1 package jalview.analysis;
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3 import jalview.datamodel.*;
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5 import jalview.util.*;
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9 public class AlignmentUtil {
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11 private AlignmentUtil() {
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14 public static int[][] percentIdentity2(AlignmentI align) {
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15 return percentIdentity2(align,0,align.getWidth()-1);
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18 public static int[][] percentIdentity2(AlignmentI align, int start, int end) {
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19 int [][] cons2 = new int[align.getWidth()][24];
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20 // Initialize the array
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21 for (int j=0;j<24;j++) {
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22 for (int i=0; i < align.getWidth();i++) {
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29 public static int getPixelHeight(int i, int j,int charHeight) {
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39 public static Vector substitution_rates (AlignmentI align, int start, int end) {
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41 Vector rates = new Vector();
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43 int len = (end-start+1);
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45 // Turn seqs into char arrays
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47 int[][] seqint = new int[align.getHeight()][len];
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50 for (int j = 0; j < align.getHeight(); j++) {
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52 SequenceI seq = align.getSequenceAt(j);
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54 for (int i = 0 ; i < len; i++) {
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55 char c = seq.getCharAt(start + i - 1);
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59 } else if (c == 'C') {
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61 } else if (c == 'T') {
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63 } else if (c == 'G') {
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74 // print_matrix(seqint,2,len); for (int j = 0; j < align.getHeight(); j++) {
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76 for (int j = 0; j < align.getHeight(); j++) {
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78 for (int k = 0; k < align.getHeight(); k++) {
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80 int counts[][] = new int[4][4];
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82 int tots[] = new int[4];
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84 int fulltots[] = new int[4];
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86 for (int i = 0 ; i < len; i++) {
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90 // System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);
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91 if (seqint[j][i] >= 0 &&
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92 seqint[k][i] >= 0) {
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93 counts[seqint[k][i]][seqint[j][i]]++;
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95 // print_matrix(counts,4,4);
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96 tots[seqint[j][i]]++;
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99 if (seqint[j][i] != -1) {
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100 fulltots[seqint[j][i]]++;
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108 System.out.println();
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110 System.out.println("Sequence " + align.getSequenceAt(j).getName() + " " + align.getSequenceAt(k).getName());
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112 System.out.println();
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113 print_matrix(counts,4,4);
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114 System.out.println();
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118 double[][] out = new double[4][4];// = constant_multiply_matrix(counts,1.0/tot,4,4);
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120 for (int i = 0; i < 4; i++) {
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121 for (int jj = 0; jj < 4; jj++) {
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122 out[i][jj] = (double)counts[i][jj]/tots[jj];
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126 print_matrix(out,4,4);
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127 System.out.println();
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130 System.out.print("RATES\t");
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131 System.out.print(align.getSequenceAt(j).getName() + "\t" + align.getSequenceAt(k).getName() + "\t");
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133 for (int i = 0; i < 4; i++) {
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134 for (int jj = 0; jj < 4; jj++) {
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135 Format.print(System.out,"%4.3f\t",out[i][jj]);
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138 System.out.println();
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140 for (int i = 0; i < 4; i++) {
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141 Format.print(System.out,"%4.3f\t",(double)fulltots[i]*1.0/fulltot);
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144 System.out.println();
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145 System.out.print("\nGC ");
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147 Format.print(System.out,"%4.3f\t",(double)(100*fulltots[1]+fulltots[3])/fulltot);
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149 System.out.print((fulltots[1]+fulltots[3]) + "\t" + fulltot);
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152 System.out.println();
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154 rates.addElement(out);
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162 public static double[][] constant_multiply_matrix(int[][] matrix, double c,int n, int m) {
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163 double[][] out = new double[n][m];
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165 for (int i = 0; i < n; i++) {
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166 for (int j = 0; j < m; j++) {
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168 out[i][j] = matrix[i][j]*c;
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175 public static void print_matrix(int[][] matrix, int n, int m) {
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178 for (int i = 0; i < n; i++) {
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179 for (int j = 0; j < m; j++) {
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181 System.out.print(matrix[i][j] + "\t");
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183 System.out.println();
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186 public static void print_matrix(double[][] matrix, int n, int m) {
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189 for (int i = 0; i < n; i++) {
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190 for (int j = 0; j < m; j++) {
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192 Format.print(System.out,"%4.3f\t",matrix[i][j]);
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195 System.out.println();
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199 public static Hashtable findKmers(SequenceI seq, int start, int end, Vector kmers) {
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201 Hashtable pos = new Hashtable();
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203 for (int j = 0; j < kmers.size(); j++) {
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205 String kmer = ((Sequence)kmers.elementAt(j)).getSequence();
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206 Sequence kmerseq = (Sequence)kmers.elementAt(j);
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208 if (end < seq.getLength()) {
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210 String str = seq.getSequence(start,end);
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214 while (str.indexOf(kmer,i) != -1) {
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216 // System.out.println("STring " + str + " " + i);
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217 int coord = str.indexOf(kmer,i);
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219 pos.put(new Integer(coord),new Integer(kmerseq.getLength()));
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