*/
package jalview.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
import jalview.math.Matrix;
/**
* A class that models a substitution score matrix for any given alphabet of
- * symbols
+ * symbols. Instances of this class are immutable and thread-safe, so the same
+ * object is returned from calls to getInstance().
*/
-public class ScoreMatrix extends SimilarityScoreModel implements
- PairwiseScoreModelI
+public class ScoreMatrix extends SimilarityScoreModel
+ implements PairwiseScoreModelI
{
private static final char GAP_CHARACTER = Comparison.GAP_DASH;
*/
public ScoreMatrix(String theName, char[] alphabet, float[][] values)
{
+ this(theName, null, alphabet, values);
+ }
+
+ /**
+ * Constructor given a name, description, symbol alphabet, and matrix of
+ * scores for pairs of symbols. The matrix should be square and of the same
+ * size as the alphabet, for example 20x20 for a 20 symbol alphabet.
+ *
+ * @param theName
+ * Unique, human readable name for the matrix
+ * @param theDescription
+ * descriptive display name suitable for use in menus
+ * @param alphabet
+ * the symbols to which scores apply
+ * @param values
+ * Pairwise scores indexed according to the symbol alphabet
+ */
+ public ScoreMatrix(String theName, String theDescription, char[] alphabet,
+ float[][] values)
+ {
if (alphabet.length != values.length)
{
throw new IllegalArgumentException(
this.matrix = values;
this.name = theName;
+ this.description = theDescription;
this.symbols = alphabet;
symbolIndex = buildSymbolIndex(alphabet);
* <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
* <li>and so on</li>
* </ul>
+ * This method is thread-safe.
*/
@Override
public MatrixI findSimilarities(AlignmentView seqstrings,
* @param params
* @return
*/
- protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
+ protected MatrixI findSimilarities(String[] seqs,
+ SimilarityParamsI params)
{
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)
return new String(symbols);
}
- public void setDescription(String desc)
- {
- description = desc;
- }
-
public float getMinimumScore()
{
return minValue;
{
return maxValue;
}
+
+ @Override
+ public ScoreModelI getInstance(AlignmentViewPanel avp)
+ {
+ return this;
+ }
}