}\r
\r
String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
- SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
-\r
+ SequenceI[] sequences = null;\r
+ try{\r
+ sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
+ }catch(java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
if ( (sequences != null) && (sequences.length > 0))\r
{\r
AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);\r
public void run()\r
{\r
SequenceI[] sequences = null;\r
- sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
-\r
+ try{\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol,\r
+ format);\r
+ }catch(java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
if ((sequences != null) && (sequences.length > 0))\r
{\r
currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
if (treeFile != null)\r
{\r
if (treeFile.indexOf("://") == -1)\r
- treeFile = getCodeBase() + treeFile;\r
+ treeFile = getCodeBase() + treeFile;\r
\r
try\r
{\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
- getCodeBase() + treeFile, "URL");\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL");\r
fin.parse();\r
\r
if (fin.getTree() != null)\r
TreePanel tp = null;\r
tp = new TreePanel(currentAlignFrame.viewport,\r
currentAlignFrame.viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase() + treeFile);\r
+ fin, "FromFile", treeFile);\r
addFrame(tp, treeFile, 600, 500);\r
currentAlignFrame.addTreeMenuItem(tp, treeFile);\r
}\r