X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=a2f38e2269ebc0c239cb5ca89db0ea70165db1d2;hb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;hp=6e7e19e7481274c3b26dacb2a29444154fbc2989;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 6e7e19e..a2f38e2 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -1,40 +1,67 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
+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
 {
 
-  @Test(groups ={ "Functional" })
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Functional" })
   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);
+    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[]
+    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 });
+    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[]
@@ -99,7 +126,7 @@ public class MapListTest
       if (mmap[1][i - 1] == -1)
       {
         System.out.print(i + "=XXX");
-  
+
       }
       else
       {
@@ -160,7 +187,7 @@ public class MapListTest
       if (mmap[1][i - 1] == -1)
       {
         System.out.print(i + "=XXX");
-  
+
       }
       else
       {
@@ -219,16 +246,14 @@ public class MapListTest
    * Tests for method that locates ranges in the 'from' map for given range in
    * the 'to' map.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testLocateInFrom_noIntrons()
   {
     /*
      * Simple mapping with no introns
      */
-    int[] codons = new int[]
-    { 1, 12 };
-    int[] protein = new int[]
-    { 1, 4 };
+    int[] codons = new int[] { 1, 12 };
+    int[] protein = new int[] { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals("[1, 3]", Arrays.toString(ml.locateInFrom(1, 1)));
     assertEquals("[4, 6]", Arrays.toString(ml.locateInFrom(2, 2)));
@@ -251,17 +276,15 @@ public class MapListTest
    * Tests for method that locates ranges in the 'from' map for given range in
    * the 'to' map.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testLocateInFrom_withIntrons()
   {
     /*
      * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
      * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
      */
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein =
-    { 1, 4 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals("[2, 3, 5, 5]", Arrays.toString(ml.locateInFrom(1, 1)));
     assertEquals("[6, 7, 9, 9]", Arrays.toString(ml.locateInFrom(2, 2)));
@@ -274,16 +297,14 @@ public class MapListTest
    * Tests for method that locates ranges in the 'to' map for given range in the
    * 'from' map.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testLocateInTo_noIntrons()
   {
     /*
      * Simple mapping with no introns
      */
-    int[] codons = new int[]
-    { 1, 12 };
-    int[] protein = new int[]
-    { 1, 4 };
+    int[] codons = new int[] { 1, 12 };
+    int[] protein = new int[] { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals("[1, 1]", Arrays.toString(ml.locateInTo(1, 3)));
     assertEquals("[2, 2]", Arrays.toString(ml.locateInTo(4, 6)));
@@ -314,20 +335,18 @@ public class MapListTest
    * Tests for method that locates ranges in the 'to' map for given range in the
    * 'from' map.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testLocateInTo_withIntrons()
   {
     /*
      * Exons at positions [2, 3, 5] [6, 7, 9] [10, 12, 14] [16, 17, 18] i.e.
      * 2-3, 5-7, 9-10, 12-12, 14-14, 16-18
      */
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
     /*
      * Mapped proteins at positions 1, 3, 4, 6 in the sequence
      */
-    int[] protein =
-    { 1, 1, 3, 4, 6, 6 };
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
     MapList ml = new MapList(codons, protein, 3, 1);
 
     /*
@@ -357,13 +376,11 @@ public class MapListTest
   /**
    * Test equals method.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testEquals()
   {
-    int[] codons = new int[]
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein = new int[]
-    { 1, 4 };
+    int[] codons = new int[] { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = new int[] { 1, 4 };
     MapList ml = new MapList(codons, protein, 3, 1);
     MapList ml1 = new MapList(codons, protein, 3, 1); // same values
     MapList ml2 = new MapList(codons, protein, 2, 1); // fromRatio differs
@@ -406,27 +423,23 @@ public class MapListTest
   /**
    * Test for the method that flattens a list of ranges into a single array.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetRanges()
   {
     List<int[]> ranges = new ArrayList<int[]>();
-    ranges.add(new int[]
-    { 2, 3 });
-    ranges.add(new int[]
-    { 5, 6 });
+    ranges.add(new int[] { 2, 3 });
+    ranges.add(new int[] { 5, 6 });
     assertEquals("[2, 3, 5, 6]", Arrays.toString(MapList.getRanges(ranges)));
   }
 
   /**
    * Check state after construction
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testConstructor()
   {
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein =
-    { 1, 1, 3, 4, 6, 6 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
     MapList ml = new MapList(codons, protein, 3, 1);
     assertEquals(3, ml.getFromRatio());
     assertEquals(2, ml.getFromLowest());
@@ -449,6 +462,36 @@ public class MapListTest
     assertEquals("{[2, 3], [5, 7], [9, 10], [12, 12], [14, 14], [16, 18]}",
             prettyPrint(ml2.getFromRanges()));
     assertEquals("{[1, 1], [3, 4], [6, 6]}", prettyPrint(ml2.getToRanges()));
+
+    /*
+     * reverse direction
+     */
+    codons = new int[] { 9, 6 };
+    protein = new int[] { 100, 91, 80, 79 };
+    ml = new MapList(codons, protein, 3, 1);
+    assertEquals(6, ml.getFromLowest());
+    assertEquals(9, ml.getFromHighest());
+    assertEquals(79, ml.getToLowest());
+    assertEquals(100, ml.getToHighest());
+  }
+
+  /**
+   * Test constructor can merge consecutive ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testConstructor_mergeRanges()
+  {
+    int[] codons = { 2, 3, 3, 7, 9, 10, 12, 12, 14, 14, 16, 17 };
+    int[] protein = { 1, 1, 1, 3, 6, 6 };
+    MapList ml = new MapList(codons, protein, 3, 1);
+    assertEquals(3, ml.getFromRatio());
+    assertEquals(2, ml.getFromLowest());
+    assertEquals(17, ml.getFromHighest());
+    assertEquals(1, ml.getToLowest());
+    assertEquals(6, ml.getToHighest());
+    assertEquals("{[2, 7], [9, 10], [12, 12], [14, 14], [16, 17]}",
+            prettyPrint(ml.getFromRanges()));
+    assertEquals("{[1, 3], [6, 6]}", prettyPrint(ml.getToRanges()));
   }
 
