X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=12d13697121f85911bbef645f1730f93d988cfa8;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=b1f0edb83284bdf2711ccb36a1372c527debc9f0;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index b1f0edb..12d1369 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -23,12 +23,15 @@ package jalview.gui;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 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.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -49,13 +52,13 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
@@ -70,7 +73,7 @@ import javax.swing.ToolTipManager;
  */
 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         MouseListener, MouseWheelListener, MouseMotionListener,
-        ActionListener, AdjustmentListener, Scrollable
+        ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
 {
   String HELIX = MessageManager.getString("label.helix");
 
@@ -156,6 +159,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     // and then set our own listener to consume all mousewheel events
     ap.annotationScroller.addMouseWheelListener(this);
     renderer = new AnnotationRenderer();
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   public AnnotationPanel(AlignViewport av)
@@ -172,11 +177,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       e.consume();
       if (e.getWheelRotation() > 0)
       {
-        ap.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
       else
       {
-        ap.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
     }
     else
@@ -280,7 +285,8 @@ public class AnnotationPanel extends JPanel 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;
@@ -291,7 +297,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (av.getColumnSelection().isVisible(index))
+        if (av.getAlignment().getHiddenColumns().isVisible(index))
         {
           anot[index] = null;
         }
@@ -315,7 +321,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -338,7 +344,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -398,7 +404,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -408,8 +414,8 @@ public class AnnotationPanel extends JPanel 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;
 
       }
@@ -441,17 +447,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     StringBuilder collatedInput = new StringBuilder(64);
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
     /*
      * the selection list (read-only view) is in selection order, not
      * column order; make a copy so we can sort it
      */
-    List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
+    List<Integer> selected = new ArrayList<>(viscols.getSelected());
     Collections.sort(selected);
     for (int index : selected)
     {
       // always check for current display state - just in case
-      if (!viscols.isVisible(index))
+      if (!hidden.isVisible(index))
       {
         continue;
       }
@@ -652,15 +659,18 @@ public class AnnotationPanel extends JPanel 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();
       adjustPanelHeight();
-      ap.paintAlignment(true);
+      ap.paintAlignment(false, false);
     }
     else
     {
@@ -708,11 +718,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    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);
     }
 
     AlignmentAnnotation ann = aa[row];
@@ -812,8 +824,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       int seqIndex = av.getAlignment().findIndex(seqref);
       if (seqIndex != -1)
       {
-        text.append(", ")
-                .append(MessageManager.getString("label.sequence"))
+        text.append(", ").append(MessageManager.getString("label.sequence"))
                 .append(" ").append(seqIndex + 1);
         char residue = seqref.getCharAt(column);
         if (!Comparison.isGap(residue))
@@ -822,16 +833,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           String name;
           if (av.getAlignment().isNucleotide())
           {
-            name = ResidueProperties.nucleotideName.get(String
-                    .valueOf(residue));
-            text.append(" Nucleotide: ").append(
-                    name != null ? name : residue);
+            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)));
+            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);
@@ -905,7 +917,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+            + 1) * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -915,8 +928,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
-                .getHeight(), BufferedImage.TYPE_INT_RGB);
+        image = new BufferedImage(imgWidth,
+                ap.getAnnotationPanel().getHeight(),
+                BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
         try
@@ -946,7 +960,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       imageFresh = true;
     }
 
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(),
+            av.getRanges().getEndRes() + 1);
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -972,13 +987,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
       return;
     }
+
+    int sr = av.getRanges().getStartRes();
+    int er = av.getRanges().getEndRes() + 1;
+    int transX = 0;
+
     long stime = System.currentTimeMillis();
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.startRes;
-    int er = av.endRes + 1;
-    int transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -1034,8 +1051,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       // and draw a faded image until the calculation
       // has completed
       if (lastImageGood
-              && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
-                      .getHeight() != image.getHeight()))
+              && (fadedImage == null || fadedImage.getWidth() != imgWidth
+                      || fadedImage.getHeight() != image.getHeight()))
       {
         // System.err.println("redraw faded image ("+(fadedImage==null ?
         // "null image" : "") + " lastGood="+lastImageGood+")");
@@ -1047,8 +1064,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         fadedG.setColor(Color.white);
         fadedG.fillRect(0, 0, imgWidth, image.getHeight());
 
-        fadedG.setComposite(AlphaComposite.getInstance(
-                AlphaComposite.SRC_OVER, .3f));
+        fadedG.setComposite(
+                AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
         fadedG.drawImage(image, 0, 0, this);
 
       }
@@ -1089,8 +1106,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       return;
     }
-    lastImageGood = renderer.drawComponent(this, av, g, activeRow,
-            startRes, endRes);
+    lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
+            endRes);
     if (!lastImageGood && fadedImage == null)
     {
       fadedImage = oldFaded;
@@ -1154,4 +1171,19 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       renderer.dispose();
     }
   }
+
+  @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());
+    }
+  }
 }