JAL-2591 simplifying hidden columns usage

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e51131b..02d30bb 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -22,6 +22,9 @@ package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -43,6 +46,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -169,14 +173,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }
 
   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
-          ColumnSelection columnSelection, JalviewLite applet,
+          HiddenColumns hidden, JalviewLite applet,
           String title, boolean embedded)
   {
-    this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+    this(al, hiddenSeqs, hidden, applet, title, embedded, true);
   }
 
   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
-          ColumnSelection columnSelection, JalviewLite applet,
+          HiddenColumns hidden, JalviewLite applet,
           String title, boolean embedded, boolean addToDisplay)
   {
     if (applet != null)
@@ -219,9 +223,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.hideSequence(hiddenSeqs);
     }
-    if (columnSelection != null)
+    if (hidden != null)
     {
-      viewport.setColumnSelection(columnSelection);
+      viewport.getAlignment().setHiddenColumns(hidden);
     }
     viewport.setScaleAboveWrapped(scaleAbove.getState());
 
@@ -597,24 +601,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     case KeyEvent.VK_PAGE_UP:
       if (viewport.getWrapAlignment())
       {
-        alignPanel.scrollUp(true);
+        ranges.scrollUp(true);
       }
       else
       {
-        alignPanel.setScrollValues(ranges.getStartRes(),
-                2 * ranges.getStartSeq() - ranges.getEndSeq());
+        ranges.pageUp();
       }
       break;
 
     case KeyEvent.VK_PAGE_DOWN:
       if (viewport.getWrapAlignment())
       {
-        alignPanel.scrollUp(false);
+        ranges.scrollUp(false);
       }
       else
       {
-        alignPanel
-                .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
+        ranges.pageDown();
       }
       break;
 
@@ -1071,6 +1073,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       delete_actionPerformed();
     }
+    else if (source == createGroup)
+    {
+      createGroup_actionPerformed();
+    }
+    else if (source == unGroup)
+    {
+      unGroup_actionPerformed();
+    }
     else if (source == grpsFromSelection)
     {
       makeGrpsFromSelection_actionPerformed();
@@ -1788,7 +1798,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    List<SequenceI> sg = new Vector<SequenceI>();
+    List<SequenceI> sg = new Vector<>();
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
@@ -1901,7 +1911,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     SequenceGroup sg = viewport.getSelectionGroup();
     copiedSequences = new StringBuffer();
-    Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
+    Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
     for (int i = 0; i < sg.getSize(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
@@ -1916,7 +1926,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+      for (int[] region : viewport.getAlignment().getHiddenColumns()
+              .getHiddenRegions())
       {
         copiedHiddenColumns.addElement(new int[] {
             region[0] - hiddenOffset, region[1] - hiddenOffset });
@@ -2681,9 +2692,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean selected = conservationMenuItem.getState();
     modifyConservation.setEnabled(selected);
     viewport.setConservationSelected(selected);
-
-    // viewport.setAbovePIDThreshold(false);
-    // abovePIDThreshold.setState(false);
+    viewport.getResidueShading().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
 
@@ -2702,8 +2711,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean selected = abovePIDThreshold.getState();
     modifyPID.setEnabled(selected);
     viewport.setAbovePIDThreshold(selected);
-    // conservationMenuItem.setState(false);
-    // viewport.setConservationSelected(false);
+    if (!selected)
+    {
+      viewport.getResidueShading().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
     changeColour(viewport.getGlobalColourScheme());
 
@@ -2721,7 +2733,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
-            .getAlignment().getSequenceAt(0), null);
+            .getAlignment().getSequenceAt(0));
 
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
@@ -2813,25 +2825,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void averageDistanceTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
+    newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
+            "Average distance tree using PID");
   }
 
   public void neighbourTreeMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
+            "Neighbour joining tree using PID");
   }
 
   protected void njTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+            .getBlosum62().getName(),
+            "Neighbour joining tree using BLOSUM62");
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed()
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+            .getBlosum62().getName(),
+            "Average distance tree using BLOSUM62");
   }
 
-  void NewTreePanel(String type, String pwType, String title)
+  void newTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
     if (!viewport.getAlignment().isAligned(false))
@@ -3337,7 +3355,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
+    createGroup.addActionListener(this);
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
+    unGroup.addActionListener(this);
+
     annotationColumnSelection.setLabel(MessageManager
             .getString("action.select_by_annotation"));
     annotationColumnSelection.addActionListener(this);
@@ -4186,9 +4207,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * @param csel
    *          - columns to be selected on the alignment
    */
-  public void select(SequenceGroup sel, ColumnSelection csel)
+  public void select(SequenceGroup sel, ColumnSelection csel,
+          HiddenColumns hidden)
   {
-    alignPanel.seqPanel.selection(sel, csel, null);
+    alignPanel.seqPanel.selection(sel, csel, hidden, null);
   }
 
   public void scrollTo(int row, int column)