Package org.intermine.bio.dataconversion

Class HomologeneConverter

  • public class HomologeneConverter
extends org.intermine.bio.dataconversion.BioFileConverter
    HomoloGene data converter, to use symbol and organism to identify a gene

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      protected class  HomologeneConverter.GeneRecord
      represents a gene record in the data files

    • Constructor Summary

      Constructors 
      Constructor Description
      HomologeneConverter​(org.intermine.dataconversion.ItemWriter writer, org.intermine.metadata.Model model)
      Constructor

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void process​(java.io.Reader reader)
      void setHomologeneHomologues​(java.lang.String homologues)
      Sets the list of taxonIds of homologues that should be processed.
      void setHomologeneOrganisms​(java.lang.String taxonIds)
      Sets the list of taxonIds that should be processed.

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

        createCrossReference, createSynonym, createSynonym, getDataSet, getDataSet, getDataSource, getOrganism, getSequenceOntologyRefId, makeLocation

      • Methods inherited from class org.intermine.dataconversion.FileConverter

        getCurrentFile, setCurrentFile

      • Methods inherited from class org.intermine.dataconversion.DataConverter

        addUniqueItemId, alias, close, createItem, getItemWriter, getModel, getUniqueItemId, 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

    • Constructor Detail

      • HomologeneConverter

        public HomologeneConverter​(org.intermine.dataconversion.ItemWriter writer,
                           org.intermine.metadata.Model model)
        Constructor
        Parameters:
        writer - the ItemWriter used to handle the resultant items
        model - the Model

    • Method Detail

      • setHomologeneOrganisms

        public void setHomologeneOrganisms​(java.lang.String taxonIds)
        Sets the list of taxonIds that should be processed. All genes will be loaded.
        Parameters:
        taxonIds - a space-separated list of taxonIds

      • setHomologeneHomologues

        public void setHomologeneHomologues​(java.lang.String homologues)
        Sets the list of taxonIds of homologues that should be processed. These homologues will only be processed if they are homologues for the organisms of interest.
        Parameters:
        homologues - a space-separated list of taxonIds

      • process

        public void process​(java.io.Reader reader)
             throws java.lang.Exception
        Specified by:
        process in class org.intermine.dataconversion.FileConverter
        Throws:
        java.lang.Exception