JAL-2599 move utility method to MappingUtils

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index c944345..81b9964 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1021,70 +1021,15 @@ public class MapList
 
     for (int[] range : map.getFromRanges())
     {
-      addRange(range, fromShifts);
+      MappingUtils.addRange(range, fromShifts);
     }
     for (int[] range : map.getToRanges())
     {
-      addRange(range, toShifts);
+      MappingUtils.addRange(range, toShifts);
     }
   }
 
   /**
-   * Adds the given range to a list of ranges. If the new range just extends
-   * existing ranges, the current endpoint is updated instead.
-   * 
-   * @param range
-   * @param addTo
-   */
-  static void addRange(int[] range, List<int[]> addTo)
-  {
-    /*
-     * list is empty - add to it!
-     */
-    if (addTo.size() == 0)
-    {
-      addTo.add(range);
-      return;
-    }
-
-    int[] last = addTo.get(addTo.size() - 1);
-    boolean lastForward = last[1] >= last[0];
-    boolean newForward = range[1] >= range[0];
-
-    /*
-     * contiguous range in the same direction - just update endpoint
-     */
-    if (lastForward == newForward && last[1] == range[0])
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
-     * next range starts at +1 in forward sense - update endpoint
-     */
-    if (lastForward && newForward && range[0] == last[1] + 1)
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
-     * next range starts at -1 in reverse sense - update endpoint
-     */
-    if (!lastForward && !newForward && range[0] == last[1] - 1)
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
-     * just add the new range
-     */
-    addTo.add(range);
-  }
-
-  /**
    * Returns true if mapping is from forward strand, false if from reverse
    * strand. Result is just based on the first 'from' range that is not a single
    * position. Default is true unless proven to be false. Behaviour is not well

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index b552c21..cd8821d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -1020,4 +1020,59 @@ public final class MappingUtils
       }
     }
   }
+
+  /**
+   * Adds the given range to a list of ranges. If the new range just extends
+   * existing ranges, the current endpoint is updated instead.
+   * 
+   * @param range
+   * @param addTo
+   */
+  public static void addRange(int[] range, List<int[]> addTo)
+  {
+    /*
+     * list is empty - add to it!
+     */
+    if (addTo.size() == 0)
+    {
+      addTo.add(range);
+      return;
+    }
+  
+    int[] last = addTo.get(addTo.size() - 1);
+    boolean lastForward = last[1] >= last[0];
+    boolean newForward = range[1] >= range[0];
+  
+    /*
+     * contiguous range in the same direction - just update endpoint
+     */
+    if (lastForward == newForward && last[1] == range[0])
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at +1 in forward sense - update endpoint
+     */
+    if (lastForward && newForward && range[0] == last[1] + 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at -1 in reverse sense - update endpoint
+     */
+    if (!lastForward && !newForward && range[0] == last[1] - 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * just add the new range
+     */
+    addTo.add(range);
+  }
 }

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 029b681..fd68e96 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -599,60 +599,6 @@ public class MapListTest
     assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
   }
 
-  @Test(groups = "Functional")
-  public void testAddRange()
-  {
-    int[] range = { 1, 5 };
-    List<int[]> ranges = new ArrayList<>();
-
-    // add to empty list:
-    MapList.addRange(range, ranges);
-    assertEquals(1, ranges.size());
-    assertSame(range, ranges.get(0));
-
-    // extend contiguous (same position):
-    MapList.addRange(new int[] { 5, 10 }, ranges);
-    assertEquals(1, ranges.size());
-    assertEquals(1, ranges.get(0)[0]);
-    assertEquals(10, ranges.get(0)[1]);
-
-    // extend contiguous (next position):
-    MapList.addRange(new int[] { 11, 15 }, ranges);
-    assertEquals(1, ranges.size());
-    assertEquals(1, ranges.get(0)[0]);
-    assertEquals(15, ranges.get(0)[1]);
-
-    // change direction: range is not merged:
-    MapList.addRange(new int[] { 16, 10 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(10, ranges.get(1)[1]);
-
-    // extend reverse contiguous (same position):
-    MapList.addRange(new int[] { 10, 8 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(8, ranges.get(1)[1]);
-
-    // extend reverse contiguous (next position):
-    MapList.addRange(new int[] { 7, 6 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(6, ranges.get(1)[1]);
-
-    // change direction: range is not merged:
-    MapList.addRange(new int[] { 6, 9 }, ranges);
-    assertEquals(3, ranges.size());
-    assertEquals(6, ranges.get(2)[0]);
-    assertEquals(9, ranges.get(2)[1]);
-
-    // not contiguous: not merged
-    MapList.addRange(new int[] { 11, 12 }, ranges);
-    assertEquals(4, ranges.size());
-    assertEquals(11, ranges.get(3)[0]);
-    assertEquals(12, ranges.get(3)[1]);
-  }
-
   /**
    * Check state after construction
    */

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 097ccd4..af82ac6 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1284,4 +1284,58 @@ public class MappingUtilsTest
     assertEquals(1, ranges.size());
     assertEquals(9, ranges.get(0)[1]);
   }
+
+  @Test(groups = "Functional")
+  public void testAddRange()
+  {
+    int[] range = { 1, 5 };
+    List<int[]> ranges = new ArrayList<>();
+  
+    // add to empty list:
+    MappingUtils.addRange(range, ranges);
+    assertEquals(1, ranges.size());
+    assertSame(range, ranges.get(0));
+  
+    // extend contiguous (same position):
+    MappingUtils.addRange(new int[] { 5, 10 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(10, ranges.get(0)[1]);
+  
+    // extend contiguous (next position):
+    MappingUtils.addRange(new int[] { 11, 15 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(15, ranges.get(0)[1]);
+  
+    // change direction: range is not merged:
+    MappingUtils.addRange(new int[] { 16, 10 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(10, ranges.get(1)[1]);
+  
+    // extend reverse contiguous (same position):
+    MappingUtils.addRange(new int[] { 10, 8 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(8, ranges.get(1)[1]);
+  
+    // extend reverse contiguous (next position):
+    MappingUtils.addRange(new int[] { 7, 6 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(6, ranges.get(1)[1]);
+  
+    // change direction: range is not merged:
+    MappingUtils.addRange(new int[] { 6, 9 }, ranges);
+    assertEquals(3, ranges.size());
+    assertEquals(6, ranges.get(2)[0]);
+    assertEquals(9, ranges.get(2)[1]);
+  
+    // not contiguous: not merged
+    MappingUtils.addRange(new int[] { 11, 12 }, ranges);
+    assertEquals(4, ranges.size());
+    assertEquals(11, ranges.get(3)[0]);
+    assertEquals(12, ranges.get(3)[1]);
+  }
 }