Package org.intermine.bio.dataconversion

Class PsiComplexesConverter

  • public class PsiComplexesConverter
extends org.intermine.bio.dataconversion.BioFileConverter
    Converter to parse complexes. May expand to handle others later.

    • Constructor Summary

      Constructors 
      Constructor Description
      PsiComplexesConverter​(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 setComplexesSource​(java.lang.String identifierSource)
      Sets the database, e.g.

      • 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

      • PsiComplexesConverter

        public PsiComplexesConverter​(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

      • setComplexesSource

        public void setComplexesSource​(java.lang.String identifierSource)
        Sets the database, e.g. SGD, from which we should get the identifier
        Parameters:
        identifierSource - the data source for the identifier

      • 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