Package org.intermine.bio.web.export

Class GFF3Util

  • public final class GFF3Util
extends java.lang.Object
    Utility methods for GFF3.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static org.intermine.bio.io.gff3.GFF3Record makeGFF3Record​(org.intermine.model.bio.SequenceFeature lsf, java.util.Map<java.lang.String,​java.lang.String> soClassNameMap, java.lang.String sourceName, java.util.Map<java.lang.String,​java.util.List<java.lang.String>> extraAttributes)
      Create a GFF3Record from a SequenceFeature.
      static org.intermine.bio.io.gff3.GFF3Record makeGFF3Record​(org.intermine.model.bio.SequenceFeature lsf, java.util.Map<java.lang.String,​java.lang.String> soClassNameMap, java.lang.String sourceName, java.util.Map<java.lang.String,​java.util.List<java.lang.String>> extraAttributes, boolean makeUcscCompatible)
      Create a GFF3Record from a SequenceFeature.

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • makeGFF3Record

        public static org.intermine.bio.io.gff3.GFF3Record makeGFF3Record​(org.intermine.model.bio.SequenceFeature lsf,
                                                                  java.util.Map<java.lang.String,​java.lang.String> soClassNameMap,
                                                                  java.lang.String sourceName,
                                                                  java.util.Map<java.lang.String,​java.util.List<java.lang.String>> extraAttributes)
        Create a GFF3Record from a SequenceFeature.
        Parameters:
        lsf - the SequenceFeature
        soClassNameMap - a Map from FlyMine class names to SO term names
        sourceName - the name of the data source encoded in the GFF, so the name of your project
        extraAttributes - name/value pairs to add to the attribute field of the GFF3Record
        Returns:
        the GFF3Record or null if this lsf has no Chromosome or no Chromosome location

      • makeGFF3Record

        public static org.intermine.bio.io.gff3.GFF3Record makeGFF3Record​(org.intermine.model.bio.SequenceFeature lsf,
                                                                  java.util.Map<java.lang.String,​java.lang.String> soClassNameMap,
                                                                  java.lang.String sourceName,
                                                                  java.util.Map<java.lang.String,​java.util.List<java.lang.String>> extraAttributes,
                                                                  boolean makeUcscCompatible)
        Create a GFF3Record from a SequenceFeature.
        Parameters:
        lsf - the SequenceFeature
        soClassNameMap - a Map from FlyMine class names to SO term names
        sourceName - the name of the data source encoded in the GFF, so the name of your project
        extraAttributes - name/value pairs to add to the attribute field of the GFF3Record
        makeUcscCompatible - if true prefix 'chr' to chromosome names to work with UCSC genome browser and Galaxy
        Returns:
        the GFF3Record or null if this lsf has no Chromosome or no Chromosome location