org.biojava.nbio.core.sequence.loader

Class UniprotProxySequenceReader<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader<C>

Type Parameters:

C -

All Implemented Interfaces:

Iterable<C>, DatabaseReferenceInterface, FeaturesKeyWordInterface, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

public class UniprotProxySequenceReader<C extends Compound>
extends Object
implements ProxySequenceReader<C>, FeaturesKeyWordInterface, DatabaseReferenceInterface

Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot. This is an example of how to map external databases of proteins and features to the BioJava3 ProteinSequence. Important to call @see setUniprotDirectoryCache to allow caching of XML files so they don't need to be reloaded each time. Does not manage cache.

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_UNIPROT_BASE_URL
static Pattern	UP_AC_PATTERN

Constructor Summary

Constructors

Constructor and Description
UniprotProxySequenceReader(Document document, CompoundSet<C> compoundSet) The xml is passed in as a DOM object so we know everything about the protein.
UniprotProxySequenceReader(String accession, CompoundSet<C> compoundSet) The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object so we know everything about the protein.

Method Summary

Modifier and Type	Method and Description
int	countCompounds(C... compounds) Returns the number of times we found a compound in the Sequence
boolean	equals(Object o)
AccessionID	getAccession() Returns the AccessionID this location is currently bound with
ArrayList<AccessionID>	getAccessions() Pull uniprot accessions associated with this sequence
ArrayList<String>	getAliases() Pull uniprot protein aliases associated with this sequence Provided for backwards compatibility now that we support both gene and protein aliases via separate methods.
List<C>	getAsList() Returns the Sequence as a List of compounds
C	getCompoundAt(int position) Returns the Compound at the given biological index
CompoundSet<C>	getCompoundSet() Gets the compound set used to back this Sequence
LinkedHashMap<String,ArrayList<DBReferenceInfo>>	getDatabaseReferences() The Uniprot mappings to other database identifiers for this sequence
ArrayList<String>	getGeneAliases() Pull uniprot gene aliases associated with this sequence
String	getGeneName() Get the gene name associated with this sequence.
int	getIndexOf(C compound) Scans through the Sequence looking for the first occurrence of the given compound
SequenceView<C>	getInverse() Does the right thing to get the inverse of the current Sequence.
ArrayList<String>	getKeyWords() Pull UniProt key words which is a mixed bag of words associated with this sequence
int	getLastIndexOf(C compound) Scans through the Sequence looking for the last occurrence of the given compound
int	getLength() The sequence length
String	getOrganismName() Get the organism name assigned to this sequence
ArrayList<String>	getProteinAliases() Pull uniprot protein aliases associated with this sequence
String	getSequenceAsString() Returns the String representation of the Sequence
String	getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)
SequenceView<C>	getSubSequence(Integer bioBegin, Integer bioEnd) Returns a portion of the sequence from the different positions.
static String	getUniprotbaseURL() The current UniProt URL to deal with caching issues. www.uniprot.org is load balanced but you can access pir.uniprot.org directly.
static String	getUniprotDirectoryCache() Local directory cache of XML that can be downloaded
int	hashCode()
Iterator<C>	iterator()
static void	main(String[] args)
static <C extends Compound> UniprotProxySequenceReader<C>	parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) The passed in xml is parsed as a DOM object so we know everything about the protein.
void	setCompoundSet(CompoundSet<C> compoundSet)
void	setContents(String sequence) Once the sequence is retrieved set the contents and make sure everything this is valid Some uniprot records contain white space in the sequence.
static void	setUniprotbaseURL(String aUniprotbaseURL)
static void	setUniprotDirectoryCache(String aUniprotDirectoryCache)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

UP_AC_PATTERN

public static final Pattern UP_AC_PATTERN

DEFAULT_UNIPROT_BASE_URL

public static final String DEFAULT_UNIPROT_BASE_URL

See Also:

Constant Field Values

Constructor Detail

UniprotProxySequenceReader

public UniprotProxySequenceReader(String accession,
                                  CompoundSet<C> compoundSet)
                           throws CompoundNotFoundException,
                                  IOException

The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object so we know everything about the protein. If an error occurs throw an exception. We could have a bad uniprot id or network error

Parameters:

accession -

compoundSet -

Throws:

CompoundNotFoundException

IOException - if problems while reading the UniProt XML

UniprotProxySequenceReader

public UniprotProxySequenceReader(Document document,
                                  CompoundSet<C> compoundSet)
                           throws CompoundNotFoundException

The xml is passed in as a DOM object so we know everything about the protein. If an error occurs throw an exception. We could have a bad uniprot id

Parameters:

document -

compoundSet -

Throws:

CompoundNotFoundException

Method Detail

parseUniprotXMLString

public static <C extends Compound> UniprotProxySequenceReader<C> parseUniprotXMLString(String xml,
                                                                                       CompoundSet<C> compoundSet)

The passed in xml is parsed as a DOM object so we know everything about the protein. If an error occurs throw an exception. We could have a bad uniprot id

Parameters:

xml -

compoundSet -

Returns:

UniprotProxySequenceReader

Throws:

Exception

setCompoundSet

public void setCompoundSet(CompoundSet<C> compoundSet)

Specified by:

setCompoundSet in interface SequenceReader<C extends Compound>

setContents

public void setContents(String sequence)
                 throws CompoundNotFoundException

Once the sequence is retrieved set the contents and make sure everything this is valid Some uniprot records contain white space in the sequence. We must strip it out so setContents doesn't fail.

