Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 16db94c..d8d27d0 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -26,6 +26,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 import jalview.schemes.ResidueProperties;
@@ -59,7 +60,6 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
@@ -114,7 +114,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   public volatile BufferedImage fadedImage;
 
-  Graphics2D gg;
+  // private Graphics2D gg;
 
   public FontMetrics fm;
 
@@ -150,7 +150,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
-    ToolTipManager.sharedInstance().registerComponent(this);
+//         setBackground(Color.white);  // BH 2019
+
+           ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
     this.ap = ap;
@@ -315,7 +317,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JvOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -347,24 +349,29 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else if (action.equals(COLOUR))
     {
-      Color col = JColorChooser.showDialog(this,
-              MessageManager.getString("label.select_foreground_colour"),
-              Color.black);
-
-      for (int index : av.getColumnSelection().getSelected())
+      final Annotation[] fAnot = anot;
+      String title = MessageManager
+              .getString("label.select_foreground_colour");
+      ColourChooserListener listener = new ColourChooserListener()
       {
-        if (!av.getAlignment().getHiddenColumns().isVisible(index))
-        {
-          continue;
-        }
-
-        if (anot[index] == null)
+        @Override
+        public void colourSelected(Color c)
         {
-          anot[index] = new Annotation("", "", ' ', 0);
-        }
-
-        anot[index].colour = col;
-      }
+          HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
+          for (int index : av.getColumnSelection().getSelected())
+          {
+            if (hiddenColumns.isVisible(index))
+            {
+              if (fAnot[index] == null)
+              {
+                fAnot[index] = new Annotation("", "", ' ', 0);
+              }
+              fAnot[index].colour = c;
+            }
+        }};
+      };
+      JalviewColourChooser.showColourChooser(this,
+              title, Color.black, listener);
     }
     else
     // HELIX, SHEET or STEM
@@ -652,14 +659,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseEntered(MouseEvent evt)
   {
+    this.mouseDragging = false;
     ap.getScalePanel().mouseEntered(evt);
   }
 
   /**
-   * DOCUMENT ME!
+   * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
+   * with column selection on a mouse drag
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseExited(MouseEvent evt)
@@ -988,6 +996,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   private volatile boolean imageFresh = false;
+  private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
 
   /**
    * DOCUMENT ME!
@@ -998,17 +1007,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void paintComponent(Graphics g)
   {
-    super.paintComponent(g);
-
+         
+         // BH: note that this method is generally recommended to 
+         // call super.paintComponent(g). Otherwise, the children of this
+         // component will not be rendered. That is not needed here 
+         // because AnnotationPanel does not have any children. It is
+         // just a JPanel contained in a JViewPort. 
+
+    computeVisibleRect(visibleRect);
+    
     g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+    g.fillRect(0, 0, visibleRect.width, visibleRect.height);
 
     if (image != null)
     {
-      if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
-              || (getVisibleRect().height != g.getClipBounds().height))
+       // BH 2018 optimizing generation of new Rectangle().
+      if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width)
+            || (visibleRect.height != clipBounds.height))
       {
-        g.drawImage(image, 0, 0, this);
+
+         
+         g.drawImage(image, 0, 0, this);
         fastPaint = false;
         return;
       }
@@ -1019,6 +1038,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       return;
     }
+    Graphics2D gg;
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
@@ -1054,10 +1074,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       gg.setColor(Color.white);
       gg.fillRect(0, 0, imgWidth, image.getHeight());
       imageFresh = true;
+    } else {
+        gg = (Graphics2D) image.getGraphics();
+
     }
     
     drawComponent(gg, av.getRanges().getStartRes(),
             av.getRanges().getEndRes() + 1);
+    gg.dispose();
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -1075,7 +1099,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void fastPaint(int horizontal)
   {
-    if ((horizontal == 0) || gg == null
+    if ((horizontal == 0) || image == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1
             || av.isCalcInProgress())
@@ -1088,6 +1112,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
+    Graphics2D gg = (Graphics2D) image.getGraphics();
+
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
 
@@ -1107,6 +1133,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     gg.translate(-transX, 0);
 
+    gg.dispose();
+    
     fastPaint = true;
 
     // Call repaint on alignment panel so that repaints from other alignment
@@ -1250,7 +1278,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     ap = null;
     image = null;
     fadedImage = null;
-    gg = null;
+//    gg = null;
     _mwl = null;
 
     /*
@@ -1304,7 +1332,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
      * hscroll, status bar, insets. 
      */
     int stuff = (ap.getViewName() != null ? 30 : 0)
-            + (Platform.isAMac() ? 120 : 140);
+            + (Platform.isAMacAndNotJS() ? 120 : 140);
     int availableHeight = ap.alignFrame.getHeight() - stuff;
     int rowHeight = av.getCharHeight();