org.intermine.bio.dataconversion
Class BioGridConverter

java.lang.Object
  org.intermine.dataconversion.DataConverter
      org.intermine.dataconversion.FileConverter
          org.intermine.bio.dataconversion.BioFileConverter
              org.intermine.bio.dataconversion.BioGridConverter

public class BioGridConverter
extends BioFileConverter

DataConverter to parse biogrid data into items Genetic interactions are labeled protein interactions, so we can't store or create any objects until all experiments and interactors are processed. Holder objects are creating, storing the data processed until the interactions are processed and we know the interactionType EXPERIMENT HOLDER holds the experiment data until the experiment data are processed INTERACTOR HOLDER holds the identifier INTERACTION HOLDER holds all interaction data until the entire entry is processed invalid experiments: - human interactions use genbank IDs - dmel gene doesn't resolve - if any of the participants are invalid, we throw away the interaction

Field Summary

protected IdResolverFactory

resolverFactory

Constructor Summary

BioGridConverter(ItemWriter writer, Model model)
Constructor

Method Summary

void	process(java.io.Reader reader) Perform the currentFile conversion
void	setBiogridOrganisms(java.lang.String taxonIds) Sets the list of taxonIds that should be imported if using split input files.

Methods inherited from class org.intermine.bio.dataconversion.BioFileConverter

getDataSetItem, getDataSetItem, getDataSourceItem

Methods inherited from class org.intermine.dataconversion.FileConverter

close, 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

resolverFactory

protected IdResolverFactory resolverFactory

Constructor Detail

BioGridConverter

public BioGridConverter(ItemWriter writer,
                        Model model)

Constructor

Parameters:

writer - the ItemWriter used to handle the resultant items

model - the Model

Method Detail

process

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

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

setBiogridOrganisms

public void setBiogridOrganisms(java.lang.String taxonIds)

Sets the list of taxonIds that should be imported if using split input files.

Parameters:

taxonIds - a space-separated list of taxonIds