org.intermine.bio.dataconversion
Class BioJavaFlatFileConverter

java.lang.Object
  org.intermine.dataconversion.DataConverter
      org.intermine.dataconversion.FileConverter
          org.intermine.bio.dataconversion.BioJavaFlatFileConverter

public class BioJavaFlatFileConverter
extends FileConverter

DataConverter to parse an EMBL/Genbank/other file using BioJava and generate genomic model items.

Field Summary

protected java.util.LinkedHashMap	bioEntities
protected Item	db
protected java.util.LinkedHashMap	ids
protected ItemFactory	itemFactory
protected java.util.LinkedHashMap	taxonIds

Constructor Summary

BioJavaFlatFileConverter(ItemWriter writer)
Constructor

Method Summary

void	close() Perform any necessary clean-up after post-conversion
protected java.lang.String	getGeneIdentifierFromCDS(Feature feature) Return a gene name for the given feature.
void	process(java.io.Reader reader) Perform the currentFile conversion

Methods inherited from class org.intermine.dataconversion.FileConverter

getCurrentFile, setCurrentFile

Methods inherited from class org.intermine.dataconversion.DataConverter

alias, createItem, getItemWriter, getModel, newId, setStoreHook, store, store, store, store, store

Methods inherited from class java.lang.Object

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

Field Detail

bioEntities

protected java.util.LinkedHashMap bioEntities

db

protected Item db

ids

protected java.util.LinkedHashMap ids

itemFactory

protected ItemFactory itemFactory

taxonIds

protected java.util.LinkedHashMap taxonIds

Constructor Detail

BioJavaFlatFileConverter

public BioJavaFlatFileConverter(ItemWriter writer)
                         throws ObjectStoreException

Constructor

Parameters:

writer - the ItemWriter used to handle the resultant items

Throws:

ObjectStoreException - if there is an ObjectStore problem

Method Detail

process

public void process(java.io.Reader reader)
             throws java.lang.Exception

Description copied from class: FileConverter

Perform the currentFile conversion

Specified by:

process in class FileConverter

Parameters:

reader - BufferedReader used as input

Throws:

java.lang.Exception - if an error occurs during processing

See Also:

FileConverter.process(Reader)

getGeneIdentifierFromCDS

protected java.lang.String getGeneIdentifierFromCDS(Feature feature)

Return a gene name for the given feature. Normally /gene is returned, but some less-than-good sequencing projects don't include /gene. In those cases this method can be overridden to do something clever to find out the gene name such as reading the /product line.

Parameters:

feature - the Feature

Returns:

the name or null if the name cannot be determined

close

public void close()
           throws ObjectStoreException

Description copied from class: FileConverter

Perform any necessary clean-up after post-conversion

Overrides:

close in class FileConverter

Throws:

ObjectStoreException

See Also:

FileConverter.close()