Package com.biomatters.geneious.publicapi.implementations

Class DefaultSequenceGraphFactories.SequenceAlignmentScorer

  • Enclosing class:
    DefaultSequenceGraphFactories
    public abstract static class DefaultSequenceGraphFactories.SequenceAlignmentScorer
extends java.lang.Object
    Provides methods to supply a score for a given set of sequence residues and provide a color for a given score. Only the multiplicity but not the order of the residues in an alignment column is passed to the scorer, so this can not be used to create alignment graphs that depend on the order of the sequences, or on consistency of sequence order across columns.

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      abstract java.awt.Color getColor​(double score)
      return a Color for a score.
      abstract java.lang.Double getScore​(char[] residues, int[] residueCounts)
      Calculates the score for one alignment column based on the residues in each column.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • SequenceAlignmentScorer

        public SequenceAlignmentScorer()

    • Method Detail

      • getScore

        public abstract java.lang.Double getScore​(char[] residues,
                                          int[] residueCounts)
        Calculates the score for one alignment column based on the residues in each column. The implementation must be thread safe as this method may be called simultaneously from multiple threads.

        As of 2008-20-02, the characters passed to this method do not include endgaps. That is, if residues contains '-' then the corresponding residueCount specifies the number of internal gaps in the alignment column. It is possible that in the future a scorer may indicate whether it's interested in endgaps or not, but for now all implementations won't be able to tell the difference between e.g. a length 3 nongap column and a length 4 column containing one terminal gap.

        Parameters:
        residues - Set of characters occurring in the alignment column to be scored.
        residueCounts - an array of the same length as residues, with residueCounts[i] specifying the number of times the character residues[i] occurs in the alignment column.
        Returns:
        the score between 0 and 1 inclusive for these residues or null if these residues do not have a score.

      • getColor

        public abstract java.awt.Color getColor​(double score)
        return a Color for a score. The score is not necessarily one returned by getScore(char[],int[]) (for example in an graph averaged over multiple residue sites)
        Parameters:
        score - the score
        Returns:
        the Color for this score.