JAL-845 move main method to 'test' class (needs further work);

formatting

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index eb414b9..4c62500 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -20,7 +20,8 @@
  */
 package jalview.util;
 
-import java.util.*;
+import java.util.Enumeration;
+import java.util.Vector;
 
 /**
  * MapList Simple way of bijectively mapping a non-contiguous linear range to
@@ -39,31 +40,41 @@ public class MapList
   public boolean equals(MapList obj)
   {
     if (obj == this)
+    {
       return true;
+    }
     if (obj != null && obj.fromRatio == fromRatio && obj.toRatio == toRatio
             && obj.fromShifts != null && obj.toShifts != null)
     {
       int i, iSize = fromShifts.size(), j, jSize = obj.fromShifts.size();
       if (iSize != jSize)
+      {
         return false;
+      }
       for (i = 0, iSize = fromShifts.size(), j = 0, jSize = obj.fromShifts
               .size(); i < iSize;)
       {
         int[] mi = (int[]) fromShifts.elementAt(i++);
         int[] mj = (int[]) obj.fromShifts.elementAt(j++);
         if (mi[0] != mj[0] || mi[1] != mj[1])
+        {
           return false;
+        }
       }
       iSize = toShifts.size();
       jSize = obj.toShifts.size();
       if (iSize != jSize)
+      {
         return false;
+      }
       for (i = 0, j = 0; i < iSize;)
       {
         int[] mi = (int[]) toShifts.elementAt(i++);
         int[] mj = (int[]) obj.toShifts.elementAt(j++);
         if (mi[0] != mj[0] || mi[1] != mj[1])
+        {
           return false;
+        }
       }
       return true;
     }
@@ -157,9 +168,13 @@ public class MapList
   private void ensureRange(int[] limits, int pos)
   {
     if (limits[0] > pos)
+    {
       limits[0] = pos;
+    }
     if (limits[1] < pos)
+    {
       limits[1] = pos;
+    }
   }
 
   public MapList(int from[], int to[], int fromRatio, int toRatio)
@@ -499,7 +514,9 @@ public class MapList
     int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol
     // position
     if (fromStart == null || fromEnd == null)
+    {
       return null;
+    }
     int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
     return iv;
   }
@@ -519,7 +536,9 @@ public class MapList
     int toStart[] = shiftFrom(start);
     int toEnd[] = shiftFrom(end);
     if (toStart == null || toEnd == null)
+    {
       return null;
+    }
     int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
     return iv;
   }
@@ -612,7 +631,9 @@ public class MapList
       i++;
     }
     if (fs == fe && fe == -1)
+    {
       return null;
+    }
     Vector ranges = new Vector();
     if (fs <= fe)
     {
@@ -623,7 +644,9 @@ public class MapList
       iv = new int[]
       { iv[0], iv[1] };// clone
       if (i == fs)
+      {
         iv[0] = startpos;
+      }
       while (i != fe)
       {
         ranges.addElement(iv); // add initial range
@@ -633,7 +656,9 @@ public class MapList
         i++;
       }
       if (i == fe)
+      {
         iv[1] = endpos;
+      }
       ranges.addElement(iv); // add only - or final range
     }
     else
@@ -750,223 +775,6 @@ public class MapList
   }
 