   /**
@@ -478,13 +521,11 @@ public class MapListTest
   /**
    * Test the method that creates an inverse mapping
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetInverse()
   {
-    int[] codons =
-    { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
-    int[] protein =
-    { 1, 1, 3, 4, 6, 6 };
+    int[] codons = { 2, 3, 5, 7, 9, 10, 12, 12, 14, 14, 16, 18 };
+    int[] protein = { 1, 1, 3, 4, 6, 6 };
 
     MapList ml = new MapList(codons, protein, 3, 1);
     MapList ml2 = ml.getInverse();
@@ -498,14 +539,279 @@ public class MapListTest
             prettyPrint(ml2.getFromRanges()));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testToString()
   {
-    MapList ml = new MapList(new int[]
-    { 1, 5, 10, 15, 25, 20 }, new int[]
-    { 51, 1 }, 1, 3);
+    MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
+        51, 1 }, 1, 3);
     String s = ml.toString();
-    assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
+    assertEquals("[ [1, 5] [10, 15] [25, 20] ] 1:3 to [ [51, 1] ]", s);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testAddMapList()
+  {
+    MapList ml = new MapList(new int[] { 11, 15, 20, 25, 35, 30 },
+            new int[] { 72, 22 }, 1, 3);
+    assertEquals(11, ml.getFromLowest());
+    assertEquals(35, ml.getFromHighest());
+    assertEquals(22, ml.getToLowest());
+    assertEquals(72, ml.getToHighest());
+
+    MapList ml2 = new MapList(new int[] { 2, 4, 37, 40 }, new int[] { 12,
+        17, 78, 83, 88, 96 }, 1, 3);
+    ml.addMapList(ml2);
+    assertEquals(2, ml.getFromLowest());
+    assertEquals(40, ml.getFromHighest());
+    assertEquals(12, ml.getToLowest());
+    assertEquals(96, ml.getToHighest());
+
+    String s = ml.toString();
+    assertEquals(
+            "[ [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()
+  {
+    MapList ml = new MapList(new int[] { 11, 15 }, new int[] { 72, 58 }, 1,
+            3);
+
+    MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
+            1, 3);
+    ml.addMapList(ml2);
+    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[]>();
+
+    // 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
+   */
+  @Test(groups = { "Functional" })
+  public void testConstructor_withLists()
+  {
+    /*
+     * reverse direction
+     */
+    int[][] codons = new int[][] { { 9, 6 } };
+    int[][] protein = new int[][] { { 100, 91 }, { 80, 79 } };
+    MapList ml = new MapList(Arrays.asList(codons), Arrays.asList(protein),
+            3, 1);
+    assertEquals(6, ml.getFromLowest());
+    assertEquals(9, ml.getFromHighest());
+    assertEquals(79, ml.getToLowest());
+    assertEquals(100, ml.getToHighest());
+  }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse from
+   * range. Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsFromForwardStrand()
+  {
+    // [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());
+  }
+
+  /**
+   * Test the method that merges a list of ranges where possible
+   */
+  @Test(groups = { "Functional" })
+  public void testCoalesceRanges()
+  {
+    assertNull(MapList.coalesceRanges(null));
+    List<int[]> ranges = new ArrayList<int[]>();
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+    ranges.add(new int[] { 1, 3 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // add non-contiguous range:
+    ranges.add(new int[] { 5, 6 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // 'contiguous' range in opposite direction is not merged:
+    ranges.add(new int[] { 7, 6 });
+    assertSame(ranges, MapList.coalesceRanges(ranges));
+
+    // merging in forward direction:
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 4, 5 });
+    ranges.add(new int[] { 5, 5 });
+    ranges.add(new int[] { 5, 7 });
+    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();
+    ranges.add(new int[] { 7, 5 });
+    ranges.add(new int[] { 5, 4 });
+    ranges.add(new int[] { 4, 4 });
+    ranges.add(new int[] { 3, 1 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(1, merged.size());
+    assertArrayEquals(new int[] { 7, 1 }, merged.get(0));
+
+    // merging with switches of direction:
+    ranges.clear();
+    ranges.add(new int[] { 1, 3 });
+    ranges.add(new int[] { 4, 5 });
+    ranges.add(new int[] { 5, 5 });
+    ranges.add(new int[] { 6, 6 });
+    ranges.add(new int[] { 12, 10 });
+    ranges.add(new int[] { 9, 8 });
+    ranges.add(new int[] { 8, 8 });
+    ranges.add(new int[] { 7, 7 });
+    merged = MapList.coalesceRanges(ranges);
+    assertEquals(2, merged.size());
+    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<int[]>();
+    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));
+  }
 }