Specified by:

setContents in interface SequenceReader<C extends Compound>

Parameters:

sequence -

Throws:

CompoundNotFoundException

getLength

public int getLength()

The sequence length

Specified by:

getLength in interface Sequence<C extends Compound>

Returns:

getCompoundAt

public C getCompoundAt(int position)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<C extends Compound>

Parameters:

position -

Returns:

getIndexOf

public int getIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the first occurrence of the given compound

Specified by:

getIndexOf in interface Sequence<C extends Compound>

Parameters:

compound -

Returns:

getLastIndexOf

public int getLastIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the last occurrence of the given compound

Specified by:

getLastIndexOf in interface Sequence<C extends Compound>

Parameters:

compound -

Returns:

toString

public String toString()

Overrides:

toString in class Object

Returns:

getSequenceAsString

public String getSequenceAsString()

Description copied from interface: Sequence

Returns the String representation of the Sequence

Specified by:

getSequenceAsString in interface Sequence<C extends Compound>

Returns:

getAsList

public List<C> getAsList()

Description copied from interface: Sequence

Returns the Sequence as a List of compounds

Specified by:

getAsList in interface Sequence<C extends Compound>

Returns:

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getInverse

public SequenceView<C> getInverse()

Description copied from interface: Sequence

Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.

Specified by:

getInverse in interface Sequence<C extends Compound>

Returns:

getSequenceAsString

public String getSequenceAsString(Integer bioBegin,
                                  Integer bioEnd,
                                  Strand strand)

Parameters:

bioBegin -

bioEnd -

strand -

Returns:

getSubSequence

public SequenceView<C> getSubSequence(Integer bioBegin,
                                      Integer bioEnd)

Description copied from interface: Sequence

Returns a portion of the sequence from the different positions. This is indexed from 1

Specified by:

getSubSequence in interface Sequence<C extends Compound>

Parameters:

bioBegin -

bioEnd -

Returns:

iterator

public Iterator<C> iterator()

Specified by:

iterator in interface Iterable<C extends Compound>

Returns:

getCompoundSet

public CompoundSet<C> getCompoundSet()

Description copied from interface: Sequence

Gets the compound set used to back this Sequence

Specified by:

getCompoundSet in interface Sequence<C extends Compound>

Returns:

getAccession

public AccessionID getAccession()

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

Returns:

getAccessions

public ArrayList<AccessionID> getAccessions()
                                     throws XPathExpressionException

Pull uniprot accessions associated with this sequence

Returns:

Throws:

XPathExpressionException

getAliases

public ArrayList<String> getAliases()
                             throws XPathExpressionException

Pull uniprot protein aliases associated with this sequence Provided for backwards compatibility now that we support both gene and protein aliases via separate methods.

Returns:

Throws:

XPathExpressionException

getProteinAliases

public ArrayList<String> getProteinAliases()
                                    throws XPathExpressionException

Pull uniprot protein aliases associated with this sequence

Returns:

Throws:

XPathExpressionException

getGeneAliases

public ArrayList<String> getGeneAliases()
                                 throws XPathExpressionException

Pull uniprot gene aliases associated with this sequence

Returns:

Throws:

XPathExpressionException

countCompounds

public int countCompounds(C... compounds)

Description copied from interface: Sequence

Returns the number of times we found a compound in the Sequence

Specified by:

countCompounds in interface Sequence<C extends Compound>

Parameters:

compounds -

Returns:

getUniprotbaseURL

public static String getUniprotbaseURL()

The current UniProt URL to deal with caching issues. www.uniprot.org is load balanced but you can access pir.uniprot.org directly.

Returns:

the uniprotbaseURL

setUniprotbaseURL

public static void setUniprotbaseURL(String aUniprotbaseURL)

Parameters:

aUniprotbaseURL - the uniprotbaseURL to set

getUniprotDirectoryCache

public static String getUniprotDirectoryCache()

Local directory cache of XML that can be downloaded

Returns:

the uniprotDirectoryCache

setUniprotDirectoryCache

public static void setUniprotDirectoryCache(String aUniprotDirectoryCache)

Parameters:

aUniprotDirectoryCache - the uniprotDirectoryCache to set

main

public static void main(String[] args)

getGeneName

public String getGeneName()

Get the gene name associated with this sequence.

Returns:

getOrganismName

public String getOrganismName()

Get the organism name assigned to this sequence

Returns:

getKeyWords

public ArrayList<String> getKeyWords()

Pull UniProt key words which is a mixed bag of words associated with this sequence

Specified by:

getKeyWords in interface FeaturesKeyWordInterface

Returns:

getDatabaseReferences

public LinkedHashMap<String,ArrayList<DBReferenceInfo>> getDatabaseReferences()

The Uniprot mappings to other database identifiers for this sequence

Specified by:

getDatabaseReferences in interface DatabaseReferenceInterface

Returns: