X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=86dcc39b267c2239216a2427ca5f0dd00fa06021;hb=ec60264ef3fc40b2edd23b446a36f6562b2f33a1;hp=2520de0e54a932d23c493680326e516396546c8f;hpb=2ad6ae4687351167ea0f706a2fe8574f7460104c;p=jalview.git

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 2520de0..86dcc39 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -27,15 +27,25 @@ import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.gui.JvOptionPane;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class MapListTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testSomething()
   {
@@ -381,7 +391,9 @@ public class MapListTest
     MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
 
     assertTrue(ml.equals(ml));
+    assertEquals(ml.hashCode(), ml.hashCode());
     assertTrue(ml.equals(ml1));
+    assertEquals(ml.hashCode(), ml1.hashCode());
     assertTrue(ml1.equals(ml));
 
     assertFalse(ml.equals(null));
@@ -416,7 +428,7 @@ public class MapListTest
   @Test(groups = { "Functional" })
   public void testGetRanges()
   {
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     ranges.add(new int[] { 2, 3 });
     ranges.add(new int[] { 5, 6 });
     assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
@@ -535,8 +547,7 @@ public class MapListTest
     MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
         51, 1 }, 1, 3);
     String s = ml.toString();
-    assertEquals("[ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
-            s);
+    assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
   }
 
   @Test(groups = { "Functional" })
@@ -559,10 +570,25 @@ public class MapListTest
 
     String s = ml.toString();
     assertEquals(
-            "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] To [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
+            "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] 1:3 to [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
             s);
   }
 
+  /**
+   * Test that confirms adding a map twice does nothing
+   */
+  @Test(groups = { "Functional" })
+  public void testAddMapList_sameMap()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[] { 72, 22 }, 1, 3);
+    String before = ml.toString();
+    ml.addMapList(ml);
+    assertEquals(before, ml.toString());
+    ml.addMapList(new MapList(ml));
+    assertEquals(before, ml.toString());
+  }
+
   @Test(groups = { "Functional" })
   public void testAddMapList_contiguous()
   {
@@ -572,14 +598,14 @@ public class MapListTest
     MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
             1, 3);
     ml.addMapList(ml2);
-    assertEquals("[ [11, 16] ] To [ [72, 53] ]", ml.toString());
+    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<int[]>();
+    List<int[]> ranges = new ArrayList<>();
 
     // add to empty list:
     MapList.addRange(range, ranges);
@@ -655,14 +681,17 @@ public class MapListTest
   @Test(groups = { "Functional" })
   public void testIsFromForwardStrand()
   {
-    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
-            new int[] { 20, 11 }, 1, 1);
+    // [3-9] declares forward strand
+    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 }, new int[] {
+        20, 11 }, 1, 1);
     assertTrue(ml.isFromForwardStrand());
 
+    // [11-5] declares reverse strand ([13-14] is ignored)
     ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
             new int[] { 20, 11 }, 1, 1);
     assertFalse(ml.isFromForwardStrand());
 
+    // all single position ranges - defaults to forward strand
     ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
             1);
     assertTrue(ml.isFromForwardStrand());
@@ -675,7 +704,7 @@ public class MapListTest
   public void testCoalesceRanges()
   {
     assertNull(MapList.coalesceRanges(null));
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertSame(ranges, MapList.coalesceRanges(ranges));
     ranges.add(new int[] { 1, 3 });
     assertSame(ranges, MapList.coalesceRanges(ranges));
@@ -697,6 +726,12 @@ public class MapListTest
     List<int[]> merged = MapList.coalesceRanges(ranges);
     assertEquals(1, merged.size());
     assertArrayEquals(new int[] { 1, 7 }, merged.get(0));
+    // verify input list is unchanged
+    assertEquals(4, ranges.size());
+    assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
+    assertArrayEquals(new int[] { 4, 5 }, ranges.get(1));
+    assertArrayEquals(new int[] { 5, 5 }, ranges.get(2));
+    assertArrayEquals(new int[] { 5, 7 }, ranges.get(3));
 
