JAL-2600 updates following review

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 1a5dc05..39b718d 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -25,8 +25,12 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -45,10 +49,11 @@ 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;
 
@@ -100,7 +105,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   public AnnotationPanel(AlignmentPanel ap)
   {
-    MAC = new jalview.util.Platform().isAMac();
+    new jalview.util.Platform();
+    MAC = Platform.isAMac();
     this.ap = ap;
     av = ap.av;
     setLayout(null);
@@ -113,12 +119,15 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
     renderer = new AnnotationRenderer();
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   public AnnotationPanel(AlignViewport av)
   {
     this.av = av;
     renderer = new AnnotationRenderer();
+
   }
 
   @Override
@@ -162,7 +171,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     {
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (av.getColumnSelection().isVisible(index))
+        if (av.getAlignment().getHiddenColumns().isVisible(index))
         {
           anot[index] = null;
         }
@@ -186,7 +195,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       {
         // TODO: JAL-2001 - provide a fast method to list visible selected
         // columns
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -208,7 +217,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -241,7 +250,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       else if (evt.getActionCommand().equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -267,7 +277,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -346,7 +356,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
             && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -354,10 +365,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       PopupMenu pop = new PopupMenu(
               MessageManager.getString("label.structure_type"));
       MenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
+
+      if (av.getAlignment().isNucleotide())
       {
         item = new MenuItem(STEM);
         item.addActionListener(this);
@@ -459,11 +468,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth()
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      column = av.getColumnSelection().adjustForHiddenColumns(column);
+      column = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(column);
     }
 
     if (row > -1 && column < aa[row].annotations.length
@@ -472,9 +483,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       StringBuilder text = new StringBuilder();
       text.append(MessageManager.getString("label.column")).append(" ")
               .append(column + 1);
-      if (aa[row].annotations[column].description != null)
+      String description = aa[row].annotations[column].description;
+      if (description != null && description.length() > 0)
       {
-        text.append("  ").append(aa[row].annotations[column].description);
+        text.append("  ").append(description);
       }
 
       /*
@@ -493,9 +505,28 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
           char residue = seqref.getCharAt(column);
           if (!Comparison.isGap(residue))
           {
+            text.append(" ");
+            String name;
+            if (av.getAlignment().isNucleotide())
+            {
+              name = ResidueProperties.nucleotideName.get(String
+                      .valueOf(residue));
+              text.append(" Nucleotide: ").append(
+                      name != null ? name : residue);
+            }
+            else
+            {
+              name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+                      : ResidueProperties.aa2Triplet.get(String
+                              .valueOf(residue)));
+              text.append(" Residue: ").append(
+                      name != null ? name : residue);
+            }
             int residuePos = seqref.findPosition(column);
-            text.append(": ").append(residue).append(" (")
-                    .append(residuePos).append(")");
+            text.append(" (").append(residuePos).append(")");
+            // int residuePos = seqref.findPosition(column);
+            // text.append(residue).append(" (")
+            // .append(residuePos).append(")");
           }
         }
       }
@@ -595,7 +626,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
 
     g.drawImage(image, 0, 0, this);
   }
@@ -612,7 +644,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.copyArea(0, 0, imgWidth, getSize().height,
             -horizontal * av.getCharWidth(), 0);
-    int sr = av.startRes, er = av.endRes + 1, transX = 0;
+    int sr = av.getRanges().getStartRes(), er = av.getRanges().getEndRes() + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -724,4 +756,19 @@ 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)
+    // Both scrolling and resizing change viewport ranges: scrolling changes
+    // both start and end points, but resize only changes end values.
+    // Here we only want to fastpaint on a scroll, with resize using a normal
+    // paint, so scroll events are identified as changes to the horizontal or
+    // vertical start value.
+    if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
+    {
+      fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+  }
 }