- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if ((sequences != null) && (sequences.length > 0)) {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences),\r
- jlapplet);\r
- addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
- } else {\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
+\r
+ if ((sequences != null) && (sequences.length > 0))\r
+ {\r
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
+ applet, file);\r
+ if (embedded)\r
+ currentAlignFrame.setEmbedded();\r
+\r
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
+\r
+\r
+ String treeFile = applet.getParameter("treeFile");\r
+ if (treeFile != null)\r
+ {\r
+ if (treeFile.indexOf("://") == -1)\r
+ treeFile = getCodeBase() + treeFile;\r
+\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+ getCodeBase() + treeFile, "URL");\r
+ fin.parse();\r
+\r
+ if (fin.getTree() != null)\r
+ {\r
+ TreePanel tp = null;\r
+ tp = new TreePanel(currentAlignFrame.viewport,\r
+ currentAlignFrame.viewport.getAlignment().getSequences(),\r
+ fin, "FromFile", applet.getCodeBase() + treeFile);\r
+ addFrame(tp, treeFile, 600, 500);\r
+ currentAlignFrame.addTreeMenuItem(tp, treeFile);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ String param = getParameter("features");\r
+ if (param != null)\r
+ {\r
+ if (param.indexOf("://") == -1)\r
+ param = getCodeBase() + param;\r
+\r
+ currentAlignFrame.parseFeaturesFile(param);\r
+ }\r
+\r
+ param = getParameter("annotations");\r
+ if (param != null)\r
+ {\r
+ if (param.indexOf("://") == -1)\r
+ param = getCodeBase() + param;\r
+\r
+ new AnnotationReader().readAnnotationFile(\r
+ currentAlignFrame.viewport.getAlignment(),\r
+ param);\r
+\r
+ currentAlignFrame.alignPanel.fontChanged();\r
+ }\r
+\r
+\r
+ String pdbfile = applet.getParameter("PDBFILE");\r
+ if(pdbfile!=null)\r
+ {\r
+ if(pdbfile.indexOf("://")==-1)\r
+ pdbfile = getCodeBase() + pdbfile;\r
+\r
+ String sequence = applet.getParameter("PDBSEQ");\r
+\r
+ if(sequence!=null)\r
+ {\r
+ new MCview.AppletPDBViewer(pdbfile, "URL",\r
+ (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),\r
+ currentAlignFrame.getSeqcanvas());\r
+ }\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r