JAL-2388 Finished split of hidden columns and selected columns

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index fd4b364..ceae253 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1812,7 +1812,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
      * Check for selection in a view of which this one is a dna/protein
      * complement.
      */
-    if (selectionFromTranslation(seqsel, colsel, source))
+    if (selectionFromTranslation(seqsel, colsel, hidden, source))
     {
       return;
     }
@@ -1946,7 +1946,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -1969,9 +1970,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     /*
      * Map column selection
      */
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
-            av);
+    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+    // av);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
+    av.getAlignment().setHiddenColumns(hs);
 
     ap.scalePanelHolder.repaint();
     ap.repaint();

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4b1eb56..4d69fa4 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -498,7 +498,7 @@ public class ColumnSelection
    * @param res
    *          int
    */
-  public void hideSelectedColumns(int col, AlignmentI al)
+  public void hideSelectedColumns(int col, HiddenColumns hidden)
   {
     /*
      * deselect column (whether selected or not!)
@@ -531,7 +531,7 @@ public class ColumnSelection
       min = max;
     }
 
-    al.getHiddenColumns().hideColumns(min, max);
+    hidden.hideColumns(min, max);
   }
 
 

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 282e826..063ab7d 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1956,8 +1956,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          HiddenColumns hidden,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
     // handles selection messages...
@@ -1982,7 +1981,7 @@ public class SeqPanel extends JPanel implements MouseListener,
      * Check for selection in a view of which this one is a dna/protein
      * complement.
      */
-    if (selectionFromTranslation(seqsel, colsel, source))
+    if (selectionFromTranslation(seqsel, colsel, hidden, source))
     {
       return;
     }
@@ -2077,7 +2076,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -2100,9 +2100,13 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * Map column selection
      */
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
-            av);
+    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+    // av);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
+    av.getAlignment().setHiddenColumns(hs);
 
     PaintRefresher.Refresh(this, av.getSequenceSetId());
 

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index dcf0f5d..e89dcfb 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -83,8 +83,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private List<int[]> hiddenColumnsList;
-
   private HiddenColumns hiddenColumns;
 
   private List<String> hiddenSeqRefs;
@@ -667,12 +665,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if (hiddenCols != null && !hiddenCols.isEmpty())
     {
-      HiddenColumns hidden = new HiddenColumns();
+      hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
       for (String rangeString : rangeStrings)
       {
         String[] range = rangeString.split("-");
-        hidden.hideColumns(Integer.valueOf(range[0]),
+        hiddenColumns.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
     }

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 44a55ec..33c43d3 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -509,18 +509,20 @@ public final class MappingUtils
    * @param mapTo
    * @return
    */
-  public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
-          AlignViewportI mapFrom, AlignViewportI mapTo)
+  public static void mapColumnSelection(ColumnSelection colsel,
+          HiddenColumns hiddencols, AlignViewportI mapFrom,
+          AlignViewportI mapTo, ColumnSelection newColSel,
+          HiddenColumns newHidden)
   {
     boolean targetIsNucleotide = mapTo.isNucleotide();
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
     List<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
-    ColumnSelection mappedColumns = new ColumnSelection();
+    // ColumnSelection mappedColumns = new ColumnSelection();
 
     if (colsel == null)
     {
-      return mappedColumns;
+      return; // mappedColumns;
     }
 
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
@@ -534,16 +536,16 @@ public final class MappingUtils
 
     for (Integer sel : colsel.getSelected())
     {
-      mapColumn(sel.intValue(), codonFrames, mappedColumns, fromSequences,
+      mapColumn(sel.intValue(), codonFrames, newColSel, fromSequences,
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : colsel.getListOfCols())
+    for (int[] hidden : hiddencols.getListOfCols())
     {
-      mapHiddenColumns(hidden, codonFrames, mappedColumns, fromSequences,
+      mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
               toSequences, fromGapChar);
     }
-    return mappedColumns;
+    return; // mappedColumns;
   }
 
   /**

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a70e382..9c8c233 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1356,7 +1356,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (start == end)
     {
-      colSel.hideSelectedColumns(start, alignment);
+      colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
     }
     else
     {

