JAL-1759 merge from develop

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 4036347..97752f2 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,17 +20,43 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 import jalview.util.MessageManager;
 
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JColorChooser;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.Scrollable;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
 /**
  * AnnotationPanel displays visible portion of annotation rows below unwrapped
  * alignment
@@ -113,7 +139,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public AnnotationPanel(AlignmentPanel ap)
   {
 
-    MAC = new jalview.util.Platform().isAMac();
+    MAC = jalview.util.Platform.isAMac();
 
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
@@ -215,7 +241,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     // update annotation label display
-    ap.alabels.setScrollOffset(-evt.getValue());
+    ap.getAlabels().setScrollOffset(-evt.getValue());
   }
 
   /**
@@ -289,7 +315,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         int index = av.getColumnSelection().columnAt(i);
 
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
@@ -307,14 +335,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (evt.getActionCommand().equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
-              "Choose foreground colour", Color.black);
+              MessageManager.getString("label.select_foreground_colour"), Color.black);
 
       for (int i = 0; i < av.getColumnSelection().size(); i++)
       {
         int index = av.getColumnSelection().columnAt(i);
 
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
@@ -373,14 +403,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         int index = av.getColumnSelection().columnAt(i);
 
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        anot[index].secondaryStructure = type;
+        
+        anot[index].secondaryStructure = type != 'S' ? type : label
+                .length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
 
       }
@@ -406,7 +440,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       int index = columnSelection.columnAt(i);
       // always check for current display state - just in case
       if (!viscols.isVisible(index))
+      {
         continue;
+      }
       String tlabel = null;
       if (anot[index] != null)
       { // LML added stem code
@@ -530,7 +566,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    ap.scalePanel.mousePressed(evt);
+    ap.getScalePanel().mousePressed(evt);
 
   }
 
@@ -546,7 +582,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretch = -1;
     graphStretchY = -1;
     mouseDragging = false;
-    ap.scalePanel.mouseReleased(evt);
+    ap.getScalePanel().mouseReleased(evt);
   }
 
   /**
@@ -558,7 +594,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseEntered(MouseEvent evt)
   {
-    ap.scalePanel.mouseEntered(evt);
+    ap.getScalePanel().mouseEntered(evt);
   }
 
   /**
@@ -570,7 +606,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseExited(MouseEvent evt)
   {
-    ap.scalePanel.mouseExited(evt);
+    ap.getScalePanel().mouseExited(evt);
   }
 
   /**
@@ -596,7 +632,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else
     {
-      ap.scalePanel.mouseDragged(evt);
+      ap.getScalePanel().mouseDragged(evt);
     }
   }
 
@@ -673,10 +709,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               && aa[row].annotations[res].description != null
               && aa[row].annotations[res].description.length() > 0)
       {
-        this.setToolTipText("<html>"
-                + JvSwingUtils
-                        .wrapTooltip(aa[row].annotations[res].description)
-                + "</html>");
+        this.setToolTipText(JvSwingUtils
+                        .wrapTooltip(true, aa[row].annotations[res].description));
       }
       else
       {
@@ -723,10 +757,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
           int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
     if (av.validCharWidth)
     {
@@ -734,9 +768,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       char s = seq.getCharAt(res);
 
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s), charOffset + x1,
-              (y1 + av.charHeight) - pady);
+              (y1 + av.getCharHeight()) - pady);
     }
 
   }
@@ -765,15 +799,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
     if (imgWidth < 1)
+    {
       return;
+    }
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+        image = new BufferedImage(imgWidth, ap.getAnnotationPanel().getHeight(),
                 BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
@@ -831,7 +867,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
     long stime = System.currentTimeMillis();
-    gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+    gg.copyArea(0, 0, imgWidth, getHeight(),
+            -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
     int sr = av.startRes;
     int er = av.endRes + 1;
@@ -839,7 +876,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
-      transX = (er - sr - horizontal) * av.charWidth;
+      transX = (er - sr - horizontal) * av.getCharWidth();
       sr = er - horizontal;
     }
     else if (horizontal < 0)
@@ -924,7 +961,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
 
     g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+    g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
 
     g.setFont(av.getFont());
     if (fm == null)
@@ -977,15 +1014,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public int[] getVisibleVRange()
   {
-    if (ap != null && ap.alabels != null)
+    if (ap != null && ap.getAlabels() != null)
     {
-      int sOffset = -ap.alabels.scrollOffset;
+      int sOffset = -ap.getAlabels().getScrollOffset();
       int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
       bounds[0] = sOffset;
       bounds[1] = visHeight;
       return bounds;
     }
     else
+    {
       return null;
+    }
   }
 }