JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)

[jalview.git] / test / jalview / util / MappingUtilsTest.java

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index d4cf98a..dd789d6 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
 
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
@@ -50,6 +51,7 @@ import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Iterator;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -913,9 +915,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 4]", Arrays.toString(regions.next()));
 
     /*
      * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
@@ -930,9 +932,9 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(1, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
@@ -944,7 +946,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(2, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
+    assertEquals(0, dnaHidden.getNumberOfRegions());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
@@ -959,9 +961,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
 
     /*
      * Combine hiding columns 1 and 3 to get discontiguous hidden columns
@@ -974,10 +976,10 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(3, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(2, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+    regions = dnaHidden.iterator();
+    assertEquals(2, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
   }
 
   @Test(groups = { "Functional" })
@@ -1283,4 +1285,33 @@ public class MappingUtilsTest
     assertEquals(1, ranges.size());
     assertEquals(9, ranges.get(0)[1]);
   }
+  
+  @Test(groups = "Functional")
+  public void testListToArray()
+  {
+    List<int[]> ranges = new ArrayList<>();
+    
+    int[] result = MappingUtils.listToArray(ranges);
+    assertEquals(result.length, 0);
+    ranges.add(new int[] {24, 12});
+    result = MappingUtils.listToArray(ranges);
+    assertEquals(result.length, 2);
+    assertEquals(result[0], 24);
+    assertEquals(result[1], 12);
+    ranges.add(new int[] {-7, 30});
+    result = MappingUtils.listToArray(ranges);
+    assertEquals(result.length, 4);
+    assertEquals(result[0], 24);
+    assertEquals(result[1], 12);
+    assertEquals(result[2], -7);
+    assertEquals(result[3], 30);
+    try
+    {
+      MappingUtils.listToArray(null);
+      fail("Expected exception");
+    } catch (NullPointerException e)
+    {
+      // expected
+    }
+  }
 }