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 6debd87..e5f2daa 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -106,7 +106,7 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     // hide column 5 (and adjacent):
-    cs.hideSelectedColumns(5, al);
+    cs.hideSelectedColumns(5, al.getHiddenColumns());
     // 4,5,6 now hidden:
     List<int[]> hidden = al.getHiddenColumns().getListOfCols();
     assertEquals(1, hidden.size());
@@ -120,7 +120,7 @@ public class ColumnSelectionTest
     cs.addElement(4);
     cs.addElement(5);
     cs.addElement(6);
-    cs.hideSelectedColumns(4, al);
+    cs.hideSelectedColumns(4, al.getHiddenColumns());
     hidden = al.getHiddenColumns().getListOfCols();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
@@ -132,7 +132,7 @@ public class ColumnSelectionTest
     cs.addElement(4);
     cs.addElement(5);
     cs.addElement(6);
-    cs.hideSelectedColumns(6, al);
+    cs.hideSelectedColumns(6, al.getHiddenColumns());
     hidden = al.getHiddenColumns().getListOfCols();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
@@ -143,7 +143,7 @@ public class ColumnSelectionTest
     cs = new ColumnSelection();
     cs.addElement(4);
     cs.addElement(6);
-    cs.hideSelectedColumns(5, al);
+    cs.hideSelectedColumns(5, al.getHiddenColumns());
     hidden = al.getHiddenColumns().getListOfCols();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index be658d5..5eaecd3 100644 (file)
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -242,7 +242,7 @@ public class HiddenColumnsTest
             Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
 
     // hidden column on gap after end of sequence - should not affect bounds
-    colsel.hideSelectedColumns(13, al);
+    colsel.hideSelectedColumns(13, al.getHiddenColumns());
     assertEquals(
             Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
                 seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
@@ -253,7 +253,7 @@ public class HiddenColumnsTest
     cs.revealAllHiddenColumns(colsel);
     // hidden column on gap before beginning of sequence - should vis bounds by
     // one
-    colsel.hideSelectedColumns(0, al);
+    colsel.hideSelectedColumns(0, al.getHiddenColumns());
     assertEquals(
             Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
                 seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
@@ -310,12 +310,12 @@ public class HiddenColumnsTest
 
     ColumnSelection colsel = new ColumnSelection();
     HiddenColumns cs = al.getHiddenColumns();
-    colsel.hideSelectedColumns(5, al);
+    colsel.hideSelectedColumns(5, al.getHiddenColumns());
     List<int[]> hidden = cs.getListOfCols();
     assertEquals(1, hidden.size());
     assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
 
-    colsel.hideSelectedColumns(3, al);
+    colsel.hideSelectedColumns(3, al.getHiddenColumns());
     assertEquals(2, hidden.size());
     // two hidden ranges, in order:
     assertSame(hidden, cs.getListOfCols());
@@ -324,7 +324,7 @@ public class HiddenColumnsTest
 
     // hiding column 4 expands [3, 3] to [3, 4]
     // and merges to [5, 5] to make [3, 5]
-    colsel.hideSelectedColumns(4, al);
+    colsel.hideSelectedColumns(4, al.getHiddenColumns());
     hidden = cs.getListOfCols();
     assertEquals(1, hidden.size());
     assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 78a867e..bd97ad8 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.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();
+    List<int[]> hidden = dnaHidden.getListOfCols();
     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.hideSelectedColumns(1);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    hidden = dnaSelection.getListOfCols();
+    proteinSelection.hideSelectedColumns(1, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    hidden = dnaHidden.getListOfCols();
     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.hideSelectedColumns(2);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    assertTrue(dnaSelection.getListOfCols().isEmpty());
+    proteinSelection.hideSelectedColumns(2, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    assertTrue(dnaHidden.getListOfCols().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.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();
+    hidden = dnaHidden.getListOfCols();
     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.hideSelectedColumns(1);
-    proteinSelection.hideSelectedColumns(3);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
-    hidden = dnaSelection.getListOfCols();
+    proteinSelection.hideSelectedColumns(1, hiddenCols);
+    proteinSelection.hideSelectedColumns(3, hiddenCols);
+    MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+            proteinView, dnaView, dnaSelection, dnaHidden);
+    hidden = dnaHidden.getListOfCols();
     assertEquals(2, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
     assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));