Package org.intermine.bio.dataconversion

Class NcbiGeneConverter

  • public class NcbiGeneConverter
extends org.intermine.bio.dataconversion.BioFileConverter
    Ncbi gene info converter

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static org.apache.log4j.Logger LOG  

    • Constructor Summary

      Constructors 
      Constructor Description
      NcbiGeneConverter​(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)
      Read the NCBI gene_info file and create genes setting identifiers, organism and synonyms.
      void setOrganisms​(java.lang.String taxonIds)
      Set the organisms to include by a space separated list of taxon ids.

      • 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

      • LOG

        protected static final org.apache.log4j.Logger LOG

    • Constructor Detail

      • NcbiGeneConverter

        public NcbiGeneConverter​(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

      • setOrganisms

        public void setOrganisms​(java.lang.String taxonIds)
        Set the organisms to include by a space separated list of taxon ids.
        Parameters:
        taxonIds - the organisms to include

      • process

        public void process​(java.io.Reader reader)
             throws java.lang.Exception
        Read the NCBI gene_info file and create genes setting identifiers, organism and synonyms.
        Specified by:
        process in class org.intermine.dataconversion.FileConverter
        Throws:
        java.lang.Exception