Merge branch 'bug/JAL-2592userDefinedScheme' into develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 016ee85..f4dd851 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -53,6 +53,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -166,7 +167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public AlignViewControllerI avc;
 
-  List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
+  List<AlignmentPanel> alignPanels = new ArrayList<>();
 
   /**
    * Last format used to load or save alignments in this window
@@ -233,7 +234,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param height
    *          height of frame.
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
           int width, int height)
   {
     this(al, hiddenColumns, width, height, null);
@@ -250,7 +251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param sequenceSetId
    *          (may be null)
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
           int width, int height, String sequenceSetId)
   {
     this(al, hiddenColumns, width, height, sequenceSetId, null);
@@ -269,7 +270,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param viewId
    *          (may be null)
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
           int width, int height, String sequenceSetId, String viewId)
   {
     setSize(width, height);
@@ -288,7 +289,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
-          ColumnSelection hiddenColumns, int width, int height)
+          HiddenColumns hiddenColumns, int width, int height)
   {
     setSize(width, height);
 
@@ -395,8 +396,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addKeyListener();
 
-    final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
-    final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+    final List<AlignmentPanel> selviews = new ArrayList<>();
+    final List<AlignmentPanel> origview = new ArrayList<>();
     final String menuLabel = MessageManager
             .getString("label.copy_format_from");
     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
@@ -409,7 +410,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 origview.clear();
                 origview.add(alignPanel);
                 // make an array of all alignment panels except for this one
-                List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
+                List<AlignmentPanel> aps = new ArrayList<>(
                         Arrays.asList(Desktop.getAlignmentPanels(null)));
                 aps.remove(AlignFrame.this.alignPanel);
                 return aps.toArray(new AlignmentPanel[aps.size()]);
@@ -688,26 +689,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          if (viewport.getWrapAlignment())
-          {
-            alignPanel.scrollUp(true);
-          }
-          else
-          {
-            alignPanel.setScrollValues(vpRanges.getStartRes(),
-                    2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
-          }
+          vpRanges.pageUp();
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          if (viewport.getWrapAlignment())
-          {
-            alignPanel.scrollUp(false);
-          }
-          else
-          {
-            alignPanel.setScrollValues(vpRanges.getStartRes(),
-                    vpRanges.getEndSeq());
-          }
+          vpRanges.pageDown();
           break;
         }
       }
@@ -1192,8 +1177,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
               exportData.getOmitHidden(), exportData.getStartEndPostions(),
-              f.getCacheSuffixDefault(format),
-              viewport.getColumnSelection());
+              f.getCacheSuffixDefault(format), viewport.getAlignment()
+                      .getHiddenColumns());
 
       if (output == null)
       {
@@ -1271,8 +1256,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
               .formatSequences(format, exportData.getAlignment(),
                       exportData.getOmitHidden(),
-                      exportData.getStartEndPostions(),
-                      viewport.getColumnSelection()));
+ exportData
+                              .getStartEndPostions(), viewport
+                              .getAlignment().getHiddenColumns()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
               "label.alignment_output_command",
               new Object[] { e.getActionCommand() }), 600, 500);
@@ -1320,9 +1306,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       alignmentToExport = viewport.getAlignment();
     }
-    alignmentStartEnd = alignmentToExport
-            .getVisibleStartAndEndIndex(viewport.getColumnSelection()
-                    .getHiddenColumns());
+    alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
             omitHidden, alignmentStartEnd, settings);
     return ed;
@@ -1731,7 +1716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    List<SequenceI> sg = new ArrayList<SequenceI>();
+    List<SequenceI> sg = new ArrayList<>();
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
@@ -1750,7 +1735,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    List<SequenceI> invertGroup = new ArrayList<SequenceI>();
+    List<SequenceI> invertGroup = new ArrayList<>();
 
