UniRefEntry (The Kraken Interfaces)

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uk.ac.ebi.kraken.interfaces.uniref
Interface UniRefEntry

All Superinterfaces:: Serializable

public interface UniRefEntry
extends Serializable
extends Serializable

Encapsulates the data found in all UniRef entries. These databases contain slightly different data items but their XML representation was unified recently so that all three share a common schema. So we have gone for a common object model

Method Summary
`List<UniRefMember>`	`getMembers()` Returns the members of this UniRefEntry.
`UniRefEntryName`	`getName()` Returns the name of this UniRefEntry.
`UniRefRepresentativeMember`	`getRepresentativeMember()` Returns the representative member of this UniRefEntry.
`UniRefDatabase`	`getUniRefDatabase()` Returns the UniRefDatabase.
`UniRefEntryId`	`getUniRefEntryId()` Returns the id of this UniRefEntry.
`Date`	`getUpdate()` Returns the last update of this UniRefEntry.
`void`	`setMembers(List<UniRefMember> members)` Sets the members of this UniRefEntry to a given list.
`void`	`setName(UniRefEntryName name)` Sets the name of this UniRefEntry to a given value.
`void`	`setRepresentativeMember(UniRefRepresentativeMember representativeMember)` Sets the representative representativeMember of this UniRefEntry to a given value.
`void`	`setUniRefDatabase(UniRefDatabase db)` Sets the UniRefDatabase.
`void`	`setUniRefEntryId(UniRefEntryId id)` Sets the id of this UniRefEntry to a given value.
`void`	`setUpdate(Date lastUpdate)` Sets the last update of this UniRefEntry to a given value.

Method Detail

getRepresentativeMember

UniRefRepresentativeMember getRepresentativeMember()

Returns the representative member of this UniRefEntry. This data item can be found at the following positions in the XML format of the entry:

 ...
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
   <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
     <property type="UniProtKB accession" value="P99999" />
     <property type="UniProtKB accession" value="P00001" />
     <property type="UniProtKB accession" value="Q6NUR2" />
     <property type="UniProtKB accession" value="Q6NX69" />
     <property type="UniProtKB accession" value="Q96BV4" />
     <property type="UniParc ID" value="UPI0000128BBF" />
     <property type="UniRef90 ID" value="UniRef90_P99999"/>
     <property type="UniRef50 ID" value="UniRef50_P99999"/>
     <property type="protein name" value="Cytochrome c" />
     <property type="NCBI taxonomy" value="9606" />
     <property type="source organism" value="Homo sapiens" />
     <property type="length" value="104" />
     <property type="overlap region" value="2-105" />
   </dbReference>
   <sequence length="104" checksum="D47C9B513DF1C5C2">
     GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWG
     EDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
   </sequence>
 </representativeMember>
 <member>
   <dbReference type="UniProtKB ID" id="Q5RFH4_PONPY" >
     <property type="UniProtKB accession" value="Q5RFH4" />
 ...

Returns:: The representative member of this UniRefEntry.

setRepresentativeMember

void setRepresentativeMember(UniRefRepresentativeMember representativeMember)

Sets the representative representativeMember of this UniRefEntry to a given value. This data item can be found at the following positions in the XML format of the entry:

 ...
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
   <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
     <property type="UniProtKB accession" value="P99999" />
     <property type="UniProtKB accession" value="P00001" />
     <property type="UniProtKB accession" value="Q6NUR2" />
     <property type="UniProtKB accession" value="Q6NX69" />
     <property type="UniProtKB accession" value="Q96BV4" />
     <property type="UniParc ID" value="UPI0000128BBF" />
     <property type="UniRef90 ID" value="UniRef90_P99999"/>
     <property type="UniRef50 ID" value="UniRef50_P99999"/>
     <property type="protein name" value="Cytochrome c" />
     <property type="NCBI taxonomy" value="9606" />
     <property type="source organism" value="Homo sapiens" />
     <property type="length" value="104" />
     <property type="overlap region" value="2-105" />
   </dbReference>
   <sequence length="104" checksum="D47C9B513DF1C5C2">
     GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWG
     EDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
   </sequence>
 </representativeMember>
 <representativeMember>
   <dbReference type="UniProtKB ID" id="Q5RFH4_PONPY" >
     <property type="UniProtKB accession" value="Q5RFH4" />
 ...

