- ps.print("\"Seq"+seq+"\"");
- for (int ev=0;ev<symm.rows; ev++)
- {
-
- ps.print(","+component(seq, ev));
- }
- ps.println();
- }*/
+ result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
+ similarityParams);
+ }
+ else if (scoreModel instanceof DistanceScoreModelI)
+ {
+ /*
+ * find distances and convert to similarity scores
+ * reverseRange(false) preserves but reverses the min-max range
+ */
+ result = ((DistanceScoreModelI) scoreModel).findDistances(av,
+ similarityParams);
+ result.reverseRange(false);
+ }
+ else
+ {
+ System.err
+ .println("Unexpected type of score model, cannot calculate similarity");
+ }
+
+ return result;
+ }
+
+ public void setJvCalcMode(boolean calcMode)
+ {
+ this.jvCalcMode = calcMode;
+ }
+
+ /**
+ * Answers the N dimensions of the NxN PCA matrix. This is the number of
+ * sequences involved in the pairwise score calculation.
+ *
+ * @return
+ */
+ public int getHeight()
+ {
+ // TODO can any of seqs[] be null?
+ return seqs.getSequences().length;