     for (SequenceI seq : viewport.getAlignment().getSequences())
     {
@@ -1883,10 +1868,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     ArrayList<int[]> hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<int[]>();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
-              .getSelectionGroup().getEndRes();
-      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+      hiddenColumns = new ArrayList<>();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
+              .getHiddenColumns().getHiddenColumnsCopy();
+      for (int[] region : hiddenRegions)
       {
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
@@ -1992,7 +1979,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
-      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+      ArrayList<Integer> newGraphGroups = new ArrayList<>();
       int fgroup = -1;
 
       if (newAlignment)
@@ -2824,7 +2811,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   protected List<String> getExistingViewNames(List<Component> comps)
   {
-    List<String> existingNames = new ArrayList<String>();
+    List<String> existingNames = new ArrayList<>();
     for (Component comp : comps)
     {
       if (comp instanceof AlignmentPanel)
@@ -2958,7 +2945,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    repaint();
+    alignPanel.paintAlignment(true);
     viewport.sendSelection();
   }
 
@@ -2966,7 +2953,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    // alignPanel.paintAlignment(true);
   }
 
   /**
@@ -3213,10 +3199,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
     alignPanel.paintAlignment(true);
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
   }
 
   /**
@@ -3272,11 +3254,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     JInternalFrame frame = new JInternalFrame();
-    OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
             "label.overview_params", new Object[] { this.getTitle() }),
-            frame.getWidth(), frame.getHeight());
+            true, frame.getWidth(), frame.getHeight(), true, true);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -3285,6 +3267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
+        overview.dispose();
         alignPanel.setOverviewPanel(null);
       };
     });
@@ -3342,7 +3325,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * 'User Defined' opens a panel to configure or load a
      * user-defined colour scheme
      */
-    if (ResidueColourScheme.USER_DEFINED.equals(name))
+    if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
     {
       new UserDefinedColours(alignPanel);
       return;
@@ -3758,7 +3741,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     List<Component> comps = PaintRefresher.components.get(viewport
             .getSequenceSetId());
-    List<TreePanel> treePanels = new ArrayList<TreePanel>();
+    List<TreePanel> treePanels = new ArrayList<>();
     for (Component comp : comps)
     {
       if (comp instanceof TreePanel)
@@ -4018,7 +4001,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void run()
       {
-        final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
+        final List<JMenuItem> legacyItems = new ArrayList<>();
         try
         {
           // System.err.println("Building ws menu again "
@@ -4033,7 +4016,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // TODO: group services by location as well as function and/or
           // introduce
           // object broker mechanism.
-          final Vector<JMenu> wsmenu = new Vector<JMenu>();
+          final Vector<JMenu> wsmenu = new Vector<>();
           final IProgressIndicator af = me;
 
           /*
@@ -4401,8 +4384,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    List<String> files = new ArrayList<String>();
-    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
+    List<String> files = new ArrayList<>();
+    List<DataSourceType> protocols = new ArrayList<>();
 
     try
     {
@@ -4422,8 +4405,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         /**
          * Object[] { String,SequenceI}
          */
-        ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
-        ArrayList<String> filesnotmatched = new ArrayList<String>();
+        ArrayList<Object[]> filesmatched = new ArrayList<>();
+        ArrayList<String> filesnotmatched = new ArrayList<>();
         for (int i = 0; i < files.size(); i++)
         {
           String file = files.get(i).toString();
@@ -4655,9 +4638,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     viewport.getAlignment(), 0, false);
             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
             viewport.getAlignment().setSeqrep(repseq);
-            ColumnSelection cs = new ColumnSelection();
+            HiddenColumns cs = new HiddenColumns();
             cs.hideInsertionsFor(repseq);
-            viewport.setColumnSelection(cs);
+            viewport.getAlignment().setHiddenColumns(cs);
             isAnnotation = true;
           }
           // else if (IdentifyFile.FeaturesFile.equals(format))
@@ -5414,7 +5397,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> cdnaSeqs = new ArrayList<>();
     for (SequenceI aaSeq : alignment.getSequences())
     {
       for (AlignedCodonFrame acf : mappings)