import jalview.util.Comparison;
/**
- * A class to provide sequence pairwise similarity based on residue identity
+ * A class to provide sequence pairwise similarity based on residue identity.
+ * Instances of this class are immutable and thread-safe.
*/
public class PIDModel extends SimilarityScoreModel implements
PairwiseScoreModelI
{
private static final String NAME = "PID";
- private String description;
-
/**
* Constructor
*/
return NAME;
}
+ /**
+ * Answers null for description. If a display name is needed, use getName() or
+ * an internationalized string built from the name.
+ */
@Override
public String getDescription()
{
- return description;
+ return null;
}
@Override
* Computes similarity scores based on pairwise percentage identity of
* sequences. For consistency with Jalview 2.10.1's SeqSpace mode PCA
* calculation, the percentage scores are rescaled to the width of the
- * sequences (as if counts of identical residues).
+ * sequences (as if counts of identical residues). This method is thread-safe.
*/
@Override
public MatrixI findSimilarities(AlignmentView seqData,
/**
* A distance score is computed in the usual way (by reversing the range of
* the similarity score results), and then rescaled to percentage values
- * (reversing the rescaling to count values done in findSimilarities)
+ * (reversing the rescaling to count values done in findSimilarities). This
+ * method is thread-safe.
*/
@Override
public MatrixI findDistances(AlignmentView seqData,