Package org.intermine.bio.dataconversion

Class EnsemblComparaConverter

  • public class EnsemblComparaConverter
extends org.intermine.bio.dataconversion.BioFileConverter
    Converter that process 4 column text file and produces homologues.

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected org.intermine.bio.dataconversion.IdResolver rslv  

    • Constructor Summary

      Constructors 
      Constructor Description
      EnsemblComparaConverter​(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 setEnsemblcomparaHomologues​(java.lang.String taxonIds)
      Sets the list of organisms to process only if the genes are homologues for organism of interest.
      void setEnsemblcomparaOrganisms​(java.lang.String taxonIds)
      Process all homologues for this organism.

      • 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

    • Field Detail

      • rslv

        protected org.intermine.bio.dataconversion.IdResolver rslv

    • Constructor Detail

      • EnsemblComparaConverter

        public EnsemblComparaConverter​(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

      • setEnsemblcomparaOrganisms

        public void setEnsemblcomparaOrganisms​(java.lang.String taxonIds)
        Process all homologues for this organism.
        Parameters:
        taxonIds - list of taxon IDs to process

      • setEnsemblcomparaHomologues

        public void setEnsemblcomparaHomologues​(java.lang.String taxonIds)
        Sets the list of organisms to process only if the genes are homologues for organism of interest. Otherwise ignore.
        Parameters:
        taxonIds - list of taxon IDs to process

      • 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