X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=492cbb66dab6f444f9d3be8d0aad629f0cdafbe7;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=853ebd5eed5d0056ebed320923bd2d03ea9b1be7;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 853ebd5..492cbb66 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -24,7 +24,6 @@ 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.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
@@ -40,7 +39,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 
 import java.awt.Color;
@@ -198,10 +199,10 @@ public class MappingUtilsTest
      * viewport).
      */
     AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
-            "FASTA");
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
-            "FASTA");
+            FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1);
@@ -269,11 +270,11 @@ public class MappingUtilsTest
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format)
+  protected AlignmentI loadAlignment(final String data, FileFormatI format)
           throws IOException
   {
     AlignmentI a = new FormatAdapter().readFile(data,
-            AppletFormatAdapter.PASTE, format);
+            DataSourceType.PASTE, format);
     a.setDataset(null);
     return a;
   }
@@ -352,11 +353,11 @@ public class MappingUtilsTest
      */
     AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
             + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
-            "FASTA");
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(
             ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n",
-            "FASTA");
+            FileFormat.Fasta);
     protein.setDataset(null);
 
     // map first dna to first protein seq
@@ -467,10 +468,11 @@ public class MappingUtilsTest
      * viewport).
      */
     AlignmentI cdna = loadAlignment(
-            ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA");
+            ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n",
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n",
-            "FASTA");
+            FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
@@ -550,10 +552,10 @@ public class MappingUtilsTest
      */
     AlignmentI cdna = loadAlignment(
             ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n",
-            "FASTA");
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(
-            ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA");
+            ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);
@@ -862,6 +864,10 @@ public class MappingUtilsTest
   public void testGetLength()
   {
     assertEquals(0, MappingUtils.getLength(null));
+
+    /*
+     * [start, end] ranges
+     */
     List<int[]> ranges = new ArrayList<int[]>();
     assertEquals(0, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 1, 1 });
@@ -870,6 +876,15 @@ public class MappingUtilsTest
     assertEquals(10, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 20, 10 });
     assertEquals(21, MappingUtils.getLength(ranges));
+
+    /*
+     * [start, end, start, end...] ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 5, 8, 4 });
+    ranges.add(new int[] { 8, 2 });
+    ranges.add(new int[] { 12, 12 });
+    assertEquals(18, MappingUtils.getLength(ranges));
   }
 
   @Test(groups = { "Functional" })
@@ -911,4 +926,107 @@ public class MappingUtilsTest
     assertFalse(MappingUtils.contains(ranges, -45));
   }
 
+  /**
+   * Test the method that drops positions from the start of a mapped range
+   */
+  @Test(groups = "Functional")
+  public void testRemoveStartPositions()
+  {
+    int[] ranges = new int[] { 1, 10 };
+    int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
+    assertEquals("[1, 10]", Arrays.toString(adjusted));
+
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[2, 10]", Arrays.toString(adjusted));
+    assertEquals("[1, 10]", Arrays.toString(ranges));
+
+    ranges = adjusted;
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[3, 10]", Arrays.toString(adjusted));
+    assertEquals("[2, 10]", Arrays.toString(ranges));
+
+    ranges = new int[] { 2, 3, 10, 12 };
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[3, 3, 10, 12]", Arrays.toString(adjusted));
+    assertEquals("[2, 3, 10, 12]", Arrays.toString(ranges));
+
+    ranges = new int[] { 2, 2, 8, 12 };
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[8, 12]", Arrays.toString(adjusted));
+    assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges));
+
+    ranges = new int[] { 2, 2, 8, 12 };
+    adjusted = MappingUtils.removeStartPositions(2, ranges);
+    assertEquals("[9, 12]", Arrays.toString(adjusted));
+    assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges));
+
+    ranges = new int[] { 2, 2, 4, 4, 9, 12 };
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[4, 4, 9, 12]", Arrays.toString(adjusted));
+    assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges));
+
+    ranges = new int[] { 2, 2, 4, 4, 9, 12 };
+    adjusted = MappingUtils.removeStartPositions(2, ranges);
+    assertEquals("[9, 12]", Arrays.toString(adjusted));
+    assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges));
+
+    ranges = new int[] { 2, 3, 9, 12 };
+    adjusted = MappingUtils.removeStartPositions(3, ranges);
+    assertEquals("[10, 12]", Arrays.toString(adjusted));
+    assertEquals("[2, 3, 9, 12]", Arrays.toString(ranges));
+  }
+
+  /**
+   * Test the method that drops positions from the start of a mapped range, on
+   * the reverse strand
+   */
+  @Test(groups = "Functional")
+  public void testRemoveStartPositions_reverseStrand()
+  {
+    int[] ranges = new int[] { 10, 1 };
+    int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
+    assertEquals("[10, 1]", Arrays.toString(adjusted));
+    assertEquals("[10, 1]", Arrays.toString(ranges));
+  
+    ranges = adjusted;
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[9, 1]", Arrays.toString(adjusted));
+    assertEquals("[10, 1]", Arrays.toString(ranges));
+  
+    ranges = adjusted;
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[8, 1]", Arrays.toString(adjusted));
+    assertEquals("[9, 1]", Arrays.toString(ranges));
+  
+    ranges = new int[] { 12, 11, 9, 6 };
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[11, 11, 9, 6]", Arrays.toString(adjusted));
+    assertEquals("[12, 11, 9, 6]", Arrays.toString(ranges));
+  
+    ranges = new int[] { 12, 12, 8, 4 };
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[8, 4]", Arrays.toString(adjusted));
+    assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
+  
+    ranges = new int[] { 12, 12, 8, 4 };
+    adjusted = MappingUtils.removeStartPositions(2, ranges);
+    assertEquals("[7, 4]", Arrays.toString(adjusted));
+    assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
+  
+    ranges = new int[] { 12, 12, 10, 10, 8, 4 };
+    adjusted = MappingUtils.removeStartPositions(1, ranges);
+    assertEquals("[10, 10, 8, 4]", Arrays.toString(adjusted));
+    assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
+  
+    ranges = new int[] { 12, 12, 10, 10, 8, 4 };
+    adjusted = MappingUtils.removeStartPositions(2, ranges);
+    assertEquals("[8, 4]", Arrays.toString(adjusted));
+    assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
+  
+    ranges = new int[] { 12, 11, 8, 4 };
+    adjusted = MappingUtils.removeStartPositions(3, ranges);
+    assertEquals("[7, 4]", Arrays.toString(adjusted));
+    assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
+  }
+
 }