JAL-2491 First port to applet

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 065c503..13332d3 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -438,8 +438,9 @@ public class AlignViewport extends AlignmentViewport implements
     int seqOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
-      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.setFollowingComplementScroll(false);
       complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.setFollowingComplementScroll(true);
     }
   }
 

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 0ec7adf..cf7f51e 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -29,6 +29,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -47,10 +48,11 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
 
 public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         AdjustmentListener, ActionListener, MouseListener,
-        MouseMotionListener
+        MouseMotionListener, ViewportListenerI
 {
   AlignViewport av;
 
@@ -122,6 +124,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
   {
     this.av = av;
     renderer = new AnnotationRenderer();
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   @Override
@@ -749,4 +752,15 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport range changes (e.g. alignment panel was scrolled)
+    if (evt.getPropertyName().equals("startres")
+            || evt.getPropertyName().equals("endres"))
+    {
+      fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+  }
 }

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index abcbd70..cad5de5 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
@@ -28,9 +29,10 @@ import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Panel;
+import java.beans.PropertyChangeEvent;
 import java.util.List;
 
-public class IdCanvas extends Panel
+public class IdCanvas extends Panel implements ViewportListenerI
 {
   protected AlignViewport av;
 
@@ -55,6 +57,7 @@ public class IdCanvas extends Panel
     setLayout(null);
     this.av = av;
     PaintRefresher.Register(this, av.getSequenceSetId());
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
@@ -393,4 +396,15 @@ public class IdCanvas extends Panel
     }
     return false;
   }
+
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport range changes (e.g. alignment panel was scrolled)
+    if (evt.getPropertyName().equals("startseq")
+            || evt.getPropertyName().equals("endseq"))
+    {
+      fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+  }
 }

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index e47c50a..7c67edd 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -401,7 +401,7 @@ public class IdPanel extends Panel implements MouseListener,
     if (av.getRanges().getStartSeq() > index
             || av.getRanges().getEndSeq() < index)
     {
-      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -429,7 +429,7 @@ public class IdPanel extends Panel implements MouseListener,
       running = true;
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
           int seq = av.getRanges().getStartSeq();

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 3ef2936..786e9c2 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.ViewportListenerI;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -35,9 +36,10 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
 
 public class OverviewPanel extends Panel implements Runnable,
-        MouseMotionListener, MouseListener
+        MouseMotionListener, MouseListener, ViewportListenerI
 {
   private OverviewDimensions od;
 
@@ -81,6 +83,9 @@ public class OverviewPanel extends Panel implements Runnable,
             (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    av.getRanges().addPropertyChangeListener(this);
+
     addComponentListener(new ComponentAdapter()
     {
 
@@ -332,7 +337,7 @@ public class OverviewPanel extends Panel implements Runnable,
    * changed
    * 
    */
-  public void setBoxPosition()
+  private void setBoxPosition()
   {
     od.setBoxPosition(av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
@@ -358,4 +363,10 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    setBoxPosition();
+  }
+
 }

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 15d82a5..a1e4f3d 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -25,6 +25,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -38,10 +39,11 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
 import java.util.List;
 
 public class ScalePanel extends Panel implements MouseMotionListener,
-        MouseListener
+        MouseListener, ViewportListenerI
 {
 
   protected int offy = 4;
@@ -71,6 +73,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     addMouseListener(this);
     addMouseMotionListener(this);
 
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   @Override
@@ -462,4 +465,11 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     }
   }
 
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport change events (e.g. alignment panel was scrolled)
+    repaint();
+  }
+
 }

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 89df11f..b025f32 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
@@ -34,8 +35,9 @@ import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Panel;
+import java.beans.PropertyChangeEvent;
 
-public class SeqCanvas extends Panel
+public class SeqCanvas extends Panel implements ViewportListenerI
 {
   FeatureRenderer fr;
 
@@ -64,6 +66,8 @@ public class SeqCanvas extends Panel
     sr = new SequenceRenderer(av);
     PaintRefresher.Register(this, av.getSequenceSetId());
     updateViewport();
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   int avcharHeight = 0, avcharWidth = 0;
@@ -431,7 +435,7 @@ public class SeqCanvas extends Panel
 
     av.setWrappedWidth(cWidth);
 
-    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth - 1);
 
     int endx;
     int ypos = hgap;
@@ -858,4 +862,35 @@ public class SeqCanvas extends Panel
     repaint();
   }
 
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    if (!av.getWrapAlignment())
+    {
+      if (evt.getPropertyName().equals("startres")
+              || evt.getPropertyName().equals("endres"))
+      {
+        // Make sure we're not trying to draw a panel
+        // larger than the visible window
+        ViewportRanges vpRanges = av.getRanges();
+        int scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+        if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
+        {
+          scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
+        }
+        else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
+        {
+          scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
+        }
+        fastPaint(scrollX, 0);
+      }
+      else if (evt.getPropertyName() == "startseq"
+              || evt.getPropertyName() == "endseq")
+      {
+        fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+      }
+    }
+
+  }
+
 }

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 0e12703..347cceb 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -223,24 +223,24 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     endEditing();
     if (av.getWrapAlignment())
     {
-      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
     }
     else
     {
       ViewportRanges ranges = av.getRanges();
       while (seqCanvas.cursorY < ranges.getStartSeq())
       {
-        ap.scrollUp(true);
+        ranges.scrollUp(true);
       }
       while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
       {
-        ap.scrollUp(false);
+        ranges.scrollUp(false);
       }
       while (seqCanvas.cursorX < av.getColumnSelection()
               .adjustForHiddenColumns(ranges.getStartRes()))
       {
 
-        if (!ap.scrollRight(false))
+        if (!ranges.scrollRight(false))
         {
           break;
         }
@@ -248,7 +248,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       while (seqCanvas.cursorX > av.getColumnSelection()
               .adjustForHiddenColumns(ranges.getEndRes()))
       {
-        if (!ap.scrollRight(true))
+        if (!ranges.scrollRight(true))
         {
           break;
         }
@@ -740,10 +740,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (av.isFollowHighlight())
     {
+      // don't allow highlight of protein/cDNA to also scroll a complementary
+      // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+      // over residue to change abruptly, causing highlighted residue in panel 2
+      // to change, causing a scroll in panel 1 etc)
+      ap.setFollowingComplementScroll(false);
       if (ap.scrollToPosition(results, true))
       {
         ap.alignFrame.repaint();
       }
+      ap.setFollowingComplementScroll(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
@@ -1751,24 +1757,24 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (mouseDragging && evt.getY() < 0
                   && av.getRanges().getStartSeq() > 0)
           {
-            running = ap.scrollUp(true);
+            running = av.getRanges().scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height
                   && av.getAlignment().getHeight() > av.getRanges()
                           .getEndSeq())
           {
-            running = ap.scrollUp(false);
+            running = av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = ap.scrollRight(false);
+            running = av.getRanges().scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = ap.scrollRight(true);
+            running = av.getRanges().scrollRight(true);
           }
         }
 

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index abd473d..cd69bdc 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -984,10 +984,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   {
     if (av.getWrapAlignment())
     {
-
-    }
-    else
-    {
       if (evt.getPropertyName().equals("startres")
               || evt.getPropertyName().equals("endres"))
       {