Package org.intermine.bio.web.export

Class GFF3Exporter

  • All Implemented Interfaces:
    org.intermine.web.logic.export.Exporter
    public class GFF3Exporter
extends java.lang.Object
implements org.intermine.web.logic.export.Exporter
    Exports LocatedSequenceFeature objects in GFF3 format.

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String FLY_LINK
      for the gff header, link to taxomony
      static java.util.Set<java.lang.String> GFF_FIELDS
      the fields we don't want to display as attributes
      static java.lang.String WORM_LINK
      for the gff header, link to taxomony

      • Fields inherited from interface org.intermine.web.logic.export.Exporter

        UNIX_SEPARATOR, WINDOWS_SEPARATOR

    • Constructor Summary

      Constructors 
      Constructor Description
      GFF3Exporter​(java.io.PrintWriter out, java.util.List<java.lang.Integer> indexes, java.util.Map<java.lang.String,​java.lang.String> soClassNames, java.util.List<java.lang.String> attributesNames, java.lang.String sourceName, java.util.Set<java.lang.String> organisms, boolean makeUcscCompatible)
      Constructor.
      GFF3Exporter​(java.io.PrintWriter out, java.util.List<java.lang.Integer> indexes, java.util.Map<java.lang.String,​java.lang.String> soClassNames, java.util.List<java.lang.String> attributesNames, java.lang.String sourceName, java.util.Set<java.lang.String> organisms, boolean makeUcscCompatible, java.util.List<org.intermine.pathquery.Path> paths)
      Constructor.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean canExport​(java.util.List<java.lang.Class<?>> clazzes)
      static boolean canExportStatic​(java.util.List<java.lang.Class<?>> clazzes)  
      void export​(java.util.Iterator<? extends java.util.List<org.intermine.api.results.ResultElement>> resultIt)  
      void export​(java.util.Iterator<? extends java.util.List<org.intermine.api.results.ResultElement>> resultIt, java.util.Collection<org.intermine.pathquery.Path> unionPathCollection, java.util.Collection<org.intermine.pathquery.Path> newPathCollection)
      int getWrittenResultsCount()

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • GFF_FIELDS

        public static final java.util.Set<java.lang.String> GFF_FIELDS
        the fields we don't want to display as attributes

      • WORM_LINK

        public static final java.lang.String WORM_LINK
        for the gff header, link to taxomony
        See Also:
        Constant Field Values

      • FLY_LINK

        public static final java.lang.String FLY_LINK
        for the gff header, link to taxomony
        See Also:
        Constant Field Values

    • Constructor Detail

      • GFF3Exporter

        public GFF3Exporter​(java.io.PrintWriter out,
                    java.util.List<java.lang.Integer> indexes,
                    java.util.Map<java.lang.String,​java.lang.String> soClassNames,
                    java.util.List<java.lang.String> attributesNames,
                    java.lang.String sourceName,
                    java.util.Set<java.lang.String> organisms,
                    boolean makeUcscCompatible)
        Constructor.
        Parameters:
        out - output stream
        indexes - index of column with exported sequence
        soClassNames - mapping
        attributesNames - names of attributes that are printed in record, they are names of columns in results table, they are in the same order as corresponding columns in results table
        sourceName - name of Mine to put in GFF source column
        organisms - taxon id of the organisms
        makeUcscCompatible - true if chromosome ids should be prefixed by 'chr'

      • GFF3Exporter

        public GFF3Exporter​(java.io.PrintWriter out,
                    java.util.List<java.lang.Integer> indexes,
                    java.util.Map<java.lang.String,​java.lang.String> soClassNames,
                    java.util.List<java.lang.String> attributesNames,
                    java.lang.String sourceName,
                    java.util.Set<java.lang.String> organisms,
                    boolean makeUcscCompatible,
                    java.util.List<org.intermine.pathquery.Path> paths)
        Constructor.
        Parameters:
        out - output stream
        indexes - index of column with exported sequence
        soClassNames - mapping
        attributesNames - names of attributes that are printed in record, they are names of columns in results table, they are in the same order as corresponding columns in results table
        sourceName - name of Mine to put in GFF source column
        organisms - taxon id of the organisms
        makeUcscCompatible - true if chromosome ids should be prefixed by 'chr'
        paths - paths

    • Method Detail

      • export

        public void export​(java.util.Iterator<? extends java.util.List<org.intermine.api.results.ResultElement>> resultIt,
                   java.util.Collection<org.intermine.pathquery.Path> unionPathCollection,
                   java.util.Collection<org.intermine.pathquery.Path> newPathCollection)
        Specified by:
        export in interface org.intermine.web.logic.export.Exporter

      • export

        public void export​(java.util.Iterator<? extends java.util.List<org.intermine.api.results.ResultElement>> resultIt)
        Specified by:
        export in interface org.intermine.web.logic.export.Exporter

      • canExport

        public boolean canExport​(java.util.List<java.lang.Class<?>> clazzes)
        Specified by:
        canExport in interface org.intermine.web.logic.export.Exporter

      • canExportStatic

        public static boolean canExportStatic​(java.util.List<java.lang.Class<?>> clazzes)
        Parameters:
        clazzes - classes of result row
        Returns:
        true if this exporter can export result composed of specified classes

      • getWrittenResultsCount

        public int getWrittenResultsCount()
        Specified by:
        getWrittenResultsCount in interface org.intermine.web.logic.export.Exporter