Parameters:: representativeMember - The representative representativeMember of this UniRefEntry.

getUniRefDatabase

UniRefDatabase getUniRefDatabase()

Returns the UniRefDatabase. This will give you info on what type UniRef100-50 also the version no and release date

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Returns:: The UniRefDatabase of this UniRefEntry.

setUniRefDatabase

void setUniRefDatabase(UniRefDatabase db)

Sets the UniRefDatabase. This will give you info on what type UniRef100-50 also the version no and release date

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

getUniRefEntryId

UniRefEntryId getUniRefEntryId()

Returns the id of this UniRefEntry. This data item can be found at the following positions in the XML format of the entry:

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Returns:: The id of this UniRefEntry.

setUniRefEntryId

void setUniRefEntryId(UniRefEntryId id)

Sets the id of this UniRefEntry to a given value. This data item can be found at the following positions in the XML format of the entry:

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Parameters:: id - The id of this UniRefEntry.

getUpdate

Date getUpdate()

Returns the last update of this UniRefEntry. This data item can be found at the following positions in the XML format of the entry:

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Returns:: The last update of this UniRefEntry.

setUpdate

void setUpdate(Date lastUpdate)

Sets the last update of this UniRefEntry to a given value. This data item can be found at the following positions in the XML format of the entry:

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Parameters:: lastUpdate - The last update of this UniRefEntry.

getName

UniRefEntryName getName()

Returns the name of this UniRefEntry. This data item can be found at the following positions in the XML format of the entry:

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Returns:: The name of this UniRefEntry.

setName

void setName(UniRefEntryName name)

Sets the name of this UniRefEntry to a given value. This data item can be found at the following positions in the XML format of the entry:

 <UniRef100 releaseDate="2005-06-30" version="45" xmlns="http://uniprot.org/uniref">
 <entry id="UniRef100_P99999" updated="2005-02-01">
 <name>Cytochrome c</name>
 <representativeMember>
 <dbReference type="UniProtKB ID" id="CYC_HUMAN" >
 <property type="UniProtKB accession" value="P99999" />
 ...

Parameters:: name - The name of this UniRefEntry.

getMembers

List<UniRefMember> getMembers()

Returns the members of this UniRefEntry. This data item can be found at the following positions in the XML format of the entry:

 ...
     </sequence>
   </representativeMember>
   <member>
     <dbReference type="UniProtKB ID" id="Q5RFH4_PONPY" >
       <property type="UniProtKB accession" value="Q5RFH4" />
       <property type="UniParc ID" value="UPI000013EAA0" />
       <property type="protein name" value="Hypothetical protein DKFZp468F1016" />
       <property type="NCBI taxonomy" value="9600" />
       <property type="source organism" value="Pongo pygmaeus" />
       <property type="length" value="105" />
       <property type="overlap region" value="1-105" />
     </dbReference>
   </member>
   <member>
     <dbReference type="UniProtKB ID" id="CYC_GORGO" >
       <property type="UniProtKB accession" value="Q6WUX8" />
       <property type="UniParc ID" value="UPI0000128BBF" />
       <property type="protein name" value="Cytochrome c" />
       <property type="NCBI taxonomy" value="9595" />
       <property type="source organism" value="Gorilla gorilla gorilla" />
       <property type="length" value="104" />
       <property type="overlap region" value="2-105" />
     </dbReference>
   </member>
 </entry>
 </UniRef100>

Returns:: The members of this UniRefEntry.

setMembers

void setMembers(List<UniRefMember> members)

Sets the members of this UniRefEntry to a given list. This data item can be found at the following positions in the XML format of the entry:

 ...
     </sequence>
   </representativeMember>
   <member>
     <dbReference type="UniProtKB ID" id="Q5RFH4_PONPY" >
       <property type="UniProtKB accession" value="Q5RFH4" />
       <property type="UniParc ID" value="UPI000013EAA0" />
       <property type="protein name" value="Hypothetical protein DKFZp468F1016" />
       <property type="NCBI taxonomy" value="9600" />
       <property type="source organism" value="Pongo pygmaeus" />
       <property type="length" value="105" />
       <property type="overlap region" value="1-105" />
     </dbReference>
   </member>
   <member>
     <dbReference type="UniProtKB ID" id="CYC_GORGO" >
       <property type="UniProtKB accession" value="Q6WUX8" />
       <property type="UniParc ID" value="UPI0000128BBF" />
       <property type="protein name" value="Cytochrome c" />
       <property type="NCBI taxonomy" value="9595" />
       <property type="source organism" value="Gorilla gorilla gorilla" />
       <property type="length" value="104" />
       <property type="overlap region" value="2-105" />
     </dbReference>
   </member>
 </entry>
 </UniRef100>

Parameters:: members - The members of this UniRefEntry.