- for (int i = 0; i < count; i++)
- {
- jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
- + seqs[i].getName());
- }
+ alignmentOutput = sb.toString();
+ }
+
+ public float[][] getScores()
+ {
+ return this.scores;
+ }
+
+ public float[][] getAlignmentScores()
+ {
+ return this.alignmentScores;
+ }
+
+ public String getAlignmentOutput()
+ {
+ return this.alignmentOutput;
+ }
+
+ /**
+ * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
+ *
+ * @param seqs
+ * @param scores
+ * @param totscore
+ */
+ protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
+ double totscore)
+ {
+ System.out
+ .println("Pairwise alignment scaled similarity score matrix\n");
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ System.out.println(
+ String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
+ }