Some refactoring.

.travis.yml

@@ -0,0 +1,11 @@
+language: java
+
+jdk:
+  - oraclejdk8
+
+before_install:
+    - chmod +x gradlew
+
+script: ./gradlew build jacocoTestReport
+
+after_success: ./gradlew jacocoRootReport coveralls

src/main/java/de/qaware/chronix/distance/BinaryDistance.java

@@ -0,0 +1,22 @@
+/*
+ * Arrays.java   Jul 14, 2004
+ *
+ * Copyright (c) 2004 Stan Salvador
+ * [email protected]
+ */
+
+package de.qaware.chronix.distance;
+
+
+import java.util.Arrays;
+
+public final class BinaryDistance implements DistanceFunction {
+    public double calcDistance(double[] vector1, double[] vector2) {
+        if (Arrays.equals(vector1, vector2)) {
+            return 0.0;
+        } else {
+            return 1.0;
+        }
+    }
+
+}

src/main/java/de/qaware/chronix/distance/DistanceFunction.java

@@ -0,0 +1,13 @@
+/*
+ * Arrays.java   Jul 14, 2004
+ *
+ * Copyright (c) 2004 Stan Salvador
+ * [email protected]
+ */
+
+package de.qaware.chronix.distance;
+
+
+public interface DistanceFunction {
+    double calcDistance(double[] vector1, double[] vector2);
+}

src/main/java/de/qaware/chronix/distance/DistanceFunctionFactory.java

@@ -0,0 +1,28 @@
+/*
+ * Arrays.java   Jul 14, 2004
+ *
+ * Copyright (c) 2004 Stan Salvador
+ * [email protected]
+ */
+
+package de.qaware.chronix.distance;
+
+
+public final class DistanceFunctionFactory {
+    public static DistanceFunction EUCLIDEAN_DIST_FN = new EuclideanDistance();
+    public static DistanceFunction MANHATTAN_DIST_FN = new ManhattanDistance();
+    public static DistanceFunction BINARY_DIST_FN = new BinaryDistance();
+
+    public static DistanceFunction getDistFnByName(String distFnName) {
+        switch (distFnName) {
+            case "EuclideanDistance":
+                return EUCLIDEAN_DIST_FN;
+            case "ManhattanDistance":
+                return MANHATTAN_DIST_FN;
+            case "BinaryDistance":
+                return BINARY_DIST_FN;
+            default:
+                throw new IllegalArgumentException("There is no DistanceFunction for the name " + distFnName);
+        }
+    }
+}

src/main/java/de/qaware/chronix/distance/EuclideanDistance.java

@@ -0,0 +1,20 @@
+/*
+ * Arrays.java   Jul 14, 2004
+ *
+ * Copyright (c) 2004 Stan Salvador
+ * [email protected]
+ */
+
+package de.qaware.chronix.distance;
+
+
+public final class EuclideanDistance implements DistanceFunction {
+    public double calcDistance(double[] vector1, double[] vector2) {
+        double sqSum = 0.0;
+        for (int x = 0; x < vector1.length; x++)
+            sqSum += Math.pow(vector1[x] - vector2[x], 2.0);
+
+        return Math.sqrt(sqSum);
+    }
+
+}

src/main/java/de/qaware/chronix/distance/ManhattanDistance.java

@@ -0,0 +1,20 @@
+/*
+ * Arrays.java   Jul 14, 2004
+ *
+ * Copyright (c) 2004 Stan Salvador
+ * [email protected]
+ */
+
+package de.qaware.chronix.distance;
+
+
+public final class ManhattanDistance implements DistanceFunction {
+    public double calcDistance(double[] vector1, double[] vector2) {
+        double diffSum = 0.0;
+        for (int x = 0; x < vector1.length; x++)
+            diffSum += Math.abs(vector1[x] - vector2[x]);
+
+        return diffSum;
+    }
+
+}

src/main/java/de/qaware/chronix/dtw/CostMatrix.java

@@ -15,5 +15,4 @@ interface CostMatrix
    double get(int col, int row);
 
    int size();
-
 }

src/main/java/de/qaware/chronix/dtw/DTW.java

@@ -10,23 +10,24 @@
 
 import de.qaware.chronix.matrix.ColMajorCell;
 import de.qaware.chronix.timeseries.TimeSeries;
-import de.qaware.chronix.util.DistanceFunction;
+import de.qaware.chronix.distance.DistanceFunction;
 
 import java.util.Iterator;
 
 
-public class DTW {
+public final class DTW {
+
+    private DTW() {
+        //avoid instances
+    }
 
