JAL-3019 correctly form toRange of 'traversed' MapList

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 7f1abc4..9f28ee1 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -327,6 +327,13 @@ public class MapList
     fromHighest = Integer.MIN_VALUE;
     for (int[] range : fromRange)
     {
+      if (range.length != 2)
+      {
+        // throw new IllegalArgumentException(range);
+        System.err.println(
+                "Invalid format for fromRange " + Arrays.toString(range)
+                + " may cause errors");
+      }
       fromLowest = Math.min(fromLowest, Math.min(range[0], range[1]));
       fromHighest = Math.max(fromHighest, Math.max(range[0], range[1]));
     }
@@ -335,6 +342,13 @@ public class MapList
     toHighest = Integer.MIN_VALUE;
     for (int[] range : toRange)
     {
+      if (range.length != 2)
+      {
+        // throw new IllegalArgumentException(range);
+        System.err.println("Invalid format for toRange "
+                + Arrays.toString(range)
+                + " may cause errors");
+      }
       toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
       toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
     }
@@ -1203,11 +1217,20 @@ public class MapList
     for (int[] range : getToRanges())
     {
       int[] transferred = map.locateInTo(range[0], range[1]);
-      if (transferred == null)
+      if (transferred == null || transferred.length % 2 != 0)
       {
         return null;
       }
-      toRanges.add(transferred);
+
+      /*
+       *  convert [start1, end1, start2, end2, ...] 
+       *  to [[start1, end1], [start2, end2], ...]
+       */
+      for (int i = 0; i < transferred.length;)
+      {
+        toRanges.add(new int[] { transferred[i], transferred[i + 1] });
+        i += 2;
+      }
     }
 
     return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio);

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 92bf0ce..a7a7d34 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2685,14 +2685,14 @@ public class AlignmentUtilsTests
     assertEquals(2, toMap.getFromRanges().get(0).length);
     assertEquals(1, toMap.getFromRanges().get(0)[0]);
     assertEquals(12, toMap.getFromRanges().get(0)[1]);
-    assertEquals(1, toMap.getToRanges().size());
-    assertEquals(4, toMap.getToRanges().get(0).length);
+    assertEquals(2, toMap.getToRanges().size());
+    assertEquals(2, toMap.getToRanges().get(0).length);
     assertEquals(158, toMap.getToRanges().get(0)[0]);
     assertEquals(164, toMap.getToRanges().get(0)[1]);
-    assertEquals(210, toMap.getToRanges().get(0)[2]);
-    assertEquals(214, toMap.getToRanges().get(0)[3]);
+    assertEquals(210, toMap.getToRanges().get(1)[0]);
+    assertEquals(214, toMap.getToRanges().get(1)[1]);
     // or summarised as (but toString might change in future):
-    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
             toMap.toString());
 
     /*
@@ -2704,7 +2704,7 @@ public class AlignmentUtilsTests
     assertEquals("GRCh38", toLoci.getAssemblyId());
     assertEquals("7", toLoci.getChromosomeId());
     toMap = toLoci.getMap();
-    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
             toMap.toString());
   }
 

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 1acc9e1..86dcc39 100644 (file)
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -828,22 +828,31 @@ public class MapListTest
      */
     MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8,
         11, 13 }, 1, 1);
+    assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges()));
+    assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges()));
+
     MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
         75, 90, 127 }, 1, 1);
+    assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges()));
+    assertEquals("{[40, 45], [70, 75], [90, 127]}",
+            prettyPrint(ml2.getToRanges()));
+
     MapList compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     List<int[]> fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 2);
+    assertEquals(2, fromRanges.size());
     assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0));
     assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1));
     List<int[]> toRanges = compound.getToRanges();
-    assertEquals(toRanges.size(), 2);
+    assertEquals(4, toRanges.size());
     // 5-8 maps to 44-45,70-71
     // 11-13 maps to 74-75,90
-    assertArrayEquals(new int[] { 44, 45, 70, 71 }, toRanges.get(0));
-    assertArrayEquals(new int[] { 74, 75, 90, 90 }, toRanges.get(1));
+    assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1));
+    assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2));
+    assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3));
 
     /*
      * 1:1 over 1:1 backwards ('reverse strand')
@@ -853,14 +862,15 @@ public class MapListTest
             new int[] { 1000, 901, 600, 201 }, 1, 1);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
     toRanges = compound.getToRanges();
-    assertEquals(toRanges.size(), 1);
-    assertArrayEquals(new int[] { 931, 901, 600, 582 }, toRanges.get(0));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 600, 582 }, toRanges.get(1));
 
     /*
      * 1:1 plus 1:3 should result in 1:3
@@ -870,15 +880,16 @@ public class MapListTest
             1, 3);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 3);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(3, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
     // 11-40 maps to 31-50,91-160
     toRanges = compound.getToRanges();
-    assertEquals(toRanges.size(), 1);
-    assertArrayEquals(new int[] { 31, 50, 91, 160 }, toRanges.get(0));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1));
 
     /*
      * 3:1 plus 1:1 should result in 3:1
@@ -888,15 +899,16 @@ public class MapListTest
             1, 1);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 3);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(3, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
     // 11-20 maps to 11-15, 91-95
     toRanges = compound.getToRanges();
-    assertEquals(toRanges.size(), 1);
-    assertArrayEquals(new int[] { 11, 15, 91, 95 }, toRanges.get(0));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1));
 
     /*
      * 1:3 plus 3:1 should result in 1:1
@@ -906,15 +918,16 @@ public class MapListTest
             3, 1);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0));
     // 13-72 maps 3:1 to 55-70, 121-124
     toRanges = compound.getToRanges();
-    assertEquals(toRanges.size(), 1);
-    assertArrayEquals(new int[] { 55, 70, 121, 124 }, toRanges.get(0));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1));
 
     /*
      * 3:1 plus 1:3 should result in 1:1
@@ -924,15 +937,16 @@ public class MapListTest
             1, 3);
     compound = ml1.traverse(ml2);
 
-    assertEquals(compound.getFromRatio(), 1);
-    assertEquals(compound.getToRatio(), 1);
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
     fromRanges = compound.getFromRanges();
-    assertEquals(fromRanges.size(), 1);
+    assertEquals(1, fromRanges.size());
     assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
     // 13-32 maps to 47-50,71-126
     toRanges = compound.getToRanges();
-    assertEquals(toRanges.size(), 1);
-    assertArrayEquals(new int[] { 47, 50, 71, 126 }, toRanges.get(0));
+    assertEquals(2, toRanges.size());
+    assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0));
+    assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1));
 
     /*
      * method returns null if not all regions are mapped through