <taxon>Serratia</taxon>
 </lineage>
 </organism>
 ...

Parameters:
taxonomy - The taxonomy of the UniProtEntry.

getSequence

Sequence getSequence()
Returns the Sequence annotation in the UniProtEntry.

These values can be found in the SQ line of the flat file on the marked position. 
 ...
 FT   CONFLICT     40     40       T -> I (in Ref. 7; AAH68464).
 SQ   SEQUENCE   104 AA;  11618 MW;  D47C9B513DF1C5C2 CRC64;
 GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG
 EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE
 //
 ...
In XML: 
 ...
 </feature>
 <sequence length="104" mass="11618" checksum="D47C9B513DF1C5C2" modified="1986-07-21">
 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTA
 ANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK
 ATNE
 </sequence>
 </entry>
 ...

Returns:
The Sequence of the UniProtEntry.

setSequence

void setSequence(Sequence sequence)
Sets the Sequence annotation in the UniProtEntry to a given value.

These values can be found in the SQ line of the flat file on the marked position. 
 ...
 FT   CONFLICT     40     40       T -> I (in Ref. 7; AAH68464).
 SQ   SEQUENCE   104 AA;  11618 MW;  D47C9B513DF1C5C2 CRC64;
 GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG
 EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE
 //
 ...
In XML: 
 ...
 </feature>
 <sequence length="104" mass="11618" checksum="D47C9B513DF1C5C2" modified="1986-07-21">
 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTA
 ANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK
 ATNE
 </sequence>
 </entry>
 ...

Parameters:
sequence - The new Sequence of the UniProtEntry.

getComments

Collection<Comment> getComments()
Returns:
Modifiable Collection of comments.

setComments

void setComments(Collection<Comment> comments)

getComments

<T extends Comment> List<T> getComments(CommentType type)

getDatabaseCrossReferences

Collection<DatabaseCrossReference> getDatabaseCrossReferences()
Returns the list of DatabaseCrossReferences annotated in the UniProtEntry.

These values can be found in the DR lines of the flat file on the marked position. 
 ...
 CC   -!- SIMILARITY: Belongs to the cytochrome c family.
 DR   EMBL; M22877; AAA35732.1; -.
 DR   PROSITE; PS51007; CYTC; 1.
 KW   Acetylation; Apoptosis; Direct protein sequencing; Electron transport;
 ...
In XML: 
 ...
 <comment type="similarity">
 <text>Belongs to the cytochrome c family</text>
 </comment>
 <dbReference type="EMBL" id="M22877" key="24">
   <property type="protein sequence ID" value="AAA35732.1"/>
 </dbReference>
 <dbReference type="PROSITE" id="PS51007" key="69">
   <property type="entry name" value="CYTC"/>
   <property type="match status" value="1"/>
 </dbReference>
 <keyword id="KW-0007">Acetylation</keyword>
 <keyword id="KW-0053">Apoptosis</keyword>
 ...

Returns:
The DatabaseCrossReferences annotation of the UniProtEntry.

setDatabaseCrossReferences

void setDatabaseCrossReferences(List<DatabaseCrossReference> DatabaseCrossReferences)
Sets the DatabaseCrossReference annotation of the UniProtEntry to a given list of DatabaseCrossReference values.

These values can be found in the DR lines of the flat file on the marked position. 
 ...
 CC   -!- SIMILARITY: Belongs to the cytochrome c family.
 DR   EMBL; M22877; AAA35732.1; -.
 DR   PROSITE; PS51007; CYTC; 1.
 KW   Acetylation; Apoptosis; Direct protein sequencing; Electron transport;
 ...
In XML: 
 ...
 <comment type="similarity">
 <text>Belongs to the cytochrome c family</text>
 </comment>
 <dbReference type="EMBL" id="M22877" key="24">
   <property type="protein sequence ID" value="AAA35732.1"/>
 </dbReference>
 <dbReference type="PROSITE" id="PS51007" key="69">
   <property type="entry name" value="CYTC"/>
   <property type="match status" value="1"/>
 </dbReference>
 <keyword id="KW-0007">Acetylation</keyword>
 <keyword id="KW-0053">Apoptosis</keyword>
 ...

