{\r
static int lastFrameX = 200;\r
static int lastFrameY = 200;\r
- static Applet applet;\r
boolean fileFound = true;\r
String file = "No file";\r
Button launcher = new Button("Start Jalview");\r
\r
+ AlignFrame currentAlignFrame;\r
+\r
+\r
/**\r
* init method for Jalview Applet\r
*/\r
public void init()\r
{\r
- applet = this;\r
-\r
int r = 255;\r
int g = 255;\r
int b = 255;\r
}\r
}\r
\r
+ param = getParameter("label");\r
+ if(param != null)\r
+ launcher.setLabel(param);\r
+\r
this.setBackground(new Color(r, g, b));\r
\r
- file = getParameter("file");\r
\r
+ param = getParameter("features");\r
+ if(param!=null)\r
+ {\r
+ if(param.indexOf("://")==-1)\r
+ param = getCodeBase() + param;\r
+ }\r
+ final String featuresFile = param;\r
+\r
+ file = getParameter("file");\r
+ final JalviewLite applet = this;\r
if (file != null)\r
{\r
add(launcher);\r
- file = applet.getCodeBase() + file;\r
+ if(file.indexOf("://")==-1)\r
+ file = getCodeBase() + file;\r
+\r
launcher.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
String format = jalview.io.IdentifyFile.Identify(file,\r
"URL");\r
- LoadFile(file, "URL", format);\r
- }\r
+ LoadingThread loader = new LoadingThread(file,\r
+ "URL",\r
+ format,\r
+ featuresFile,\r
+ applet);\r
+ loader.start();\r
+ }\r
});\r
}\r
else\r
}\r
}\r
\r
+\r
public static void main(String [] args)\r
{\r
if(args.length!=1)\r
}\r
\r
String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
- SequenceI[] sequences = FormatAdapter.readFile(args[0], "File", format);\r
+ SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
\r
if ( (sequences != null) && (sequences.length > 0))\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), null);\r
- addFrame(af, args[0], AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);\r
af.statusBar.setText("Successfully loaded file " + args[0]);\r
}\r
}\r
\r
- /**\r
- * Displays the given URL in a new browser window\r
- *\r
- * @param url URL to display in browser window.\r
- * <br>New window will be named "HELP_WINDOW"\r
- */\r
- public static void showURL(String url)\r
- {\r
- showURL(url, "HELP");\r
- }\r
-\r
- public static void showURL(String url, String target)\r
- {\r
- if(applet==null)\r
- {\r
- System.out.println("Not running as applet - no browser available.");\r
- }\r
- else\r
- {\r
- try\r
- {\r
- applet.getAppletContext().showDocument(new java.net.URL(url),\r
- target);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * Starts a new LoadingThread for loading an alignment file\r
- *\r
- * @param file file name including full path to file\r
- * @param protocol file or URL or paste\r
- * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview\r
- */\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
- loader.start();\r
- }\r
\r
/**\r
* Initialises and displays a new java.awt.Frame\r
frame.setVisible(true);\r
}\r
\r
+ public String getAlignment(String format)\r
+ {\r
+ return getAlignment(format, "true");\r
+ }\r
+\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
+ return reply;\r
+ }\r
+ catch (Exception ex)\r
+ {ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+\r
+ }\r
+ }\r
+\r
/**\r
* This paints the background surrounding the "Launch Jalview button"\r
* <br>\r
String file;\r
String protocol;\r
String format;\r
- JalviewLite jlapplet;\r
-\r
- public LoadingThread(String file, String protocol, String format,\r
- JalviewLite applet)\r
+ String featuresFile;\r
+ JalviewLite applet;\r
+\r
+ public LoadingThread(String file,\r
+ String protocol,\r
+ String format,\r
+ String features,\r
+ JalviewLite applet)\r
{\r
this.file = file;\r
this.protocol = protocol;\r
this.format = format;\r
- this.jlapplet = applet;\r
+ featuresFile = features;\r
+ this.applet = applet;\r
}\r
\r
public void run()\r
{\r
SequenceI[] sequences = null;\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
\r
if ((sequences != null) && (sequences.length > 0))\r
{\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
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
+ applet, file);\r
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ if(featuresFile!=null)\r
+ currentAlignFrame.parseFeaturesFile(featuresFile);\r
}\r
else\r
{\r
git://source.jalview.org / jalview.git / blobdiff