java.lang.Object
- ubic.gemma.core.loader.util.parser.BasicLineMapParser<K,T>
- - 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

All Methods Instance Methods Concrete Methods
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

- Constructor Detail
  - 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 Detail
  - 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)
```

Class BiomartEnsembleNcbiParser

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Constructor Detail

BiomartEnsembleNcbiParser

Method Detail

containsKey

get

getKeySet

getResults

parseOneLine

createBioMartEnsembleNcbi

getBioMartFields

setBioMartFields

getBioMartFieldsPerRow

getMap

setTaxon