X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=452f0027adf0935925dfa5a3e7d1a0947a4d11a1;hb=42498abb930c08393b09fc7af2564b7f210ac294;hp=74505554f45fe802fc4677c2aee01cacd3d7105b;hpb=c73c8c28e34bdcac21e89aa89b69e85dad9e0189;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 7450555..452f002 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -23,12 +23,14 @@ 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 java.awt.AlphaComposite;
 import java.awt.Color;
@@ -49,13 +51,13 @@ 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 +72,7 @@ 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");
 
@@ -123,8 +125,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   boolean mouseDragging = false;
 
-  boolean MAC = false;
-
   // for editing cursor
   int cursorX = 0;
 
@@ -142,9 +142,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
-
-    MAC = jalview.util.Platform.isAMac();
-
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -161,6 +158,8 @@ 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)
@@ -177,11 +176,11 @@ 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
@@ -296,7 +295,7 @@ 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;
         }
@@ -305,7 +304,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(this,
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -320,7 +319,7 @@ 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;
         }
@@ -343,7 +342,7 @@ 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;
         }
@@ -385,7 +384,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         aa[activeRow].hasIcons = true;
       }
 
-      String label = JOptionPane.showInputDialog(MessageManager
+      String label = JvOptionPane.showInputDialog(MessageManager
               .getString("label.enter_label_for_the_structure"), symbol);
 
       if (label == null)
@@ -403,7 +402,7 @@ 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;
         }
@@ -446,6 +445,7 @@ 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
@@ -456,15 +456,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     for (int index : selected)
     {
       // always check for current display state - just in case
-      if (!viscols.isVisible(index))
+      if (!hidden.isVisible(index))
       {
         continue;
       }
       String tlabel = null;
       if (anots[index] != null)
       { // LML added stem code
-        if (type.equals(HELIX) || type.equals(SHEET)
-                || type.equals(STEM) || type.equals(LABEL))
+        if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+                || type.equals(LABEL))
         {
           tlabel = anots[index].description;
           if (tlabel == null || tlabel.length() < 1)
@@ -713,11 +713,13 @@ 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];
@@ -819,8 +821,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         text.append(", ")
                 .append(MessageManager.getString("label.sequence"))
-                .append(" ")
-                .append(seqIndex + 1);
+                .append(" ").append(seqIndex + 1);
         char residue = seqref.getCharAt(column);
         if (!Comparison.isGap(residue))
         {
@@ -911,7 +912,8 @@ 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;
@@ -952,7 +954,8 @@ 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);
   }
@@ -982,8 +985,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.startRes;
-    int er = av.endRes + 1;
+    int sr = av.getRanges().getStartRes();
+    int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
@@ -1139,4 +1142,36 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  /**
+   * Try to ensure any references held are nulled
+   */
+  public void dispose()
+  {
+    av = null;
+    ap = null;
+    image = null;
+    fadedImage = null;
+    gg = null;
+    _mwl = null;
+
+    /*
+     * I created the renderer so I will dispose of it
+     */
+    if (renderer != null)
+    {
+      renderer.dispose();
+    }
+  }
+
+  @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());
+    }
+  }
 }