+
+ j++;
+ }
+
+ // unnecessary ?
+
+ /*
+ * for (int i=start; i <= end; i++) { int max = -1000; int maxi = -1; int
+ * maxj = -1;
+ *
+ * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
+ * maxi = i; maxj = j; } } }
+ */
+ }
+ }
+
+ /**
+ * Calculates the quality of the set of sequences
+ *
+ * @param start
+ * Start residue
+ * @param end
+ * End residue
+ */
+ public void findQuality(int start, int end)
+ {
+ quality = new Vector();
+
+ double max = -10000;
+ int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+
+ // Loop over columns // JBPNote Profiling info
+ // long ts = System.currentTimeMillis();
+ // long te = System.currentTimeMillis();
+ percentIdentity2();
+
+ int size = seqNums.size();
+ int[] lengths = new int[size];
+ double tot, bigtot, sr, tmp;
+ double[] x, xx;
+ int l, j, i, ii, i2, k, seqNum;
+
+ for (l = 0; l < size; l++)
+ {
+ lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;