Package uk.ac.ebi.uniprot.dataservice.client.alignment.blast

Interface Alignment

public interface Alignment
Details a blast alignment.

  • Method Summary

    Modifier and Type
    Method
    Description
    float
    getBitScore()
    Bit score (a normalised score) for the alignment.
    int
    getEndMatchSeq()
    Represents the position of the last amino acid from the sequence, obtained from #getMatchSeq, in relation to the entry's complete sequence
    int
    getEndQuerySeq()
    Represents the position of the last amino acid from the sequence, obtained from #getQuerySeq, in relation to the entry's complete sequence
    double
    getExpectation()
    Expectation value (E-value) for the alignment.
    float
    getGaps()
    Percentage of gaps in the alignment.
    float
    getIdentity()
    Percentage of identical bases/residues in the alignment.
    String
    getMatchSeq()
    Region of the match/target sequence in the alignment
    String
    getOverlap()
    Length of the region covered by the alignment.
    String
    getPattern()
    Consensus pattern for the alignment.
    float
    getPositives()
    Percentage of similar bases/residues in the alignment.
    float
    getProbability()
    Probability value (P-value) for the alignment.
    String
    getQuerySeq()
    Region of the query sequence in the alignment.
    int
    getScore()
    The alignment score
    int
    getSmithWatermanScore()
    Smith-Waterman alignment score.
    int
    getStartMatchSeq()
    Represents the position of the first amino acid from the sub-sequence, obtained from #getMatchSeq, in relation to the entry's complete sequence
    int
    getStartQuerySeq()
    Represents the position of the first amino acid from the sub-sequence, obtained from #getQuerySeq, in relation to the entry's complete sequence
    String
    getStrand()
    Nucleotide sequence strand.
    float
    getUngaps()
    Percentage of identical bases/residues in the alignment ignoring gaps.
    float
    getZScore()
    Z-score statistic for the alignment.

  • Method Details

    • getScore

      int getScore()
      The alignment score
      Returns:
      the score

    • getBitScore

      float getBitScore()
      Bit score (a normalised score) for the alignment.
      Returns:
      the bit score

    • getZScore

      float getZScore()
      Z-score statistic for the alignment.
      Returns:
      the Z score

    • getSmithWatermanScore

      int getSmithWatermanScore()
      Smith-Waterman alignment score.
      Returns:
      Smith-Waterman score

    • getExpectation

      double getExpectation()
      Expectation value (E-value) for the alignment.
      Returns:
      expectation value

    • getIdentity

      float getIdentity()
      Percentage of identical bases/residues in the alignment.
      Returns:
      identity as a percentage

    • getOverlap

      String getOverlap()
      Length of the region covered by the alignment.
      Returns:
      amino-acids that overlap

    • getPositives

      float getPositives()
      Percentage of similar bases/residues in the alignment.
      Returns:
      number of similar base/residues as a percentage

    • getGaps

      float getGaps()
      Percentage of gaps in the alignment.
      Returns:
      number of gaps in the alignment as a percentage

    • getUngaps

      float getUngaps()
      Percentage of identical bases/residues in the alignment ignoring gaps.
      Returns:
      number of ungapped areas in the alignment as a percentage

    • getStrand

      String getStrand()
      Nucleotide sequence strand.
      Returns:
      the sequence strand

    • getProbability

      float getProbability()
      Probability value (P-value) for the alignment.
      Returns:
      the p-value of the alignment

    • getQuerySeq

      String getQuerySeq()
      Region of the query sequence in the alignment.
      Returns:
      sub-sequence of the query sequence

    • getStartQuerySeq

      int getStartQuerySeq()
      Represents the position of the first amino acid from the sub-sequence, obtained from #getQuerySeq, in relation to the entry's complete sequence
      Returns:
      position of the first amino-acid where the query sub-sequence starts, in relation to the full sequence

    • getEndQuerySeq

      int getEndQuerySeq()
      Represents the position of the last amino acid from the sequence, obtained from #getQuerySeq, in relation to the entry's complete sequence
      Returns:
      position of the last amino-acid where the query sub-sequence starts, in relation to the full sequence

    • getMatchSeq

      String getMatchSeq()
      Region of the match/target sequence in the alignment
      Returns:
      the sub-sequence represented in the alignment for the given match entry sequence

    • getStartMatchSeq

      int getStartMatchSeq()
      Represents the position of the first amino acid from the sub-sequence, obtained from #getMatchSeq, in relation to the entry's complete sequence
      Returns:
      position of the first amino-acid where the query sub-sequence starts, in relation to the full sequence

    • getEndMatchSeq

      int getEndMatchSeq()
      Represents the position of the last amino acid from the sequence, obtained from #getMatchSeq, in relation to the entry's complete sequence
      Returns:
      position of the last amino-acid where the query sub-sequence starts, in relation to the full sequence

    • getPattern

      String getPattern()
      Consensus pattern for the alignment.
      Returns:
      alignment pattern