\r
file = getParameter("file");\r
\r
+ if(file==null)\r
+ {\r
+ //Maybe the sequences are added as parameters\r
+ StringBuffer data = new StringBuffer("PASTE");\r
+ int i=1;\r
+ while( (file=getParameter("sequence"+i))!=null)\r
+ {\r
+ data.append(file.toString()+"\n");\r
+ i++;\r
+ }\r
+ if(data.length()>5)\r
+ file = data.toString();\r
+ }\r
+\r
final JalviewLite applet = this;\r
if(getParameter("embedded")!=null\r
&& getParameter("embedded").equalsIgnoreCase("true"))\r
JalviewLite _applet)\r
{\r
file = _file;\r
- if(inArchive(file))\r
+ if(file.startsWith("PASTE"))\r
+ {\r
+ file = file.substring(5);\r
+ protocol = AppletFormatAdapter.PASTE;\r
+ }\r
+ else if(inArchive(file))\r
protocol = AppletFormatAdapter.CLASSLOADER;\r
else\r
{\r
file,\r
embedded);\r
\r
+ if(protocol==jalview.io.AppletFormatAdapter.PASTE)\r
+ currentAlignFrame.setTitle("Sequences from "+getDocumentBase());\r
\r
initialAlignFrame = currentAlignFrame;\r
\r
currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
\r
\r
- String treeFile = applet.getParameter("treeFile");\r
+ String treeFile = applet.getParameter("tree");\r
+ if(treeFile==null)\r
+ applet.getParameter("treeFile");\r
if (treeFile != null)\r
{\r
try\r
if( !inArchive(param) )\r
param = addProtocol( param );\r
\r
- currentAlignFrame.parseFeaturesFile(param);\r
+ currentAlignFrame.parseFeaturesFile(param, protocol);\r
}\r
\r
param = getParameter("showFeatureSettings");\r
if(param !=null && param.equalsIgnoreCase("true"))\r
{\r
+ currentAlignFrame.viewport.showSequenceFeatures(true);\r
currentAlignFrame.featureSettings_actionPerformed();\r
}\r
\r