+ // From Alignment.java in jalview118\r
+\r
+ public void findQuality() {\r
+ findQuality(0,maxLength-1);\r
+ }\r
+\r
+ int[][] cons2;\r
+\r
+ private void percentIdentity2() {\r
+ calcSeqNums(); // updates maxLength, too.\r
+ if (cons2==null || seqNumsChanged) {\r
+ cons2 = new int[maxLength][24];\r
+ // Initialize the array\r
+ for (int j=0;j<24;j++) {\r
+ for (int i=0; i < maxLength;i++) {\r
+ cons2[i][j] = 0;\r
+ }\r
+ }\r
+\r
+ int sqnum[];\r
+ int j = 0;\r
+ while(j < sequences.size()) {\r
+ sqnum=(int[])seqNums.elementAt(j);\r
+ for (int i = 1; i < sqnum.length; i++) {\r
+ cons2[i-1][sqnum[i]]++;\r
+ }\r
+ j++;\r
+ }\r
+\r
+ // unnecessary ?\r
+ /* for (int i=start; i <= end; i++) {\r
+ int max = -1000;\r
+ int maxi = -1;\r
+ int maxj = -1;\r
+\r
+ for (int j=0;j<24;j++) {\r
+ if (cons2[i][j] > max) {\r
+ max = cons2[i][j];\r
+ maxi = i;\r
+ maxj = j;\r
+ }\r
+\r
+ }\r
+ } */\r
+ }\r
+\r
+}\r
+\r
+\r
+public void findQuality(int start, int end) {\r
+ quality = new Vector();\r
+ double max = -10000;\r
+ String s = "";\r
+ int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();\r
+ //Loop over columns // JBPNote Profiling info\r
+ // long ts = System.currentTimeMillis();\r
+ //long te = System.currentTimeMillis();\r
+ percentIdentity2();\r
+\r
+ int size = seqNums.size();\r
+ int[] lengths = new int[size];\r
+\r
+ for (int l = 0; l < size; l++)\r
+ lengths[l] = ((int[]) seqNums.get(l)).length;\r
+\r
+ for (int j=start; j <= end; j++) {\r
+ double bigtot = 0;\r
+\r
+ // First Xr = depends on column only\r
+ double x[] = new double[24];\r
+\r
+ for (int ii=0; ii < 24; ii++) {\r
+ x[ii] = 0;\r
+ try {\r
+ for (int i2=0; i2 < 24; i2++) {\r
+ x[ii] += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;\r
+ }\r
+ } catch (Exception e) {\r
+ System.out.println("Exception : " + e);\r
+ }\r
+ //System.out.println("X " + ii + " " + x[ii]);\r
+ x[ii] /= (size);\r
+ //System.out.println("X " + ii + " " + x[ii]);\r
+ }\r
+ // Now calculate D for each position and sum\r
+ for (int k=0; k < size; k++) {\r
+ double tot = 0;\r
+ double[] xx = new double[24];\r
+ int seqNum =\r
+ ((j+1)<lengths[size])\r
+ ? ((int[]) seqNums.get(k))[j+1]\r
+ : 23; // Sequence, or gap at the end\r
+\r
+ // This is a loop over r\r
+ for (int i=0; i < 23; i++) {\r
+ double sr = 0;\r
+ try {\r
+ sr = (double)BLOSUM62[i][seqNum]+4;\r
+ } catch (Exception e) {\r
+ System.out.println("Exception in sr " + e);\r
+ }\r
+ //Calculate X with another loop over residues\r
+\r
+ // System.out.println("Xi " + i + " " + x[i] + " " + sr);\r
+ xx[i] = x[i] - sr;\r
+\r
+ tot += xx[i]*xx[i];\r
+ }\r
+ bigtot += Math.sqrt(tot);\r
+ }\r
+ // This is the quality for one column\r
+ if (max < bigtot) {max = bigtot;}\r
+ // bigtot = bigtot * (size-cons2[j][23])/size;\r
+\r
+ quality.addElement(new Double(bigtot));\r
+\r
+ s += "-";\r
+\r
+ // Need to normalize by gaps\r
+ }\r
+ double newmax=-10000;\r
+ for (int j=start; j <= end; j++) {\r
+ double tmp = ((Double)quality.elementAt(j)).doubleValue();\r
+ tmp = (max - tmp)*(size-cons2[j][23])/size;\r
+ // System.out.println(tmp+ " " + j);\r
+ quality.setElementAt(new Double(tmp),j);\r
+ if (tmp>newmax)\r
+ newmax = tmp;\r
+ }\r
+ // System.out.println("Quality " + s);\r
+ qualityRange[0] = new Double(0);\r
+ qualityRange[1] = new Double(newmax);\r
+ }\r
+\r
+\r