Parameters:
DatabaseCrossReferences - The DatabaseCrossReferences annotation of the UniProtEntry.

getDatabaseCrossReferences

<T extends DatabaseCrossReference> List<T> getDatabaseCrossReferences(DatabaseType type)

getGoTerms

List<Go> getGoTerms()

getEvidences

List<Evidence> getEvidences()
Returns the list of Evidences annotated in the UniProtEntry.

These values can be found in the **EV lines of the flat file on the marked position. 
 ...
 DR   EMBL; U93082; AAB51527.1; -.{EI1}
 KW   Plasmid{EP2}.
 **
 **   #################    INTERNAL SECTION    ############
 **EV EI1; EMBL; -; AAB51527.1; 02-APR-2004.
 **EV EP2; TrEMBL; -; AAB51527.1; 02-APR-2004.
 SQ   SEQUENCE   67 AA;  8012 MW;  57098438650D14B1 CRC64;
 ...
In XML: 
 ...
 <keyword id="KW-0614" evidence="EP2">Plasmid</keyword>
 <evidence category="import" type="EMBL" attribute="AAB51527.1" date="2004-04-02" key="EI1"/>
 <evidence category="program" type="TrEMBL" attribute="AAB51527.1" date="2004-04-02" key="EP2"/>
 <sequence length="67" mass="8012" checksum="57098438650D14B1" modified="1997-07-01">
 ...

setEvidences

void setEvidences(List<Evidence> evidences)
Sets the Evidence annotation of the UniProtEntry to a given list of Evidences.

These values can be found in the **EV lines of the flat file on the marked position. 
 ...
 DR   EMBL; U93082; AAB51527.1; -.{EI1}
 KW   Plasmid{EP2}.
 **
 **   #################    INTERNAL SECTION    ############
 **EV EI1; EMBL; -; AAB51527.1; 02-APR-2004.
 **EV EP2; TrEMBL; -; AAB51527.1; 02-APR-2004.
 SQ   SEQUENCE   67 AA;  8012 MW;  57098438650D14B1 CRC64;
 ...
In XML: 
 ...
 <keyword id="KW-0614" evidence="EP2">Plasmid</keyword>
 <evidence category="import" type="EMBL" attribute="AAB51527.1" date="2004-04-02" key="EI1"/>
 <evidence category="program" type="TrEMBL" attribute="AAB51527.1" date="2004-04-02" key="EP2"/>
 <sequence length="67" mass="8012" checksum="57098438650D14B1" modified="1997-07-01">
 ...

getUniParcEntry

@Deprecated
UniParcEntry getUniParcEntry()
Deprecated. 

The UniProt object is nolonger linked to UniParc this is now available via the ProteinData

Returns:

setUniParcEntry

@Deprecated
void setUniParcEntry(UniParcEntry uniParcEntry)
Deprecated. 

The UniProt object is nolonger linked to UniParc this is now available via the ProteinData

Parameters:
uniParcEntry -

getFeatures

List<Feature> getFeatures()

setFeatures

void setFeatures(Collection<Feature> features)

setFeatures

void setFeatures(List<Feature> features)

getFeatures

<T extends Feature> Collection<T> getFeatures(FeatureType type)

setDescription

@Deprecated
void setDescription(Description description)
Deprecated. see setProteinDescription()

Parameters:
description -

getDescription

@Deprecated
Description getDescription()
Deprecated. see getProteinDescription()

setProteinDescription

void setProteinDescription(ProteinDescription description)

getProteinDescription

ProteinDescription getProteinDescription()

setNcbiTaxonomyIds

void setNcbiTaxonomyIds(List<NcbiTaxonomyId> id)

getNcbiTaxonomyIds

List<NcbiTaxonomyId> getNcbiTaxonomyIds()

setGenes

void setGenes(List<Gene> genes)
Sets the Genes in which this protein is encoded.

