From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 8 Oct 2020 07:40:18 +0000 (+0100)
Subject: JAL-3761 failing test, formatting, method renamed
X-Git-Tag: Release_2_11_2_0~34^2~25
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=468df74e8febbe5066f9544bf7e0aa07311586ed;p=jalview.git

JAL-3761 failing test, formatting, method renamed
---

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 36fb450..e095106 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -336,7 +336,8 @@ public class MapList
    * <p>
    * The main use case for this method is when mapping cDNA sequence to its
    * protein product, based on CDS feature ranges which derive from spliced
-   * exons, but are contiguous on the cDNA sequence. For example 
+   * exons, but are contiguous on the cDNA sequence. For example
+   * 
    * <pre>
    *   CDS 1-20  // from exon1
    *   CDS 21-35 // from exon2
@@ -568,7 +569,7 @@ public class MapList
     }
     int fromRemainder = (fromCount[0] - 1) % fromRatio;
     int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio);
-    int[] toPos = countToPos(shiftFrom, toCount);
+    int[] toPos = traverseToPosition(shiftFrom, toCount);
     if (toPos == null)
     {
       return null; // throw new Error("Bad Mapping!");
@@ -617,44 +618,61 @@ public class MapList
   }
 
   /**
-   * count out pos positions into a series of intervals and return the position
+   * Reads through the given intervals until {@code count} positions have been
+   * traversed, and returns an array consisting of two values:
+   * <ul>
+   * <li>the value at the {@code count'th} position</li>
+   * <li>+1 if the last interval read is forwards, -1 if reverse direction</li>
+   * </ul>
+   * Returns null if the ranges include less than {@code count} positions, or if
+   * {@code count < 1}.
    * 
-   * @param shiftFrom
-   * @param pos
-   * @return position pos in interval set
+   * @param intervals
+   *          a list of [start, end] ranges
+   * @param count
+   *          the number of positions to traverse
+   * @return
    */
-  protected static int[] countToPos(List<int[]> shiftFrom, int pos)
+  protected static int[] traverseToPosition(List<int[]> intervals,
+          final int count)
   {
-    int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size();
-    int[] intv = { 0, 0 };
+    int traversed = 0;
+    int ivSize = intervals.size();
+    int iv = 0;
+
+    if (count < 1)
+    {
+      return null;
+    }
+
     while (iv < ivSize)
     {
-      intv = shiftFrom.get(iv++);
-      diff = intv[1] - intv[0];
+      int[] intv = intervals.get(iv++);
+      int diff = intv[1] - intv[0];
       if (diff >= 0)
       {
-        if (pos <= count + 1 + diff)
+        if (count <= traversed + 1 + diff)
         {
-          return new int[] { pos - count - 1 + intv[0], +1 };
+          return new int[] { intv[0] + (count - traversed - 1), +1 };
         }
         else
         {
-          count += 1 + diff;
+          traversed += 1 + diff;
         }
       }
       else
       {
-        if (pos <= count + 1 - diff)
+        if (count <= traversed + 1 - diff)
         {
-          return new int[] { intv[0] - (pos - count - 1), -1 };
+          return new int[] { intv[0] - (count - traversed - 1), -1 };
         }
         else
         {
-          count += 1 - diff;
+          traversed += 1 - diff;
         }
       }
     }
-    return null;// (diff<0) ? (intv[1]-1) : (intv[0]+1);
+    return null;
   }
 
   /**
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 4017055..d1a9fae 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -44,7 +44,7 @@ public class MapListTest
   {
     Cache.initLogger();
   }
-  
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -596,7 +596,8 @@ public class MapListTest
   public void testAddMapList_sameMap()
   {
     MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
-            new int[] { 72, 22 }, 1, 3);
+            new int[]
+            { 72, 22 }, 1, 3);
     String before = ml.toString();
     ml.addMapList(ml);
     assertEquals(before, ml.toString());
@@ -779,11 +780,11 @@ public class MapListTest
     assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
     assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
     assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
-    
+
     // 'subsumed' ranges are preserved
     ranges.clear();
     ranges.add(new int[] { 10, 30 });
-    ranges.add(new int[] { 15, 25 }); 
+    ranges.add(new int[] { 15, 25 });
     merged = MapList.coalesceRanges(ranges);
     assertEquals(2, merged.size());
     assertArrayEquals(new int[] { 10, 30 }, merged.get(0));
@@ -980,7 +981,7 @@ public class MapListTest
     assertEquals("[1, 12, 12, 17]", Arrays.toString(ml.locateInFrom(1, 6)));
     assertEquals("[4, 9]", Arrays.toString(ml.locateInFrom(2, 3)));
     assertEquals("[7, 12, 12, 17]", Arrays.toString(ml.locateInFrom(3, 6)));
-  
+
     assertNull(ml.locateInFrom(0, 0));
     assertNull(ml.locateInFrom(1, 7));
     assertNull(ml.locateInFrom(-1, 1));
@@ -999,15 +1000,25 @@ public class MapListTest
     assertEquals("[1, 3]", Arrays.toString(ml.locateInTo(3, 8)));
     assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(2, 11)));
     assertEquals("[1, 4]", Arrays.toString(ml.locateInTo(3, 11)));
-    
-    // we want 'greedy' mapping of base 12 to both peptides it codes for
+
+    // we want base 12 to map to both of the amino acids it codes for
     assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(12, 12)));
     assertEquals("[4, 5]", Arrays.toString(ml.locateInTo(11, 12)));
     assertEquals("[4, 6]", Arrays.toString(ml.locateInTo(11, 15)));
     assertEquals("[6, 6]", Arrays.toString(ml.locateInTo(15, 17)));
-  
+
     assertNull(ml.locateInTo(0, 0));
     assertNull(ml.locateInTo(1, 18));
     assertNull(ml.locateInTo(-1, 1));
   }
+
+  @Test(groups = { "Functional" })
+  public void testTraverseToPosition()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    assertNull(MapList.traverseToPosition(ranges, 0));
+
+    ranges.add(new int[] { 3, 6 });
+    assertNull(MapList.traverseToPosition(ranges, 0));
+  }
 }