applet can define groups as parameters

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 35fc82f..222d049 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -461,27 +461,55 @@ public class JalviewLite extends Applet
              }\r
 \r
 \r
-                String pdbfile = applet.getParameter("PDBFILE");\r
-                if(pdbfile!=null)\r
+                param = getParameter("PDBFILE");\r
+                if(param!=null)\r
                 {\r
-                  if( inArchive(pdbfile) )\r
+                  if( inArchive(param) )\r
                     protocol = AppletFormatAdapter.CLASSLOADER;\r
                   else\r
                   {\r
                     protocol = AppletFormatAdapter.URL;\r
-                    pdbfile = addProtocol(pdbfile);\r
+                    param = addProtocol(param);\r
                   }\r
 \r
                   String sequence = applet.getParameter("PDBSEQ");\r
 \r
                   if(sequence!=null)\r
                   {\r
-                    new MCview.AppletPDBViewer(pdbfile, protocol,\r
+                    new MCview.AppletPDBViewer(param, protocol,\r
                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),\r
                                                currentAlignFrame.getSeqcanvas());\r
                   }\r
 \r
                 }\r
+\r
+                int gIndex = 1;\r
+                param = getParameter("SEQUENCE_GROUP"+gIndex);\r
+                if(param!=null)\r
+                do{\r
+                  new AnnotationFile().readAnnotationFile(\r
+                   currentAlignFrame.viewport.getAlignment(),\r
+                   "JALVIEW_ANNOTATION\nSEQUENCE_GROUP\t"+param,\r
+                   AppletFormatAdapter.PASTE);\r
+                  gIndex++;\r
+                  param = applet.getParameter("SEQUENCE_GROUP"+gIndex);\r
+                  currentAlignFrame.alignPanel.repaint();\r
+                }while(param!=null);\r
+\r
+              gIndex = 1;\r
+              param = getParameter("PROPERTIES" + gIndex);\r
+              if (param != null)\r
+                do\r
+                {\r
+                  new AnnotationFile().readAnnotationFile(\r
+                      currentAlignFrame.viewport.getAlignment(),\r
+                      "JALVIEW_ANNOTATION\nPROPERTIES\t" + param,\r
+                      AppletFormatAdapter.PASTE);\r
+                  gIndex++;\r
+                  param = applet.getParameter("PROPERTIES" + gIndex);\r
+                  currentAlignFrame.alignPanel.repaint();\r
+                }\r
+                while (param != null);\r
             }\r
             else\r
             {\r