X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=097ccd4900741de81b93f066204323ac3703fca4;hb=9062c3dbd065631f01af61f47a8cbafabe9c6c8b;hp=78a867e29388844dcb48c9be69d945734233fd80;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 78a867e..097ccd4 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -33,6 +33,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -49,6 +50,7 @@ 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;
@@ -300,49 +302,60 @@ public class MappingUtilsTest
     setupMappedAlignments();
 
     ColumnSelection colsel = new ColumnSelection();
+    HiddenColumns hidden = new HiddenColumns();
 
     /*
      * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
      * in dna respectively, overall 0-4
      */
     colsel.addElement(0);
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
-            proteinView, dnaView);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+            cs, hs);
     assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());
 
     /*
      * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
      */
+    cs.clear();
     colsel.clear();
     colsel.addElement(1);
-    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+            cs, hs);
     assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
      */
+    cs.clear();
     colsel.clear();
     colsel.addElement(2);
-    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
+            dnaView, cs, hs);
     assertEquals("[]", cs.getSelected().toString());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
      * 6-9, 6-10, 5-8 respectively, overall to 5-10
      */
+    cs.clear();
     colsel.clear();
     colsel.addElement(3);
-    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
+            dnaView, cs, hs);
     assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());
 
     /*
      * Combine selection of columns 1 and 3 to get a discontiguous mapped
      * selection
      */
+    cs.clear();
     colsel.clear();
     colsel.addElement(1);
     colsel.addElement(3);
-    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
+            dnaView, cs, hs);
     assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
             .toString());
   }
@@ -407,14 +420,17 @@ public class MappingUtilsTest
     setupMappedAlignments();
 
     ColumnSelection colsel = new ColumnSelection();
+    HiddenColumns hidden = new HiddenColumns();
 
     /*
      * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
      * in protein.
      */
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
     colsel.addElement(0);
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
-            proteinView);
+    MappingUtils.mapColumnSelection(colsel, hidden, dnaView, proteinView,
+            cs, hs);
     assertEquals("[0, 1]", cs.getSelected().toString());
 
     /*
@@ -424,7 +440,9 @@ public class MappingUtilsTest
     colsel.addElement(3);
     colsel.addElement(4);
     colsel.addElement(5);
-    cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
+    cs.clear();
+    MappingUtils.mapColumnSelection(colsel, hidden, dnaView, proteinView,
+            cs, hs);
     assertEquals("[0, 1, 3]", cs.getSelected().toString());
   }
 
@@ -432,8 +450,10 @@ public class MappingUtilsTest
   public void testMapColumnSelection_null() throws IOException
   {
     setupMappedAlignments();
-    ColumnSelection cs = MappingUtils.mapColumnSelection(null, dnaView,
-            proteinView);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(null, null, dnaView, proteinView, cs,
+            hs);
     assertTrue("mapped selection not empty", cs.getSelected().isEmpty());
   }
 
@@ -670,7 +690,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
     acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
@@ -745,7 +765,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf4 = new AlignedCodonFrame();
     acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
@@ -802,7 +822,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
     acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf);
 
     AlignmentI prot = new Alignment(new SequenceI[] { protein });
@@ -882,72 +902,83 @@ public class MappingUtilsTest
     setupMappedAlignments();
 
     ColumnSelection proteinSelection = new ColumnSelection();
+    HiddenColumns hiddenCols = new HiddenColumns();
 
