}\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
\r
\r
SequenceI refSeq = null;\r
- Hashtable annotationsHash = new Hashtable();\r
public boolean readAnnotationFile(AlignmentI al,\r
String file,\r
String protocol)\r
if(sg.getSize()>0)\r
{\r
al.addGroup(sg);\r
- annotationsHash.put(sg.getName(), sg);\r
}\r
}\r
\r
//So far we have only added groups to the annotationHash,\r
//the idea is in the future properties can be added to\r
//alignments, other annotations etc\r
- SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());\r
+ if(al.getGroups()==null)\r
+ return;\r
+ SequenceGroup sg = null;\r
+\r
+ String name = st.nextToken();\r
+\r
+ Vector groups = al.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ sg = (SequenceGroup)groups.elementAt(i);\r
+ if(sg.getName().equals(name))\r
+ break;\r
+ else\r
+ sg = null;\r
+ }\r
\r
if(sg!=null)\r
{\r