   /**
-   * test routine. not incremental.
-   * 
-   * @param ml
-   * @param fromS
-   * @param fromE
-   */
-  public static void testMap(MapList ml, int fromS, int fromE)
-  {
-    for (int from = 1; from <= 25; from++)
-    {
-      int[] too = ml.shiftFrom(from);
-      System.out.print("ShiftFrom(" + from + ")==");
-      if (too == null)
-      {
-        System.out.print("NaN\n");
-      }
-      else
-      {
-        System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
-        System.out.print("\t+--+\t");
-        int[] toofrom = ml.shiftTo(too[0]);
-        if (toofrom != null)
-        {
-          if (toofrom[0] != from)
-          {
-            System.err.println("Mapping not reflexive:" + from + " "
-                    + too[0] + "->" + toofrom[0]);
-          }
-          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
-                  + " % " + toofrom[1] + " (" + toofrom[2] + ")");
-        }
-        else
-        {
-          System.out.println("ShiftTo(" + too[0] + ")=="
-                  + "NaN! - not Bijective Mapping!");
-        }
-      }
-    }
-    int mmap[][] = ml.makeFromMap();
-    System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
-            + mmap[0][2] + " " + mmap[0][3] + " ");
-    for (int i = 1; i <= mmap[1].length; i++)
-    {
-      if (mmap[1][i - 1] == -1)
-      {
-        System.out.print(i + "=XXX");
-
-      }
-      else
-      {
-        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
-      }
-      if (i % 20 == 0)
-      {
-        System.out.print("\n");
-      }
-      else
-      {
-        System.out.print(",");
-      }
-    }
-    // test range function
-    System.out.print("\nTest locateInFrom\n");
-    {
-      int f = mmap[0][2], t = mmap[0][3];
-      while (f <= t)
-      {
-        System.out.println("Range " + f + " to " + t);
-        int rng[] = ml.locateInFrom(f, t);
-        if (rng != null)
-        {
-          for (int i = 0; i < rng.length; i++)
-          {
-            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        System.out.print("\nReversed\n");
-        rng = ml.locateInFrom(t, f);
-        if (rng != null)
-        {
-          for (int i = 0; i < rng.length; i++)
-          {
-            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        System.out.print("\n");
-        f++;
-        t--;
-      }
-    }
-    System.out.print("\n");
-    mmap = ml.makeToMap();
-    System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
-            + mmap[0][2] + " " + mmap[0][3] + " ");
-    for (int i = 1; i <= mmap[1].length; i++)
-    {
-      if (mmap[1][i - 1] == -1)
-      {
-        System.out.print(i + "=XXX");
-
-      }
-      else
-      {
-        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
-      }
-      if (i % 20 == 0)
-      {
-        System.out.print("\n");
-      }
-      else
-      {
-        System.out.print(",");
-      }
-    }
-    System.out.print("\n");
-    // test range function
-    System.out.print("\nTest locateInTo\n");
-    {
-      int f = mmap[0][2], t = mmap[0][3];
-      while (f <= t)
-      {
-        System.out.println("Range " + f + " to " + t);
-        int rng[] = ml.locateInTo(f, t);
-        if (rng != null)
-        {
-          for (int i = 0; i < rng.length; i++)
-          {
-            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        System.out.print("\nReversed\n");
-        rng = ml.locateInTo(t, f);
-        if (rng != null)
-        {
-          for (int i = 0; i < rng.length; i++)
-          {
-            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
-          }
-        }
-        else
-        {
-          System.out.println("No range!");
-        }
-        f++;
-        t--;
-        System.out.print("\n");
-      }
-    }
-
-  }
-
-  public static void main(String argv[])
-  {
-    MapList ml = new MapList(new int[]
-    { 1, 5, 10, 15, 25, 20 }, new int[]
-    { 51, 1 }, 1, 3);
-    MapList ml1 = new MapList(new int[]
-    { 1, 3, 17, 4 }, new int[]
-    { 51, 1 }, 1, 3);
-    MapList ml2 = new MapList(new int[]
-    { 1, 60 }, new int[]
-    { 1, 20 }, 3, 1);
-    // test internal consistency
-    int to[] = new int[51];
-    MapList.testMap(ml, 1, 60);
-    MapList mldna = new MapList(new int[]
-    { 2, 2, 6, 8, 12, 16 }, new int[]
-    { 1, 3 }, 3, 1);
-    int[] frm = mldna.locateInFrom(1, 1);
-    testLocateFrom(mldna, 1, 1, new int[]
-    { 2, 2, 6, 7 });
-    MapList.testMap(mldna, 1, 3);
-    /*
-     * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
-     * toofrom=ml.shiftFrom(too[0]);
-     * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
-     * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
-     */
-    System.out.print("Success?\n"); // if we get here - something must be
-    // working!
-  }
-
-  private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
-  {
-    int[] frm = mldna.locateInFrom(i, j);
-    if (frm == ks || java.util.Arrays.equals(frm, ks))
-    {
-      System.out.println("Success test locate from " + i + " to " + j);
-    }
-    else
-    {
-      System.err.println("Failed test locate from " + i + " to " + j);
-      for (int c = 0; c < frm.length; c++)
-      {
-        System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
-      }
-      System.err.println("Expected");
-      for (int c = 0; c < ks.length; c++)
-      {
-        System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));
-      }
-    }
-  }
-
-  /**
    * 
    * @return a MapList whose From range is this maplist's To Range, and vice
    *         versa

