Package ubic.gemma.core.loader.util.biomart

Class BiomartEnsembleNcbiParser

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineMapParser<String,Ensembl2NcbiValueObject>

ubic.gemma.core.loader.util.parser.LineMapParser<String,Ensembl2NcbiValueObject>

ubic.gemma.core.loader.util.biomart.BiomartEnsembleNcbiParser

All Implemented Interfaces:

LineParser<Ensembl2NcbiValueObject>, Parser<Ensembl2NcbiValueObject>

public class BiomartEnsembleNcbiParser
extends LineMapParser<String,Ensembl2NcbiValueObject>

Parser for BioMart file. The taxon and the attributes in the file are essential for construction so that the parser is configured to parse the file in the correct fashion for the taxon. The biomart file is taxon spefic which means that the file is generated from bioamrt after providing taxon as a query parameter. It is of the gemma type LineMapParser which means that after parsing a Map of BioMartEnsembleNcbi value objects are returned keyed on ensembl peptide id. Parsing is triggered by calling super class method parse which then calls child method parse oneline.

Author:

ldonnison

Field Summary

Fields inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser

COMMENT_MARK, log

Fields inherited from interface ubic.gemma.core.loader.util.parser.LineParser

MIN_PARSED_LINES_FOR_UPDATE, PARSE_ALERT_TIME_FREQUENCY_MS

Fields inherited from interface ubic.gemma.core.loader.util.parser.Parser

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
BiomartEnsembleNcbiParser(Taxon taxon, String[] attributesInFile)	Class needs to be initialised with taxon and which attributes have been used in query for biomart and thus what columns are in this file.

Method Summary

Modifier and Type	Method	Description
boolean	containsKey(String key)	Method that returns a particular BioMartEnsembleNcbi based on a peptide id.
Ensembl2NcbiValueObject	createBioMartEnsembleNcbi(String[] fields)	Given an array of strings representing the line to parse then create a BioMartEnsembleNcbi value object with some validation.
Ensembl2NcbiValueObject	get(String key)	Method that returns a particular BioMartEnsembleNcbi based on a peptide id.
String[]	getBioMartFields()
int	getBioMartFieldsPerRow()	Based on what attributes were set on the original file then calculate how many columns should be in file.
Collection<String>	getKeySet()	Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file
Map<String,Ensembl2NcbiValueObject>	getMap()
Collection<Ensembl2NcbiValueObject>	getResults()	Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file
Ensembl2NcbiValueObject	parseOneLine(String line)	Method to parse one biomart line, note that there is a many to many relationship between ensemble ids and entrez gene ids.
void	setBioMartFields(String[] bioMartFields)
void	setTaxon(Taxon taxon)

Methods inherited from class ubic.gemma.core.loader.util.parser.LineMapParser

getKey, parse, put

Methods inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser

parse, parse

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.util.parser.Parser

getUniqueResult

Constructor Details

BiomartEnsembleNcbiParser

public BiomartEnsembleNcbiParser(Taxon taxon,
 String[] attributesInFile)

Class needs to be initialised with taxon and which attributes have been used in query for biomart and thus what columns are in this file.

Parameters:

taxon - Taxon for the current file being processed

attributesInFile - The attributes that were queried for in Biomart

Method Details

containsKey

public boolean containsKey(String key)

Method that returns a particular BioMartEnsembleNcbi based on a peptide id.

Specified by:

containsKey in class BasicLineMapParser<String,Ensembl2NcbiValueObject>

Returns:

boolean to indicate whether map contains particular peptide key.

get

public Ensembl2NcbiValueObject get(String key)

Method that returns a particular BioMartEnsembleNcbi based on a peptide id.

Specified by:

get in class BasicLineMapParser<String,Ensembl2NcbiValueObject>

Returns:

BioMartEnsembleNcbi associated with that peptide id.

getKeySet

public Collection<String> getKeySet()

Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file

Specified by:

getKeySet in class BasicLineMapParser<String,Ensembl2NcbiValueObject>

Returns:

Collection of Strings representing the peptide ids in the map

getResults

public Collection<Ensembl2NcbiValueObject> getResults()

Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file

Specified by:

getResults in interface Parser<Ensembl2NcbiValueObject>

Specified by:

getResults in class BasicLineMapParser<String,Ensembl2NcbiValueObject>

Returns:

Collection of BioMartEnsembleNcbi value objects

parseOneLine

public Ensembl2NcbiValueObject parseOneLine(String line)

Method to parse one biomart line, note that there is a many to many relationship between ensemble ids and entrez gene ids.

Specified by:

parseOneLine in interface LineParser<Ensembl2NcbiValueObject>

Specified by:

parseOneLine in class BasicLineMapParser<String,Ensembl2NcbiValueObject>

Parameters:

line - line to parse

Returns:

BioMartEnsembleNcbi Value object representing the line parsed

createBioMartEnsembleNcbi

public Ensembl2NcbiValueObject createBioMartEnsembleNcbi(String[] fields)
                                                  throws NumberFormatException,
FileFormatException

Given an array of strings representing the line to parse then create a BioMartEnsembleNcbi value object with some validation. That is if a duplicate record keyed on peptide id is found then that means that it maps to more than one entrez gene id. As such check that the duplicate and currently processed record share the same ensemble gene id as a sanity check. Add the entrez gene to the existing collection of entrez genes.

Parameters:

fields - Parsed line split on delimiter

Returns:

BioMartEnsembleNcbi value object

Throws:

NumberFormatException - Parsing a number that is not one

FileFormatException - Validation than when a duplicate record is found then the peptide id is the same the ensemble gene id should be the same.

getBioMartFields

public String[] getBioMartFields()

setBioMartFields

public void setBioMartFields(String[] bioMartFields)

getBioMartFieldsPerRow

public int getBioMartFieldsPerRow()

Based on what attributes were set on the original file then calculate how many columns should be in file.

Returns:

Number of columns in file.

getMap

public Map<String,Ensembl2NcbiValueObject> getMap()

setTaxon

public void setTaxon(Taxon taxon)