Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java
- Timestamp:
- 07/14/14 23:27:01 (10 years ago)
- File:
-
- 1 edited
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branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java
r1592 r1612 39 39 private SubstitutionMatrix submat; 40 40 41 public NeedlemanWunsch(int[] input1, int[] input2, SubstitutionMatrix submat,42 float threshold) {43 this.input1 = input1;44 this.input2 = input2;45 length1 = input1.length;46 length2 = input2.length;47 this.submat = submat;48 49 // System.out.println("Starting SmithWaterman algorithm with a "50 // + submat.getClass() + " Substitution Matrix: " +51 // submat.getClass().getCanonicalName());52 53 matrix = new MatrixEntry[length1 + 1][length2 + 1];54 alignment = new ArrayList<NumberSequence>();55 56 for (int i = 0; i < length1+1; i++) {57 for (int j = 0; j < length2+1; j++) {58 matrix[i][j] = new MatrixEntry();59 }60 }61 62 buildMatrix();63 traceback();64 }65 41 66 42 /** … … 289 265 } 290 266 267 @Override 268 public void align(int[] input1, int[] input2, SubstitutionMatrix submat, 269 float threshold) { 270 this.input1 = input1; 271 this.input2 = input2; 272 length1 = input1.length; 273 length2 = input2.length; 274 this.submat = submat; 275 276 // System.out.println("Starting SmithWaterman algorithm with a " 277 // + submat.getClass() + " Substitution Matrix: " + 278 // submat.getClass().getCanonicalName()); 279 280 matrix = new MatrixEntry[length1 + 1][length2 + 1]; 281 alignment = new ArrayList<NumberSequence>(); 282 283 for (int i = 0; i < length1+1; i++) { 284 for (int j = 0; j < length2+1; j++) { 285 matrix[i][j] = new MatrixEntry(); 286 } 287 } 288 289 buildMatrix(); 290 traceback(); 291 292 } 293 291 294 292 295
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