JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index ee8c9ca..c06f7b1 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -25,9 +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;
@@ -46,10 +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
+public class AnnotationPanel extends Panel
+        implements AwtRenderPanelI, AdjustmentListener, ActionListener,
+        MouseListener, MouseMotionListener, ViewportListenerI
 {
   AlignViewport av;
 
@@ -115,12 +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
@@ -146,7 +153,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     if (anot.length < av.getColumnSelection().getMax())
     {
-      Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+      Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+              + 2];
       System.arraycopy(anot, 0, temp, 0, anot.length);
       anot = temp;
       aa[activeRow].annotations = anot;
@@ -162,12 +170,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
-        // of
-        // annotation if selection includes hidden columns
-        anot[sel] = null;
+        if (av.getAlignment().getHiddenColumns().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -188,7 +196,7 @@ 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;
         }
@@ -210,7 +218,7 @@ 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;
         }
@@ -270,7 +278,7 @@ 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;
         }
@@ -280,8 +288,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        anot[index].secondaryStructure = type != 'S' ? type : label
-                .length() == 0 ? ' ' : label.charAt(0);
+        anot[index].secondaryStructure = type != 'S' ? type
+                : label.length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
       }
     }
@@ -346,7 +354,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+    if ((evt.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
             && activeRow != -1)
     {
       if (av.getColumnSelection() == null
@@ -418,16 +427,20 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
   {
     if (graphStretch > -1)
     {
-      av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
-              - evt.getY();
-      if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+      av.getAlignment()
+              .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+                      - evt.getY();
+      if (av.getAlignment()
+              .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
       {
-        av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+        av.getAlignment()
+                .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
       }
       graphStretchY = evt.getY();
       av.calcPanelHeight();
       needValidating = true;
-      ap.paintAlignment(true);
+      // TODO: only update overview visible geometry
+      ap.paintAlignment(true, false);
     }
     else
     {
@@ -461,11 +474,13 @@ 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
@@ -474,9 +489,10 @@ 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);
       }
 
       /*
@@ -495,9 +511,29 @@ 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(")");
           }
         }
       }
@@ -597,14 +633,15 @@ 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);
   }
 
   public void fastPaint(int horizontal)
   {
-    if (horizontal == 0
+    if (horizontal == 0 || gg == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1)
     {
@@ -614,7 +651,8 @@ 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
     {
@@ -726,4 +764,19 @@ 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());
+    }
+  }
 }