Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9f79999..d613ea7 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,6 +33,7 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -55,6 +56,7 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
@@ -111,6 +113,8 @@ import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
@@ -346,7 +350,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     buildSortByAnnotationScoresMenu();
     buildTreeMenu();
     
-    if (viewport.wrapAlignment)
+    if (viewport.getWrapAlignment())
     {
       wrapMenuItem_actionPerformed(null);
     }
@@ -358,6 +362,59 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addKeyListener();
 
+    final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
+    final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+    ViewSelectionMenu vsel = new ViewSelectionMenu("Transfer colours from",
+            new ViewSetProvider()
+            {
+
+              @Override
+              public AlignmentPanel[] getAllAlignmentPanels()
+              {
+                origview.clear();
+                origview.add(alignPanel);
+                return Desktop.getAlignmentPanels(null);
+              }
+            }, selviews, new ItemListener()
+            {
+
+              @Override
+              public void itemStateChanged(ItemEvent e)
+              {
+                if (origview.size() > 0)
+                {
+                  ViewStyleI vs = selviews.get(0).getAlignViewport()
+                          .getViewStyle();
+                  origview.get(0).getAlignViewport().setViewStyle(vs);
+                  AlignViewportI complement = origview.get(0)
+                          .getAlignViewport().getCodingComplement();
+                  if (complement != null)
+                  {
+                    AlignFrame af = Desktop.getAlignFrameFor(complement);
+                    if (complement.isNucleotide())
+                    {
+                      complement.setViewStyle(vs);
+                      vs.setCharWidth(vs.getCharWidth() / 3);
+                    }
+                    else
+                    {
+                      int rw = vs.getCharWidth();
+                      vs.setCharWidth(rw * 3);
+                      complement.setViewStyle(vs);
+                      vs.setCharWidth(rw);
+                    }
+                    af.alignPanel.updateLayout();
+                    af.setMenusForViewport();
+                  }
+                  origview.get(0).updateLayout();
+                  origview.get(0).setSelected(true);
+                  origview.get(0).alignFrame.setMenusForViewport();
+
+                }
+              }
+            });
+    formatMenu.add(vsel);
+
   }
 
   /**
@@ -553,7 +610,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          if (viewport.wrapAlignment)
+          if (viewport.getWrapAlignment())
           {
             alignPanel.scrollUp(true);
           }
@@ -564,7 +621,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          if (viewport.wrapAlignment)
+          if (viewport.getWrapAlignment())
           {
             alignPanel.scrollUp(false);
           }
@@ -829,17 +886,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
-    colourTextMenuItem.setSelected(av.showColourText);
+    colourTextMenuItem.setSelected(av.isShowColourText());
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     conservationMenuItem.setSelected(av.getConservationSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
     idRightAlign.setSelected(av.isRightAlignIds());
-    centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
-    renderGapsMenuItem.setSelected(av.renderGaps);
-    wrapMenuItem.setSelected(av.wrapAlignment);
-    scaleAbove.setVisible(av.wrapAlignment);
-    scaleLeft.setVisible(av.wrapAlignment);
-    scaleRight.setVisible(av.wrapAlignment);
+    centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
+    renderGapsMenuItem.setSelected(av.isRenderGaps());
+    wrapMenuItem.setSelected(av.getWrapAlignment());
+    scaleAbove.setVisible(av.getWrapAlignment());
+    scaleLeft.setVisible(av.getWrapAlignment());
+    scaleRight.setVisible(av.getWrapAlignment());
     annotationPanelMenuItem.setState(av.isShowAnnotation());
     /*
      * Show/hide annotations only enabled if annotation panel is shown
@@ -848,8 +905,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    viewBoxesMenuItem.setSelected(av.showBoxes);
-    viewTextMenuItem.setSelected(av.showText);
+    viewBoxesMenuItem.setSelected(av.getShowBoxes());
+    viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
     showGroupConsensus.setSelected(av.isShowGroupConsensus());
     showGroupConservation.setSelected(av.isShowGroupConservation());
@@ -861,10 +918,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getGlobalColourScheme()));
 
     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
-    hiddenMarkers.setState(av.showHiddenMarkers);
+    hiddenMarkers.setState(av.getShowHiddenMarkers());
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
-    showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
-    showDbRefsMenuitem.setSelected(av.isShowDbRefs());
+    showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
+    showDbRefsMenuitem.setSelected(av.isShowDBRefs());
     autoCalculate.setSelected(av.autoCalculateConsensus);
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
@@ -2721,7 +2778,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       newap.av.getAlignment().deleteAllAnnotations(false);
     }
 
-    newap.av.gatherViewsHere = false;
+    newap.av.setGatherViewsHere(false);
 
     if (viewport.viewName == null)
     {
@@ -2744,7 +2801,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (alignPanels.size() == 2)
     {
-      viewport.gatherViewsHere = true;
+      viewport.setGatherViewsHere(true);
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
     return newap;
@@ -2865,7 +2922,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
-    viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+    viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -2910,7 +2967,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(wrapMenuItem.isSelected());
     scaleRight.setVisible(wrapMenuItem.isSelected());
     viewport.setWrapAlignment(wrapMenuItem.isSelected());
-    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+    alignPanel.updateLayout();
   }
 
   @Override
@@ -3214,11 +3271,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
-    alignPanel.setAnnotationVisible(setVisible);
     this.showAllSeqAnnotations.setEnabled(setVisible);
     this.hideAllSeqAnnotations.setEnabled(setVisible);
     this.showAllAlAnnotations.setEnabled(setVisible);
     this.hideAllAlAnnotations.setEnabled(setVisible);
+    alignPanel.updateLayout();
   }
 
   @Override
@@ -3460,11 +3517,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
       }
       else
       {
-        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
       }
 
       if (viewport.getConservationSelected())
@@ -3527,7 +3584,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 || cs instanceof PIDColourScheme
                 || cs instanceof Blosum62ColourScheme)
         {
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
 
           sg.cs.setConsensus(AAFrequency.calculate(
                   sg.getSequences(viewport.getHiddenRepSequences()),
@@ -3535,7 +3592,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         else
         {
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
         }
 
         if (viewport.getConservationSelected())
@@ -5418,7 +5475,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
-    viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+    viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
   }
 
   /*
@@ -5430,7 +5487,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
-    viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+    viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
   }
 
   /**
@@ -5868,7 +5925,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
     }
     if (tabbedPane != null
-            & alignPanels.indexOf(alignmentPanel) != tabbedPane
+            && tabbedPane.getTabCount() > 0
+            && alignPanels.indexOf(alignmentPanel) != tabbedPane
                     .getSelectedIndex())
     {
       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));