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)

Author:

rkrimmel

Message:

Added automatically created javadoc, still needs to be commented properly though

File:

• branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (9 diffs)

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

@@ +1 @@
+/*
+ * 
+ */
 package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
 
@@ -8 +11 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants;
 
+// TODO: Auto-generated Javadoc
+/**
+ * The Class SmithWatermanRepeated.
+ */
 public class SmithWatermanRepeated implements AlignmentAlgorithm {
 
-        /**
-         * The first input
-         */
+        /** The first input. */
         private int[] input1;
 
-        /**
-         * The second input String
-         */
+        /** The second input String. */
         private int[] input2;
 
-        /**
-         * The lengths of the input
-         */
+        /** The lengths of the input. */
         private int length1, length2;
 
@@ -31 +32 @@
         private MatrixEntry[][] matrix;
 
+        /** The alignment. */
         private ArrayList<NumberSequence> alignment;
 
+        /** The score threshold. */
         private float scoreThreshold;
 
-        /**
-         * Substitution matrix to calculate scores
-         */
+        /** Substitution matrix to calculate scores. */
         private SubstitutionMatrix submat;
 
+        /**
+         * Instantiates a new smith waterman repeated.
+         */
         public SmithWatermanRepeated() {
 
         }
 
+        /* (non-Javadoc)
+         * @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)
+         */
         @Override
         public void align(NumberSequence input1, NumberSequence input2,
@@ -219 +226 @@
         }
 
+        /* (non-Javadoc)
+         * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#getMatches()
+         */
         @Override
         public ArrayList<Match> getMatches() {
@@ -265 +275 @@
         /**
          * Get the maximum value in the score matrix.
+         *
+         * @return the max score
          */
         @Override
@@ -282 +294 @@
         }
 
+        /* (non-Javadoc)
+         * @see de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm#printAlignment()
+         */
         @Override
         public void printAlignment() {
@@ -312 +327 @@
 
         /**
-         * print the dynmaic programming matrix
+         * print the dynmaic programming matrix.
          */
         @Override
@@ -337 +352 @@
         }
 
+        /**
+         * Sets the alignment.
+         *
+         * @param alignment the new alignment
+         */
         public void setAlignment(ArrayList<NumberSequence> alignment) {
                 this.alignment = alignment;
@@ -355 +375 @@
         }
 
+        /**
+         * Traceback.
+         */
         public void traceback() {
                 MatrixEntry tmp = matrix[length1 + 1][0].getPrevious();