Package org.intermine.bio.web.model

Class GenomicRegion

  • All Implemented Interfaces:
    java.lang.Comparable<GenomicRegion>
    public class GenomicRegion
extends java.lang.Object
implements java.lang.Comparable<GenomicRegion>
    This Java bean represents one record of Chromosome coordinates from user input The record should be in BED format: "chr\tstart\tend".

    • Constructor Detail

      • GenomicRegion

        public GenomicRegion()
        Default constructor a new GenomicRegion must use setters to set start, end, extendedRegionSize

    • Method Detail

      • setOrganism

        public void setOrganism​(java.lang.String organism)
        Parameters:
        organism - short name

      • getOrganism

        public java.lang.String getOrganism()
        Returns:
        organism

      • getChr

        public java.lang.String getChr()
        Returns:
        chr

      • setChr

        public void setChr​(java.lang.String chr)
        Parameters:
        chr - chromosome

      • getStart

        public java.lang.Integer getStart()
        Returns:
        start

      • setStart

        public void setStart​(java.lang.Integer start)
        Parameters:
        start - start position

      • getEnd

        public java.lang.Integer getEnd()
        Returns:
        end

      • setEnd

        public void setEnd​(java.lang.Integer end)
        Parameters:
        end - end position

      • getExtendedStart

        public java.lang.Integer getExtendedStart()
        Returns:
        the extendedStart

      • setExtendedStart

        public void setExtendedStart​(java.lang.Integer extendedStart)
        Parameters:
        extendedStart - the extendedStart to set

      • getExtendedEnd

        public java.lang.Integer getExtendedEnd()
        Returns:
        the extendedEnd

      • setExtendedEnd

        public void setExtendedEnd​(java.lang.Integer extendedEnd)
        Parameters:
        extendedEnd - the extendedEnd to set

      • getExtendedRegionSize

        public int getExtendedRegionSize()
        Returns:
        the extendedRegionSize

      • setExtendedRegionSize

        public void setExtendedRegionSize​(int extendedRegionSize)
        Parameters:
        extendedRegionSize - the extendedRegionSize to set

      • setTag

        public void setTag​(java.lang.Integer tag)
        Parameters:
        tag - as integer

      • getTag

        public java.lang.Integer getTag()
        Returns:
        tag value

      • setMinusStrand

        public void setMinusStrand​(java.lang.Boolean minusStrand)
        Parameters:
        minusStrand - as Boolean

      • setMinusStrand

        public void setMinusStrand​(boolean minusStrand)
        Parameters:
        minusStrand - as boolean

      • getMinusStrand

        public java.lang.Boolean getMinusStrand()
        Returns:
        minusStrand value

      • getOriginalRegion

        public java.lang.String getOriginalRegion()
        Make a string of orginal region if extended
        Returns:
        chr:start..end

      • getExtendedRegion

        public java.lang.String getExtendedRegion()
        Returns:
        chr:extendedStart..extenededEnd

      • getFullRegionInfo

        public java.lang.String getFullRegionInfo()
        Returns:
        chr:extendedStart..extenededEnd|chr:start..end

      • equals

        public boolean equals​(java.lang.Object obj)
        Overrides:
        equals in class java.lang.Object
        Parameters:
        obj - a GenomicRegion object
        Returns:
        boolean

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
        Returns:
        hashCode

      • compareTo

        public int compareTo​(GenomicRegion gr)
        Specified by:
        compareTo in interface java.lang.Comparable<GenomicRegion>

      • isOverlapped

        public boolean isOverlapped​(GenomicRegion gr)
        Test if two regions are overlapped.
        Parameters:
        gr - GenomicRegion
        Returns:
        A boolean value