X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMapListTest.java;h=d2db258583b1cf946c01c5a0d47eacdba93f948a;hb=353109c11d706b29ae5bc9606f0e12223aa45a98;hp=9699af9edf52f3f1ab50a91fec2026922a07727b;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 9699af9..d2db258 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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()
   {
@@ -804,4 +814,130 @@ public class MapListTest
     assertEquals(1, merged.size());
     assertArrayEquals(new int[] { 9, 0 }, merged.get(0));
   }
+
+  /**
+   * Test the method that compounds ('traverses') two mappings
+   */
+  @Test
+  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);
+    MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70,
+        75, 90, 127 }, 1, 1);
+    MapList compound = ml1.traverse(ml2);
+
+    assertEquals(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    List<int[]> fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 2);
+    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);
+    // 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));
+
+    /*
+     * 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(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    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));
+
+    /*
+     * 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(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 3);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    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));
+
+    /*
+     * 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(compound.getFromRatio(), 3);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    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));
+
+    /*
+     * 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(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    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));
+
+    /*
+     * 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(compound.getFromRatio(), 1);
+    assertEquals(compound.getToRatio(), 1);
+    fromRanges = compound.getFromRanges();
+    assertEquals(fromRanges.size(), 1);
+    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));
+
+    /*
+     * 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);
+  }
 }