-    // FUNCTIONS
     public static double calcWarpCost(WarpPath path, TimeSeries tsI, TimeSeries tsJ, DistanceFunction distFn) {
         double totalCost = 0.0;
 
         for (int p = 0; p < path.size(); p++) {
             final ColMajorCell currWarp = path.get(p);
-            totalCost += distFn.calcDistance(tsI.getMeasurementVector(currWarp.getCol()),
-                    tsJ.getMeasurementVector(currWarp.getRow()));
+            totalCost += distFn.calcDistance(tsI.getMeasurementVector(currWarp.getCol()), tsJ.getMeasurementVector(currWarp.getRow()));
         }
-
         return totalCost;
     }
 
@@ -73,20 +74,20 @@ public static double getWarpDistBetween(TimeSeries tsI, TimeSeries tsJ, Distance
 
         // Minimum Cost is at (maxI,maxJ)
         return currCol[maxJ];
-    }  // end getWarpDistBetween(..)
+    }
 
 
     public static WarpPath getWarpPathBetween(TimeSeries tsI, TimeSeries tsJ, DistanceFunction distFn) {
-        return DynamicTimeWarp(tsI, tsJ, distFn).getPath();
+        return dynamicTimeWarp(tsI, tsJ, distFn).getPath();
     }
 
 
     public static TimeWarpInfo getWarpInfoBetween(TimeSeries tsI, TimeSeries tsJ, DistanceFunction distFn) {
-        return DynamicTimeWarp(tsI, tsJ, distFn);
+        return dynamicTimeWarp(tsI, tsJ, distFn);
     }
 
 
-    private static TimeWarpInfo DynamicTimeWarp(TimeSeries tsI, TimeSeries tsJ, DistanceFunction distFn) {
+    private static TimeWarpInfo dynamicTimeWarp(TimeSeries tsI, TimeSeries tsJ, DistanceFunction distFn) {
         //     COST MATRIX:
         //   5|_|_|_|_|_|_|E| E = min Global Cost
         //   4|_|_|_|_|_|_|_| S = Start point
@@ -124,33 +125,10 @@ private static TimeWarpInfo DynamicTimeWarp(TimeSeries tsI, TimeSeries tsJ, Dist
                                 costMatrix[i][j - 1]));
                 costMatrix[i][j] = minGlobalCost + distFn.calcDistance(tsI.getMeasurementVector(i),
                         tsJ.getMeasurementVector(j));
-            }  // end for loop
-        }  // end for loop
+            }
+        }
+
 
-/*
-// writes a section of the cost matrix to a file
-try
-{
-final PrintWriter out = new PrintWriter(new FileWriter("matrix1.csv"));
-for (int j=maxJ; j>=0; j--)
-{
-   for (int i=0; i<=maxI; i++)
-   {
-      out.print(costMatrix[i][j]);
-      if (i != maxI)
-         out.print(",");
-   }
-   out.println();
-}
-out.flush();
-out.close();
-}
-catch (Exception e)
-{
-   System.out.println(e);
-   e.printStackTrace();
-}
- */
         // Minimum Cost is at (maxIi,maxJ)
         final double minimumCost = costMatrix[maxI][maxJ];
 
@@ -202,10 +180,10 @@ else if (i <= j)  // leftCost==rightCost > diagCost
 
             // Add the current step to the warp path.
             minCostPath.addFirst(i, j);
-        }  // end while loop
+        }
 
         return new TimeWarpInfo(minimumCost, minCostPath);
-    }  // end DynamicTimeWarp(..)
+    }
 
 
     public static double getWarpDistBetween(TimeSeries tsI, TimeSeries tsJ, SearchWindow window, DistanceFunction distFn) {
@@ -225,37 +203,35 @@ public static double getWarpDistBetween(TimeSeries tsI, TimeSeries tsJ, SearchWi
 
         // Get an iterator that traverses the window cells in the order that the cost matrix is filled.
         //    (first to last row (1..maxI), bottom to top (1..MaxJ)
-        final Iterator matrixIterator = window.iterator();
+        final Iterator<ColMajorCell> matrixIterator = window.iterator();
 
