Package org.biojava.nbio.core.search.io

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

java.lang.Object
org.biojava.nbio.core.search.io.Hsp<S,C>
public abstract class Hsp<S extends Sequence<C>,C extends Compound> extends 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 Details

    • 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, String hspQseq, String hspHseq, String hspIdentityString, Double percentageIdentity, Integer mismatchCount)

  • Method Details

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(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 Object
      Returns:
      true if HSP alignments are the same, false otherwise or if alignment strings are undetermined

    • getAlignment

      public SequencePair<S,C> getAlignment()

    • 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 String getHspQseq()
      HSP aligned query sequence string
      Returns:

    • getHspHseq

      public String getHspHseq()
      HSP aligned hit sequence string
      Returns:

    • getHspIdentityString

      public String getHspIdentityString()
      Identity string representing correspondence between aligned residues
      Returns:

    • getPercentageIdentity

      public Double getPercentageIdentity()

    • getMismatchCount

      public Integer getMismatchCount()