This value can be found in the GN line of the flat file on the marked position. 
 DE   Serine proteases 1/2 precursor (EC 3.4.21.-) (Protein Jonah
 DE   99Cii/99Ciii).
 GN   Name=Jon99Cii; Synonyms=SER1, SER5, Ser99Da; ORFNames=CG7877;
 GN   and
 GN   Name=Jon99Ciii; Synonyms=SER2, SER5, Ser99Db; ORFNames=CG15519;
 OS   Drosophila melanogaster (Fruit fly).
 ...

Parameters:
genes - the List of Genes in which this protein is found.

getGenes

List<Gene> getGenes()
Returns the Genes in which this protein is encoded.

This value can be found in the GN line of the flat file on the marked position. 
 DE   Serine proteases 1/2 precursor (EC 3.4.21.-) (Protein Jonah
 DE   99Cii/99Ciii).
 GN   Name=Jon99Cii; Synonyms=SER1, SER5, Ser99Da; ORFNames=CG7877;
 GN   and
 GN   Name=Jon99Ciii; Synonyms=SER2, SER5, Ser99Db; ORFNames=CG15519;
 OS   Drosophila melanogaster (Fruit fly).
 ...

Returns:
the List of Genes in which this protein is found.

setOrganisms

@Deprecated
void setOrganisms(List<Organism> organisms)
Deprecated. 

Sets the Organisms in which this protein is found. In recent UniProt Versions only one Organism is used. For backward compatibility a List of Organisms is still supported through this interface.

This value can be found in the OS line of the flat file on the marked position. 
 GN   Name=CYP71A2; Synonyms=CYPEG4;
 OS   Solanum melongena (Eggplant) (Aubergine).
 OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
 OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
 OC   asterids; lamiids; Solanales; Solanaceae; Solanum.
 ...

Parameters:
organisms - the List of Organisms in which this protein is found.

getOrganisms

@Deprecated
List<Organism> getOrganisms()
Deprecated. 

Returns the Organisms in which this protein is found. In recent UniProt Versions only one Organism is used. For backward compatibility a List of Organisms is still supported through this interface.

This value can be found in the OS line of the flat file on the marked position. 
 GN   Name=CYP71A2; Synonyms=CYPEG4;
 OS   Solanum melongena (Eggplant) (Aubergine).
 OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
 OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
 OC   asterids; lamiids; Solanales; Solanaceae; Solanum.
 ...

Returns:
the List of Organisms in which this protein is found.

setOrganism

void setOrganism(Organism organism)
Sets the Organisms in which this protein is found. In recent UniProt Versions only one Organism is used. For backward compatibility a List of Organisms is still supported through this interface.

This value can be found in the OS line of the flat file on the marked position. 
 GN   Name=CYP71A2; Synonyms=CYPEG4;
 OS   Solanum melongena (Eggplant) (Aubergine).
 OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
 OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
 OC   asterids; lamiids; Solanales; Solanaceae; Solanum.
 ...

Parameters:
organism - the List of Organisms in which this protein is found.

getOrganism

Organism getOrganism()
Returns the Organisms in which this protein is found. In recent UniProt Versions only one Organism is used. For backward compatibility a List of Organisms is still supported through this interface.

This value can be found in the OS line of the flat file on the marked position. 
 GN   Name=CYP71A2; Synonyms=CYPEG4;
 OS   Solanum melongena (Eggplant) (Aubergine).
 OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
 OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
 OC   asterids; lamiids; Solanales; Solanaceae; Solanum.
 ...

Returns:
the List of Organisms in which this protein is found.

getOrganelles

List<Organelle> getOrganelles()

setOrganelles

void setOrganelles(List<Organelle> organelles)

hasCitations

boolean hasCitations()

getCitations

List<Citation> getCitations()

getCitations

List<Citation> getCitations(CitationTypeEnum type)

setCitations

void setCitations(List<Citation> citation)

setInternalSection

void setInternalSection(InternalSection internalSection)

getInternalSection

InternalSection getInternalSection()

getProteinExistence

ProteinExistence getProteinExistence()

setProteinExistence

void setProteinExistence(ProteinExistence proteinExistence)
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