From d19a0643d50c405995df23ef9d29f18e0204e87c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 6 Dec 2005 17:14:57 +0000
Subject: [PATCH] Make ImageMap for features as well as groups

---
 src/jalview/gui/AlignmentPanel.java |  100 ++++++++++++++++++++++++++++-------
 1 file changed, 81 insertions(+), 19 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ed00d33..e3bc620 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -809,6 +809,11 @@ public class AlignmentPanel extends GAlignmentPanel
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
     int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
 
+    if (idPanel.getWidth() == 0)
+    {
+      width += calculateIdWidth().getWidth() + 4;
+    }
+
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
@@ -897,45 +902,102 @@ public class AlignmentPanel extends GAlignmentPanel
     {
       try
       {
+        int s, sSize = av.alignment.getHeight(),
+            res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
+        StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName +
                     "\" border=\"0\" usemap=\"#Map\" >"
                     + "<map name=\"Map\">");
 
-        for (int s = 0; s < av.alignment.getHeight(); s++)
+        for (s = 0; s < sSize; s++)
         {
+          sy = s * av.charHeight + scaleHeight;
+
           SequenceI seq = av.alignment.getSequenceAt(s);
+          java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();
           SequenceGroup[] groups = av.alignment.findAllGroups(seq);
-          for (int i = 0; i < groups.length; i++)
+          for(res =0; res<alwidth; res++)
           {
-            int sy = s * av.charHeight + scaleHeight;
-            for (int res = groups[i].getStartRes();
-                 res < groups[i].getEndRes() + 1; res++)
+            text = new StringBuffer();
+            Object obj = ResidueProperties.aa2Triplet.get(
+                    seq.getCharAt(res) + "");
+            if (obj == null)
+                  continue;
+
+            String triplet = obj.toString();
+            int alIndex = seq.findPosition(res);
+            gSize = groups.length;
+            for (g = 0; g < gSize; g++)
             {
-              int alIndex = seq.findPosition(res);
-              Object obj = ResidueProperties.aa2Triplet.get(
-                  seq.getCharAt(res) + "");
-              if (obj == null)
-                continue;
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                  + (idWidth + res * av.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
 
-              String triplet = obj.toString();
+              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+            }
 
-              out.println(
-                  "<area shape=\"rect\" coords=\""
+            if (features != null)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
                   + (idWidth + res * av.charWidth) + ","
                   + sy + ","
                   + (idWidth + (res + 1) * av.charWidth) + ","
                   + (av.charHeight + sy) + "\""
                   + " onMouseOver=\"toolTip('"
-                  + alIndex + " " + triplet +
-                  "<br><em>" + groups[i].getName() +
-                  "</em>')\"; onMouseOut=\"toolTip()\"; "
-                  + " href=\"#\">");
+                  + alIndex + " " + triplet );
+              }
+                fSize = features.size();
+                for (f = 0; f < fSize; f++)
+                {
+                  SequenceFeature sf = (SequenceFeature) features.elementAt(f);
+
+                  if ( (sf.getBegin() <= seq.findPosition(res)) &&
+                      (sf.getEnd() >= seq.findPosition(res)))
+                  {
+                    if (sf.getType().equals("disulfide bond"))
+                    {
+                      if (sf.getBegin() == seq.findPosition(res)
+                          || sf.getEnd() == seq.findPosition(res))
+                      {
+                        text.append("<br>disulfide bond " + sf.getBegin() + ":" +
+                                       sf.getEnd());
+                      }
+                    }
+                    else
+                    {
+                      text.append("<br>");
+                      text.append(sf.getType());
+                      if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
+                        text.append(" " + sf.getDescription());
+
+                      if (sf.getStatus() != null && sf.getStatus().length()>0)
+                      {
+                        text.append(" (" + sf.getStatus() + ")");
+                      }
+                    }
+                  }
+
+                }
+              }
+              if(text.length()>1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
+              }
             }
           }
-        }
-
         out.println("</map></body></html>");
         out.close();
 
-- 
1.7.10.2