2.5.1 release branding

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 9bf2374..9fc994b 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,25 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.Vector;
 
 import jalview.datamodel.*;
 import jalview.util.UrlLink;
@@ -57,6 +57,7 @@ public class IdPanel extends Panel implements MouseListener,
     idCanvas.addMouseMotionListener(this);
 
     String label, url;
+    // TODO: add in group link parameter
     if (av.applet != null)
     {
       for (int i = 1; i < 10; i++)
@@ -87,26 +88,85 @@ public class IdPanel extends Panel implements MouseListener,
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if (sequence.getDescription() == null)
+    // look for non-pos features
+    StringBuffer tooltiptext = new StringBuffer();
+
+    if (sequence.getDescription() != null)
+    {
+      tooltiptext.append(sequence.getDescription());
+      tooltiptext.append("\n");
+    }
+
+    SequenceFeature sf[] = sequence.getSequenceFeatures();
+    for (int sl = 0; sf != null && sl < sf.length; sl++)
+    {
+      if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+      {
+        boolean nl = false;
+        if (sf[sl].getFeatureGroup() != null)
+        {
+          tooltiptext.append(sf[sl].getFeatureGroup());
+          nl = true;
+        }
+        ;
+        if (sf[sl].getType() != null)
+        {
+          tooltiptext.append(" ");
+          tooltiptext.append(sf[sl].getType());
+          nl = true;
+        }
+        ;
+        if (sf[sl].getDescription() != null)
+        {
+          tooltiptext.append(" ");
+          tooltiptext.append(sf[sl].getDescription());
+          nl = true;
+        }
+        ;
+        if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+        {
+          tooltiptext.append(" Score = ");
+          tooltiptext.append(sf[sl].getScore());
+          nl = true;
+        }
+        ;
+        if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
+        {
+          tooltiptext.append(" (");
+          tooltiptext.append(sf[sl].getStatus());
+          tooltiptext.append(")");
+          nl = true;
+        }
+        ;
+        if (nl)
+        {
+          tooltiptext.append("\n");
+        }
+      }
+    }
+
+    if (tooltiptext.length() == 0)
     {
+      // nothing to display - so clear tooltip if one is visible
       if (tooltip != null)
       {
         tooltip.setVisible(false);
       }
       tooltip = null;
+      tooltiptext = null;
       return;
     }
-
     if (tooltip == null)
     {
       tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
-              + sequence.getDescription(), idCanvas);
+              + tooltiptext.toString(), idCanvas);
     }
     else
     {
       tooltip.setTip(sequence.getDisplayId(true) + "\n"
-              + sequence.getDescription());
+              + tooltiptext.toString());
     }
+    tooltiptext = null;
   }
 
   public void mouseDragged(MouseEvent e)
@@ -230,8 +290,30 @@ public class IdPanel extends Panel implements MouseListener,
 
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av
-              .getAlignment().getSequenceAt(seq), links);
+      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+      // build a new links menu based on the current links + any non-positional
+      // features
+      Vector nlinks = new Vector();
+      for (int l = 0, lSize = links.size(); l < lSize; l++)
+      {
+        nlinks.addElement(links.elementAt(l));
+      }
+      SequenceFeature sf[] = sq.getSequenceFeatures();
+      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      {
+        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+        {
+          if (sf[sl].links != null && sf[sl].links.size() > 0)
+          {
+            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+            {
+              nlinks.addElement(sf[sl].links.elementAt(l));
+            }
+          }
+        }
+      }
+
+      APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
       return;