From f22d8c3bfc1892fe88b4aad3f6381e5018f175f1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Feb 2007 10:57:02 +0000
Subject: [PATCH] applet can define groups as parameters

---
 src/jalview/bin/JalviewLite.java   |   38 +++++++++++++++++++++++++++++++-----
 src/jalview/io/AnnotationFile.java |   18 ++++++++++++++---
 2 files changed, 48 insertions(+), 8 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 35fc82f..222d049 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -461,27 +461,55 @@ public class JalviewLite extends Applet
              }
 
 
-                String pdbfile = applet.getParameter("PDBFILE");
-                if(pdbfile!=null)
+                param = getParameter("PDBFILE");
+                if(param!=null)
                 {
-                  if( inArchive(pdbfile) )
+                  if( inArchive(param) )
                     protocol = AppletFormatAdapter.CLASSLOADER;
                   else
                   {
                     protocol = AppletFormatAdapter.URL;
-                    pdbfile = addProtocol(pdbfile);
+                    param = addProtocol(param);
                   }
 
                   String sequence = applet.getParameter("PDBSEQ");
 
                   if(sequence!=null)
                   {
-                    new MCview.AppletPDBViewer(pdbfile, protocol,
+                    new MCview.AppletPDBViewer(param, protocol,
                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
                                                currentAlignFrame.getSeqcanvas());
                   }
 
                 }
+
+                int gIndex = 1;
+                param = getParameter("SEQUENCE_GROUP"+gIndex);
+                if(param!=null)
+                do{
+                  new AnnotationFile().readAnnotationFile(
+                   currentAlignFrame.viewport.getAlignment(),
+                   "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\t"+param,
+                   AppletFormatAdapter.PASTE);
+                  gIndex++;
+                  param = applet.getParameter("SEQUENCE_GROUP"+gIndex);
+                  currentAlignFrame.alignPanel.repaint();
+                }while(param!=null);
+
+              gIndex = 1;
+              param = getParameter("PROPERTIES" + gIndex);
+              if (param != null)
+                do
+                {
+                  new AnnotationFile().readAnnotationFile(
+                      currentAlignFrame.viewport.getAlignment(),
+                      "JALVIEW_ANNOTATION\nPROPERTIES\t" + param,
+                      AppletFormatAdapter.PASTE);
+                  gIndex++;
+                  param = applet.getParameter("PROPERTIES" + gIndex);
+                  currentAlignFrame.alignPanel.repaint();
+                }
+                while (param != null);
             }
             else
             {
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 56040d9..8ec234d 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -225,7 +225,6 @@ public class AnnotationFile
 
 
   SequenceI refSeq = null;
-  Hashtable annotationsHash = new Hashtable();
   public boolean readAnnotationFile(AlignmentI al,
                                     String file,
                                     String protocol)
@@ -591,7 +590,6 @@ public class AnnotationFile
     if(sg.getSize()>0)
     {
       al.addGroup(sg);
-      annotationsHash.put(sg.getName(), sg);
     }
   }
 
@@ -601,7 +599,21 @@ public class AnnotationFile
     //So far we have only added groups to the annotationHash,
     //the idea is in the future properties can be added to
     //alignments, other annotations etc
-    SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());
+    if(al.getGroups()==null)
+      return;
+    SequenceGroup sg = null;
+
+    String name = st.nextToken();
+
+    Vector groups = al.getGroups();
+    for(int i=0; i<groups.size(); i++)
+    {
+      sg = (SequenceGroup)groups.elementAt(i);
+      if(sg.getName().equals(name))
+        break;
+      else
+        sg = null;
+    }
 
     if(sg!=null)
     {
-- 
1.7.10.2