Changeset 1734 for branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java
- Timestamp:
- 09/05/14 20:20:29 (10 years ago)
- File:
-
- 1 edited
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branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java
r1733 r1734 1 /* 2 * 3 */ 1 4 package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; 2 5 … … 8 11 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants; 9 12 13 // TODO: Auto-generated Javadoc 14 /** 15 * The Class SmithWatermanRepeated. 16 */ 10 17 public class SmithWatermanRepeated implements AlignmentAlgorithm { 11 18 12 /** 13 * The first input 14 */ 19 /** The first input. */ 15 20 private int[] input1; 16 21 17 /** 18 * The second input String 19 */ 22 /** The second input String. */ 20 23 private int[] input2; 21 24 22 /** 23 * The lengths of the input 24 */ 25 /** The lengths of the input. */ 25 26 private int length1, length2; 26 27 … … 31 32 private MatrixEntry[][] matrix; 32 33 34 /** The alignment. */ 33 35 private ArrayList<NumberSequence> alignment; 34 36 37 /** The score threshold. */ 35 38 private float scoreThreshold; 36 39 37 /** 38 * Substitution matrix to calculate scores 39 */ 40 /** Substitution matrix to calculate scores. */ 40 41 private SubstitutionMatrix submat; 41 42 43 /** 44 * Instantiates a new smith waterman repeated. 45 */ 42 46 public SmithWatermanRepeated() { 43 47 44 48 } 45 49 50 /* (non-Javadoc) 51 * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#align(de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence, de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence, de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix, float) 52 */ 46 53 @Override 47 54 public void align(NumberSequence input1, NumberSequence input2, … … 219 226 } 220 227 228 /* (non-Javadoc) 229 * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#getMatches() 230 */ 221 231 @Override 222 232 public ArrayList<Match> getMatches() { … … 265 275 /** 266 276 * Get the maximum value in the score matrix. 277 * 278 * @return the max score 267 279 */ 268 280 @Override … … 282 294 } 283 295 296 /* (non-Javadoc) 297 * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#printAlignment() 298 */ 284 299 @Override 285 300 public void printAlignment() { … … 312 327 313 328 /** 314 * print the dynmaic programming matrix 329 * print the dynmaic programming matrix. 315 330 */ 316 331 @Override … … 337 352 } 338 353 354 /** 355 * Sets the alignment. 356 * 357 * @param alignment the new alignment 358 */ 339 359 public void setAlignment(ArrayList<NumberSequence> alignment) { 340 360 this.alignment = alignment; … … 355 375 } 356 376 377 /** 378 * Traceback. 379 */ 357 380 public void traceback() { 358 381 MatrixEntry tmp = matrix[length1 + 1][0].getPrevious();
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