Package org.intermine.bio.web.export

Class ResidueFieldExporter

  • All Implemented Interfaces:
    org.intermine.web.logic.export.FieldExporter
    public class ResidueFieldExporter
extends java.lang.Object
implements org.intermine.web.logic.export.FieldExporter
    ResidueFieldExporter class

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static org.apache.log4j.Logger LOG  
      protected static java.lang.String PROPERTY_DESCRIPTIONLINE  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void exportField​(org.intermine.model.InterMineObject object, java.lang.String fieldName, org.intermine.objectstore.ObjectStore os, javax.servlet.http.HttpServletResponse response)
      Export a field containing residues in FASTA format.
      static org.intermine.model.InterMineObject getIMObjectForSequence​(org.intermine.objectstore.ObjectStore os, java.lang.Class clazz, org.intermine.model.bio.Sequence sequence)
      Find the IntermineObject that references the given Sequence.
      static org.intermine.model.bio.Protein getProteinForSequence​(org.intermine.objectstore.ObjectStore os, org.intermine.model.bio.Sequence sequence)
      Find the Protein that references the given Sequence.
      static org.intermine.model.bio.SequenceFeature getSequenceFeatureForSequence​(org.intermine.objectstore.ObjectStore os, org.intermine.model.bio.Sequence sequence)
      Find the SequenceFeature that references the given Sequence.

      • 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

      • PROPERTY_DESCRIPTIONLINE

        protected static final java.lang.String PROPERTY_DESCRIPTIONLINE
        See Also:
        Constant Field Values

    • Constructor Detail

      • ResidueFieldExporter

        public ResidueFieldExporter()

    • Method Detail

      • exportField

        public void exportField​(org.intermine.model.InterMineObject object,
                        java.lang.String fieldName,
                        org.intermine.objectstore.ObjectStore os,
                        javax.servlet.http.HttpServletResponse response)
        Export a field containing residues in FASTA format.
        Specified by:
        exportField in interface org.intermine.web.logic.export.FieldExporter
        Parameters:
        object - the object of interest
        fieldName - the field of the object to output - should be sequence
        os - the ObjectStore that contains the object
        response - The HTTP response we are creating - used to get the OutputStream to write to
        Throws:
        org.intermine.web.logic.export.ExportException - if the application business logic throws an exception

      • getSequenceFeatureForSequence

        public static org.intermine.model.bio.SequenceFeature getSequenceFeatureForSequence​(org.intermine.objectstore.ObjectStore os,
                                                                                    org.intermine.model.bio.Sequence sequence)
        Find the SequenceFeature that references the given Sequence.
        Parameters:
        os - the ObjectStore
        sequence - the Sequence
        Returns:
        the SequenceFeature

      • getProteinForSequence

        public static org.intermine.model.bio.Protein getProteinForSequence​(org.intermine.objectstore.ObjectStore os,
                                                                    org.intermine.model.bio.Sequence sequence)
        Find the Protein that references the given Sequence.
        Parameters:
        os - the ObjectStore
        sequence - the Sequence
        Returns:
        the Protein

      • getIMObjectForSequence

        public static org.intermine.model.InterMineObject getIMObjectForSequence​(org.intermine.objectstore.ObjectStore os,
                                                                         java.lang.Class clazz,
                                                                         org.intermine.model.bio.Sequence sequence)
        Find the IntermineObject that references the given Sequence.
        Parameters:
        os - the ObjectStore
        clazz - the class of the InterMineObject
        sequence - the Sequence
        Returns:
        the IntermineObject