Package org.intermine.bio.web.export

Class BEDUtil

  • public final class BEDUtil
extends java.lang.Object
    Utility methods for UCSC BED format. Refer to GFF3Util.java.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static org.intermine.bio.io.bed.BEDRecord makeBEDRecord​(org.intermine.model.bio.SequenceFeature lsf)
      Create a BEDRecord from a LocatedSequenceFeature.
      static org.intermine.bio.io.bed.BEDRecord makeBEDRecord​(org.intermine.model.bio.SequenceFeature lsf, boolean makeUcscCompatible)
      Create a BEDRecord from a LocatedSequenceFeature.

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • makeBEDRecord

        public static org.intermine.bio.io.bed.BEDRecord makeBEDRecord​(org.intermine.model.bio.SequenceFeature lsf)
        Create a BEDRecord from a LocatedSequenceFeature.
        Parameters:
        lsf - the LocatedSequenceFeature
        Returns:
        the BEDRecord or null if this lsf has no Chromosome or no Chromosome location

      • makeBEDRecord

        public static org.intermine.bio.io.bed.BEDRecord makeBEDRecord​(org.intermine.model.bio.SequenceFeature lsf,
                                                               boolean makeUcscCompatible)
        Create a BEDRecord from a LocatedSequenceFeature.
        Parameters:
        lsf - the LocatedSequenceFeature
        makeUcscCompatible - if true prefix 'chr' to chromosome names to work with UCSC genome browser and Galaxy
        Returns:
        the BEDRecord or null if this lsf has no Chromosome or no Chromosome location