     /*
      * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
      * in dna respectively, overall 0-4
      */
-    proteinSelection.hideSelectedColumns(0);
-    ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(
-            proteinSelection, proteinView, dnaView);
+    proteinSelection.hideSelectedColumns(0, hiddenCols);
+    ColumnSelection dnaSelection = new ColumnSelection();
+    HiddenColumns dnaHidden = new HiddenColumns();
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaSelection.getListOfCols();
-    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
      */
-    proteinSelection.revealAllHiddenColumns();
+    dnaSelection = new ColumnSelection();
+    dnaHidden = new HiddenColumns();
+    hiddenCols.revealAllHiddenColumns(proteinSelection);
     // the unhidden columns are now marked selected!
     assertEquals("[0]", proteinSelection.getSelected().toString());
     // deselect these or hideColumns will be expanded to include 0
     proteinSelection.clear();
-    proteinSelection.hideSelectedColumns(1);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    hidden = dnaSelection.getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+    proteinSelection.hideSelectedColumns(1, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
      */
-    proteinSelection.revealAllHiddenColumns();
+    dnaSelection = new ColumnSelection();
+    dnaHidden = new HiddenColumns();
+    hiddenCols.revealAllHiddenColumns(proteinSelection);
     proteinSelection.clear();
-    proteinSelection.hideSelectedColumns(2);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    assertTrue(dnaSelection.getListOfCols().isEmpty());
+    proteinSelection.hideSelectedColumns(2, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    assertEquals(0, dnaHidden.getNumberOfRegions());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
      * 6-9, 6-10, 5-8 respectively, overall to 5-10
      */
-    proteinSelection.revealAllHiddenColumns();
+    dnaSelection = new ColumnSelection();
+    dnaHidden = new HiddenColumns();
+    hiddenCols.revealAllHiddenColumns(proteinSelection);
     proteinSelection.clear();
-    proteinSelection.hideSelectedColumns(3); // 5-10 hidden in dna
+    proteinSelection.hideSelectedColumns(3, hiddenCols); // 5-10 hidden in dna
     proteinSelection.addElement(1); // 0-3 selected in dna
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaSelection.getListOfCols();
-    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
      */
-    proteinSelection.revealAllHiddenColumns();
+    dnaSelection = new ColumnSelection();
+    dnaHidden = new HiddenColumns();
+    hiddenCols.revealAllHiddenColumns(proteinSelection);
     proteinSelection.clear();
-    proteinSelection.hideSelectedColumns(1);
-    proteinSelection.hideSelectedColumns(3);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    hidden = dnaSelection.getListOfCols();
-    assertEquals(2, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+    proteinSelection.hideSelectedColumns(1, hiddenCols);
+    proteinSelection.hideSelectedColumns(3, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    regions = dnaHidden.iterator();
+    assertEquals(2, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
   }
 
   @Test(groups = { "Functional" })
@@ -958,7 +989,7 @@ public class MappingUtilsTest
     /*
      * [start, end] ranges
      */
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertEquals(0, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 1, 1 });
     assertEquals(1, MappingUtils.getLength(ranges));
@@ -981,7 +1012,7 @@ public class MappingUtilsTest
   public void testContains()
   {
     assertFalse(MappingUtils.contains(null, 1));
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertFalse(MappingUtils.contains(ranges, 1));
 
     ranges.add(new int[] { 1, 4 });
@@ -1119,4 +1150,138 @@ public class MappingUtilsTest
     assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
   }
 
+  @Test(groups = { "Functional" })
+  public void testRangeContains()
+  {
+    /*
+     * both forward ranges
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        4, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        0, 9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        -10, -9 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        1, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 12 }));
+
+    /*
+     * forward range, reverse query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        5, 5 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+        10, 0 }));
+
+    /*
+     * reverse range, forward query
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        1, 9 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        2, 10 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 6 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        6, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 20 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -3, -2 }));
+
+    /*
+     * both reverse
+     */
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        9, 1 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 2 }));
+    assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        3, 3 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        11, 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        10, 0 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        12, 11 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+        -5, -8 }));
+
+    /*
+     * bad arguments
+     */
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
+            new int[] {
+        1, 10 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
+            new int[] { 1 }));
+    assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
+    assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
+  }
+
+  @Test(groups = "Functional")
+  public void testRemoveEndPositions()
+  {
+    List<int[]> ranges = new ArrayList<>();
+
+    /*
+     * case 1: truncate last range
+     */
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 30 });
+    MappingUtils.removeEndPositions(5, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(25, ranges.get(1)[1]);
+
+    /*
+     * case 2: remove last range
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 22 });
+    MappingUtils.removeEndPositions(3, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(10, ranges.get(0)[1]);
+
+    /*
+     * case 3: truncate penultimate range
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 21 });
+    MappingUtils.removeEndPositions(3, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(9, ranges.get(0)[1]);
+
+    /*
+     * case 4: remove last two ranges
+     */
+    ranges.clear();
+    ranges.add(new int[] { 1, 10 });
+    ranges.add(new int[] { 20, 20 });
+    ranges.add(new int[] { 30, 30 });
+    MappingUtils.removeEndPositions(3, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(9, ranges.get(0)[1]);
+  }
 }