JAL-2446 merged to spike branch

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

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index b84e770..19c8438 100644 (file)
--- 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;
@@ -300,49 +301,60 @@ 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 +419,17 @@ 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 +439,9 @@ 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 +449,10 @@ 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());
   }
 
@@ -882,69 +901,80 @@ 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.hideColumns(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.getHiddenColumns();
+    List<int[]> hidden = dnaHidden.getHiddenRegions();
     assertEquals(1, hidden.size());
     assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
 
     /*
      * 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.hideColumns(1);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    hidden = dnaSelection.getHiddenColumns();
+    proteinSelection.hideSelectedColumns(1, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    hidden = dnaHidden.getHiddenRegions();
     assertEquals(1, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
      */
-    proteinSelection.revealAllHiddenColumns();
+    dnaSelection = new ColumnSelection();
+    dnaHidden = new HiddenColumns();
+    hiddenCols.revealAllHiddenColumns(proteinSelection);
     proteinSelection.clear();
-    proteinSelection.hideColumns(2);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    assertTrue(dnaSelection.getHiddenColumns().isEmpty());
+    proteinSelection.hideSelectedColumns(2, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    assertTrue(dnaHidden.getHiddenRegions().isEmpty());
 
     /*
      * 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.hideColumns(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.getHiddenColumns();
+    hidden = dnaHidden.getHiddenRegions();
     assertEquals(1, hidden.size());
     assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
 
     /*
      * 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.hideColumns(1);
-    proteinSelection.hideColumns(3);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    hidden = dnaSelection.getHiddenColumns();
+    proteinSelection.hideSelectedColumns(1, hiddenCols);
+    proteinSelection.hideSelectedColumns(3, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    hidden = dnaHidden.getHiddenRegions();
     assertEquals(2, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
     assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));