Package org.intermine.bio.web.export

Class BEDExporter

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

    • Field Summary

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

        UNIX_SEPARATOR, WINDOWS_SEPARATOR

    • Constructor Summary

      Constructors 
      Constructor Description
      BEDExporter​(java.io.PrintWriter out, java.util.List<java.lang.Integer> featureIndexes, java.lang.String sourceName, java.lang.String organismString, boolean makeUcscCompatible, java.lang.String trackDescription)
      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

    • Constructor Detail

      • BEDExporter

        public BEDExporter​(java.io.PrintWriter out,
                   java.util.List<java.lang.Integer> featureIndexes,
                   java.lang.String sourceName,
                   java.lang.String organismString,
                   boolean makeUcscCompatible,
                   java.lang.String trackDescription)
        Constructor.
        Parameters:
        out - output stream
        featureIndexes - index of column with exported sequence
        sourceName - name of Mine to put in GFF source column
        organismString - a comma separated string of organism short names
        makeUcscCompatible - true if chromosome ids should be prefixed by 'chr'
        trackDescription - track description in the header

    • Method Detail

      • 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

      • 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

      • getWrittenResultsCount

        public int getWrittenResultsCount()
        Specified by:
        getWrittenResultsCount 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