/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
try\r
{\r
UIManager.setLookAndFeel(\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
+ UIManager.getSystemLookAndFeelClassName()\r
+ // UIManager.getCrossPlatformLookAndFeelClassName()\r
//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
//"javax.swing.plaf.metal.MetalLookAndFeel"\r
//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
\r
if(file!=null)\r
{\r
+ System.out.println("Opening file: " + file);\r
\r
if (!file.startsWith("http://"))\r
{\r
\r
protocol = "File";\r
\r
- if (file.indexOf("http:") > -1)\r
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)\r
{\r
protocol = "URL";\r
}\r
\r
+\r
+\r
if (file.endsWith(".jar"))\r
format = "Jalview";\r
else\r
format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
\r
- System.out.println("Opening: " + format + " file " + file);\r
+\r
\r
AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
\r
+ if(af==null)\r
+ {\r
+ System.out.println("error");\r
+ return;\r
+ }\r
+\r
+ data = aparser.getValue("colour");\r
+ if(data!=null)\r
+ {\r
+ data.replaceAll("%20", " ");\r
+\r
+ jalview.schemes.ColourSchemeI cs =\r
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().\r
+ getAlignment(), data);\r
+\r
+ if(cs == null)\r
+ {\r
+ jalview.schemes.UserColourScheme ucs\r
+ = new jalview.schemes.UserColourScheme("white");\r
+ ucs.parseAppletParameter(data);\r
+ cs = ucs;\r
+ }\r
+\r
+ System.out.println("colour is " + data);\r
+ af.changeColour( cs );\r
+ }\r
+\r
+\r
// Must maintain ability to use the groups flag\r
data = aparser.getValue("groups");\r
if (data != null)\r
{\r
- af.parseGroupsFile(data);\r
+ af.parseFeaturesFile(data, protocol);\r
System.out.println("Added "+data);\r
}\r
data = aparser.getValue("features");\r
if (data != null)\r
{\r
- af.parseGroupsFile(data);\r
+ af.parseFeaturesFile(data, protocol);\r
System.out.println("Added "+data);\r
}\r
\r
}\r
\r
// We'll only open the default file if the desktop is visible.\r
+ // And the user\r
//////////////////////\r
if (\r
!headless\r
+ && file==null\r
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)\r
)\r
{\r
\r
if (file.endsWith(".jar"))\r
{\r
- new Jalview2XML().LoadJalviewAlign(file);\r
+ format = "Jalview";\r
}\r
else\r
{\r
format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
- new jalview.io.FileLoader().LoadFile(file, protocol, format);\r
}\r
+\r
+ fileLoader.LoadFile(file, protocol, format);\r
+\r
}\r
}\r
}\r