     // merging in reverse direction:
     ranges.clear();
@@ -723,4 +758,227 @@ public class MapListTest
     assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
     assertArrayEquals(new int[] { 12, 7 }, merged.get(1));
   }
+
+  /**
+   * Test the method that merges a list of ranges where possible
+   */
+  @Test(groups = { "Functional" })
+  public void testCoalesceRanges_withOverlap()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 2, 5 });
+
+    /*
+     * [2, 5] should extend [1, 3]
+     */
+    List<int[]> merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 5 }, merged.get(0));
+
+    /*
+     * a subsumed interval should be dropped
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 6 });
+    ranges.add(new int[] { 2, 4 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+
+    ranges.clear();
+    ranges.add(new int[] { 1, 5 });
+    ranges.add(new int[] { 1, 6 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 6 }, merged.get(0));
+
+    /*
+     * merge duplicate ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 1, 3 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 1, 3 }, merged.get(0));
+
+    /*
+     * reverse direction
+     */
+    ranges.clear();
+    ranges.add(new int[] { 9, 5 });
+    ranges.add(new int[] { 9, 4 });
+    ranges.add(new int[] { 8, 3 });
+    ranges.add(new int[] { 3, 2 });
+    ranges.add(new int[] { 1, 0 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
+  }
+
+  /**
+   * Test the method that compounds ('traverses') two mappings
+   */
+  @Test(groups = "Functional")
+  public void testTraverse()
+  {
+    /*
+     * simple 1:1 plus 1:1 forwards
+     */
+    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(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    List<int[]> fromRanges = compound.getFromRanges();
+    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(4, toRanges.size());
+    // 5-8 maps to 44-45,70-71
+    // 11-13 maps to 74-75,90
+    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')
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 70, 119 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 500 },
+            new int[] { 1000, 901, 600, 201 }, 1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0));
+    toRanges = compound.getToRanges();
+    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
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 40 }, 1, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 50, 91, 340 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(3, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-40 maps to 31-50,91-160
+    toRanges = compound.getToRanges();
+    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
+     */
+    ml1 = new MapList(new int[] { 1, 30 }, new int[] { 11, 20 }, 3, 1);
+    ml2 = new MapList(new int[] { 1, 100 }, new int[] { 1, 15, 91, 175 },
+            1, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(3, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0));
+    // 11-20 maps to 11-15, 91-95
+    toRanges = compound.getToRanges();
+    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
+     */
+    ml1 = new MapList(new int[] { 21, 40 }, new int[] { 13, 72 }, 1, 3);
+    ml2 = new MapList(new int[] { 1, 300 }, new int[] { 51, 70, 121, 200 },
+            3, 1);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    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(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
+     */
+    ml1 = new MapList(new int[] { 31, 90 }, new int[] { 13, 32 }, 3, 1);
+    ml2 = new MapList(new int[] { 11, 40 }, new int[] { 41, 50, 71, 150 },
+            1, 3);
+    compound = ml1.traverse(ml2);
+
+    assertEquals(1, compound.getFromRatio());
+    assertEquals(1, compound.getToRatio());
+    fromRanges = compound.getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0));
+    // 13-32 maps to 47-50,71-126
+    toRanges = compound.getToRanges();
+    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
+     */
+    ml1 = new MapList(new int[] { 1, 50 }, new int[] { 101, 150 }, 1, 1);
+    ml2 = new MapList(new int[] { 131, 180 }, new int[] { 201, 250 }, 1, 3);
+    compound = ml1.traverse(ml2);
+    assertNull(compound);
+  }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse 'to' range.
+   * Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsToForwardsStrand()
+  {
+    // [3-9] declares forward strand
+    MapList ml = new MapList(new int[] { 20, 11 },
+            new int[]
+            { 2, 2, 3, 9, 12, 11 }, 1, 1);
+    assertTrue(ml.isToForwardStrand());
+
+    // [11-5] declares reverse strand ([13-14] is ignored)
+    ml = new MapList(new int[] { 20, 11 },
+            new int[]
+            { 2, 2, 11, 5, 13, 14 }, 1, 1);
+    assertFalse(ml.isToForwardStrand());
+
+    // all single position ranges - defaults to forward strand
+    ml = new MapList(new int[] { 3, 1 }, new int[] { 2, 2, 4, 4, 6, 6 }, 1,
+            1);
+    assertTrue(ml.isToForwardStrand());
+  }
 }