Class Hsp<S extends Sequence<C>,​C extends Compound>


  • public abstract class Hsp<S extends Sequence<C>,​C extends Compound>
    extends java.lang.Object
    This class models a search Hsp. You will retrieve a list of this using iterator of a Hit Designed by Paolo Pavan. You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. https://github.com/paolopavan
    Author:
    Paolo Pavan
    • Constructor Detail

      • Hsp

        public Hsp​(int hspNum,
                   double hspBitScore,
                   int hspScore,
                   double hspEvalue,
                   int hspQueryFrom,
                   int hspQueryTo,
                   int hspHitFrom,
                   int hspHitTo,
                   int hspQueryFrame,
                   int hspHitFrame,
                   int hspIdentity,
                   int hspPositive,
                   int hspGaps,
                   int hspAlignLen,
                   java.lang.String hspQseq,
                   java.lang.String hspHseq,
                   java.lang.String hspIdentityString,
                   java.lang.Double percentageIdentity,
                   java.lang.Integer mismatchCount)
    • Method Detail

      • hashCode

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

        public boolean equals​(java.lang.Object obj)
        Experimental. Wants to implement conceptual comparisons of search results. Fields unrelated to search are deliberately not considered. In HSP case, alignment representation strings are considered.
        Overrides:
        equals in class java.lang.Object
        Returns:
        true if HSP alignments are the same, false otherwise or if alignment strings are undetermined
      • getHspNum

        public int getHspNum()
      • getHspBitScore

        public double getHspBitScore()
      • getHspScore

        public int getHspScore()
      • getHspEvalue

        public double getHspEvalue()
      • getHspQueryFrom

        public int getHspQueryFrom()
      • getHspQueryTo

        public int getHspQueryTo()
      • getHspHitFrom

        public int getHspHitFrom()
      • getHspHitTo

        public int getHspHitTo()
      • getHspQueryFrame

        public int getHspQueryFrame()
      • getHspHitFrame

        public int getHspHitFrame()
      • getHspIdentity

        public int getHspIdentity()
      • getHspPositive

        public int getHspPositive()
      • getHspGaps

        public int getHspGaps()
      • getHspAlignLen

        public int getHspAlignLen()
      • getHspQseq

        public java.lang.String getHspQseq()
        HSP aligned query sequence string
        Returns:
      • getHspHseq

        public java.lang.String getHspHseq()
        HSP aligned hit sequence string
        Returns:
      • getHspIdentityString

        public java.lang.String getHspIdentityString()
        Identity string representing correspondence between aligned residues
        Returns:
      • getPercentageIdentity

        public java.lang.Double getPercentageIdentity()
      • getMismatchCount

        public java.lang.Integer getMismatchCount()