+        calcCostMatrix(tsI, tsJ, distFn, costMatrix, matrixIterator);
+        // Minimum Cost is at (maxI, maxJ)
+        return costMatrix.get(maxI, maxJ);
+
+    }
+
+    private static void calcCostMatrix(TimeSeries tsI, TimeSeries tsJ, DistanceFunction distFn, CostMatrix costMatrix, Iterator<ColMajorCell> matrixIterator) {
         while (matrixIterator.hasNext()) {
-            final ColMajorCell currentCell = (ColMajorCell) matrixIterator.next();  // current cell being filled
+            final ColMajorCell currentCell = matrixIterator.next();  // current cell being filled
             final int i = currentCell.getCol();
             final int j = currentCell.getRow();
 
             if ((i == 0) && (j == 0))      // bottom left cell (first row AND first column)
                 costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(0), tsJ.getMeasurementVector(0)));
-            else if (i == 0)             // first column
+            else if (i == 0)           // first column
             {
-                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(0), tsJ.getMeasurementVector(j)) +
-                        costMatrix.get(i, j - 1));
+                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(0), tsJ.getMeasurementVector(j)) + costMatrix.get(i, j - 1));
             } else if (j == 0)             // first row
             {
-                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(i), tsJ.getMeasurementVector(0)) +
-                        costMatrix.get(i - 1, j));
+                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(i), tsJ.getMeasurementVector(0)) + costMatrix.get(i - 1, j));
             } else                         // not first column or first row
             {
-                final double minGlobalCost = Math.min(costMatrix.get(i - 1, j),
-                        Math.min(costMatrix.get(i - 1, j - 1),
-                                costMatrix.get(i, j - 1)));
-                costMatrix.put(i, j, minGlobalCost + distFn.calcDistance(tsI.getMeasurementVector(i),
-                        tsJ.getMeasurementVector(j)));
-            }  // end if
-        }  // end while loop
-
-        // Minimum Cost is at (maxI, maxJ)
-        return costMatrix.get(maxI, maxJ);
-
-    }  // end getWarpDistBetween(...)
+                final double minGlobalCost = Math.min(costMatrix.get(i - 1, j), Math.min(costMatrix.get(i - 1, j - 1), costMatrix.get(i, j - 1)));
+                costMatrix.put(i, j, minGlobalCost + distFn.calcDistance(tsI.getMeasurementVector(i), tsJ.getMeasurementVector(j)));
+            }
+        }
+    }
 
 
     public static WarpPath getWarpPathBetween(TimeSeries tsI, TimeSeries tsJ, SearchWindow window, DistanceFunction distFn) {
@@ -285,32 +261,9 @@ private static TimeWarpInfo constrainedTimeWarp(TimeSeries tsI, TimeSeries tsJ,
 
         // Get an iterator that traverses the window cells in the order that the cost matrix is filled.
         //    (first to last row (1..maxI), bottom to top (1..MaxJ)
-        final Iterator matrixIterator = window.iterator();
+        final Iterator<ColMajorCell> matrixIterator = window.iterator();
 
-        while (matrixIterator.hasNext()) {
-            final ColMajorCell currentCell = (ColMajorCell) matrixIterator.next();  // current cell being filled
-            final int i = currentCell.getCol();
-            final int j = currentCell.getRow();
-
-            if ((i == 0) && (j == 0))      // bottom left cell (first row AND first column)
-                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(0), tsJ.getMeasurementVector(0)));
-            else if (i == 0)             // first column
-            {
-                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(0), tsJ.getMeasurementVector(j)) +
-                        costMatrix.get(i, j - 1));
-            } else if (j == 0)             // first row
-            {
-                costMatrix.put(i, j, distFn.calcDistance(tsI.getMeasurementVector(i), tsJ.getMeasurementVector(0)) +
-                        costMatrix.get(i - 1, j));
-            } else                         // not first column or first row
-            {
-                final double minGlobalCost = Math.min(costMatrix.get(i - 1, j),
-                        Math.min(costMatrix.get(i - 1, j - 1),
-                                costMatrix.get(i, j - 1)));
-                costMatrix.put(i, j, minGlobalCost + distFn.calcDistance(tsI.getMeasurementVector(i),
-                        tsJ.getMeasurementVector(j)));
-            }  // end if
-        }  // end while loop
+        calcCostMatrix(tsI, tsJ, distFn, costMatrix, matrixIterator);
 
         // Minimum Cost is at (maxI, maxJ)
         final double minimumCost = costMatrix.get(maxI, maxJ);
@@ -364,11 +317,6 @@ else if (i <= j)  // leftCost==rightCost > diagCost
             minCostPath.addFirst(i, j);
         }  // end while loop
 
-        // Free any rescources associated with the costMatrix (a swap file may have been created if the swa file did not
-        //    fit into main memory).
-        costMatrix.freeMem();
-
         return new TimeWarpInfo(minimumCost, minCostPath);
-    }  // end ConstrainedTimeWarp
-
-}  // end class DtwTest
+    }
+}