From 7d4f1d8e997964bef5c351d04fbdafe4401cf5d7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 9 Sep 2008 10:09:17 +0000
Subject: [PATCH] tooltip contains non-positional features and popup contains
 URLs from non-pos features

---
 src/jalview/appletgui/IdPanel.java |   62 ++++++++++++++++++++++++++++++++----
 1 file changed, 56 insertions(+), 6 deletions(-)

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 9bf2374..b973913 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,6 +20,7 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.Vector;
 
 import jalview.datamodel.*;
 import jalview.util.UrlLink;
@@ -86,27 +87,54 @@ public class IdPanel extends Panel implements MouseListener,
     int seq = alignPanel.seqPanel.findSeq(e);
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    
+    // look for non-pos features
+    StringBuffer tooltiptext = new StringBuffer();
+    
 
-    if (sequence.getDescription() == null)
+    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 +258,30 @@ 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;
-- 
1.7.10.2