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
new file mode 100644 (file)
index 0000000..2c8e207
--- /dev/null
+++ b/test/jalview/util/MapListTest.java
@@ -0,0 +1,213 @@
+package jalview.util;
+
+import java.util.Arrays;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class MapListTest
+{
+
+  @Test
+  public void testSomething()
+  {
+    MapList ml = new MapList(new int[]
+    { 1, 5, 10, 15, 25, 20 }, new int[]
+    { 51, 1 }, 1, 3);
+    MapList ml1 = new MapList(new int[]
+    { 1, 3, 17, 4 }, new int[]
+    { 51, 1 }, 1, 3);
+    MapList ml2 = new MapList(new int[]
+    { 1, 60 }, new int[]
+    { 1, 20 }, 3, 1);
+    // test internal consistency
+    int to[] = new int[51];
+    testMap(ml, 1, 60);
+    MapList mldna = new MapList(new int[]
+    { 2, 2, 6, 8, 12, 16 }, new int[]
+    { 1, 3 }, 3, 1);
+    int[] frm = mldna.locateInFrom(1, 1);
+    testLocateFrom(mldna, 1, 1, new int[]
+    { 2, 2, 6, 7 });
+    testMap(mldna, 1, 3);
+    /*
+     * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
+     * toofrom=ml.shiftFrom(too[0]);
+     * System.out.println("ShiftFrom("+from+")=="+too[0]+" %
+     * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
+     */
+  }
+
+  private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
+  {
+    int[] frm = mldna.locateInFrom(i, j);
+    Assert.assertEquals("Failed test locate from " + i + " to " + j,
+            Arrays.toString(frm), Arrays.toString(ks));
+  }
+
+  /**
+   * test routine. not incremental.
+   * 
+   * @param ml
+   * @param fromS
+   * @param fromE
+   */
+  private void testMap(MapList ml, int fromS, int fromE)
+  {
+    // todo convert to JUnit style tests
+    for (int from = 1; from <= 25; from++)
+    {
+      int[] too = ml.shiftFrom(from);
+      System.out.print("ShiftFrom(" + from + ")==");
+      if (too == null)
+      {
+        System.out.print("NaN\n");
+      }
+      else
+      {
+        System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
+        System.out.print("\t+--+\t");
+        int[] toofrom = ml.shiftTo(too[0]);
+        if (toofrom != null)
+        {
+          if (toofrom[0] != from)
+          {
+            System.err.println("Mapping not reflexive:" + from + " "
+                    + too[0] + "->" + toofrom[0]);
+          }
+          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
+                  + " % " + toofrom[1] + " (" + toofrom[2] + ")");
+        }
+        else
+        {
+          System.out.println("ShiftTo(" + too[0] + ")=="
+                  + "NaN! - not Bijective Mapping!");
+        }
+      }
+    }
+    int mmap[][] = ml.makeFromMap();
+    System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
+            + mmap[0][2] + " " + mmap[0][3] + " ");
+    for (int i = 1; i <= mmap[1].length; i++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
+        System.out.print(i + "=XXX");
+  
+      }
+      else
+      {
+        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+      }
+      if (i % 20 == 0)
+      {
+        System.out.print("\n");
+      }
+      else
+      {
+        System.out.print(",");
+      }
+    }
+    // test range function
+    System.out.print("\nTest locateInFrom\n");
+    {
+      int f = mmap[0][2], t = mmap[0][3];
+      while (f <= t)
+      {
+        System.out.println("Range " + f + " to " + t);
+        int rng[] = ml.locateInFrom(f, t);
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
+            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        System.out.print("\nReversed\n");
+        rng = ml.locateInFrom(t, f);
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
+            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        System.out.print("\n");
+        f++;
+        t--;
+      }
+    }
+    System.out.print("\n");
+    mmap = ml.makeToMap();
+    System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "
+            + mmap[0][2] + " " + mmap[0][3] + " ");
+    for (int i = 1; i <= mmap[1].length; i++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
+        System.out.print(i + "=XXX");
+  
+      }
+      else
+      {
+        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+      }
+      if (i % 20 == 0)
+      {
+        System.out.print("\n");
+      }
+      else
+      {
+        System.out.print(",");
+      }
+    }
+    System.out.print("\n");
+    // test range function
+    System.out.print("\nTest locateInTo\n");
+    {
+      int f = mmap[0][2], t = mmap[0][3];
+      while (f <= t)
+      {
+        System.out.println("Range " + f + " to " + t);
+        int rng[] = ml.locateInTo(f, t);
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
+            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        System.out.print("\nReversed\n");
+        rng = ml.locateInTo(t, f);
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
+            System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        f++;
+        t--;
+        System.out.print("\n");
+      }
+    }
+  
+  }
+
+}