/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.bin;\r
\r
-import jalview.appletgui.AlignFrame;\r
+import java.applet.*;\r
\r
-import jalview.datamodel.*;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
\r
+import jalview.appletgui.*;\r
+import jalview.datamodel.*;\r
import jalview.io.*;\r
\r
-import java.applet.*;\r
+/**\r
+ * Jalview Applet. Runs in Java 1.18 runtime\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class JalviewLite\r
+ extends Applet\r
+{\r
\r
-import java.awt.*;\r
-import java.awt.event.*;\r
+ ///////////////////////////////////////////\r
+ //The following public methods maybe called\r
+ //externally, eg via javascript in HTML page\r
+\r
+ public String getSelectedSequences()\r
+ {\r
+ StringBuffer result = new StringBuffer("");\r
+\r
+ if (initialAlignFrame.viewport.getSelectionGroup() != null)\r
+ {\r
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
+ getSequencesInOrder(\r
+ initialAlignFrame.viewport.getAlignment());\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ result.append(seqs[i].getName() + "¬");\r
+ }\r
+ }\r
+\r
+ return result.toString();\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(), seqlimits);\r
+ return reply;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ }\r
+\r
+ public void loadAnnotation(String annotation)\r
+ {\r
+ if (new AnnotationFile().readAnnotationFile(\r
+ currentAlignFrame.getAlignViewport().getAlignment(), annotation,\r
+ AppletFormatAdapter.PASTE))\r
+ {\r
+ currentAlignFrame.alignPanel.fontChanged();\r
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ else\r
+ {\r
+ currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+ }\r
+ }\r
+\r
+ public String getFeatures(String format)\r
+ {\r
+ return currentAlignFrame.outputFeatures(false, format);\r
+ }\r
+\r
+ public String getAnnotation()\r
+ {\r
+ return currentAlignFrame.outputAnnotations(false);\r
+ }\r
+\r
+ public void loadAlignment(String text, String title)\r
+ {\r
+ Alignment al = null;\r
+ String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(text,\r
+ AppletFormatAdapter.PASTE,\r
+ format);\r
+ if (al.getHeight() > 0)\r
+ {\r
+ new AlignFrame(al, this, title, false);\r
+ }\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ ////////////////////////////////////////////////\r
+ ////////////////////////////////////////////////\r
+\r
+\r
+\r
+ static int lastFrameX = 200;\r
+ static int lastFrameY = 200;\r
+ boolean fileFound = true;\r
+ String file = "No file";\r
+ Button launcher = new Button("Start Jalview");\r
+\r
+ //The currentAlignFrame is static, it will change\r
+ //if and when the user selects a new window\r
+ public static AlignFrame currentAlignFrame;\r
+\r
+ //This is the first frame to be displayed, and does not change\r
+ AlignFrame initialAlignFrame;\r
+\r
+ boolean embedded = false;\r
+\r
+ /**\r
+ * init method for Jalview Applet\r
+ */\r
+ public void init()\r
+ {\r
+ int r = 255;\r
+ int g = 255;\r
+ int b = 255;\r
+ String param = getParameter("RGB");\r
+\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ r = Integer.parseInt(param.substring(0, 2), 16);\r
+ g = Integer.parseInt(param.substring(2, 4), 16);\r
+ b = Integer.parseInt(param.substring(4, 6), 16);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ r = 255;\r
+ g = 255;\r
+ b = 255;\r
+ }\r
+ }\r
+\r
+ param = getParameter("label");\r
+ if (param != null)\r
+ {\r
+ launcher.setLabel(param);\r
+ }\r
+\r
+ this.setBackground(new Color(r, g, b));\r
+\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
+ {\r
+ file = data.toString();\r
+ }\r
+ }\r
+\r
+ final JalviewLite applet = this;\r
+ if (getParameter("embedded") != null\r
+ && getParameter("embedded").equalsIgnoreCase("true"))\r
+ {\r
+ embedded = true;\r
+ LoadingThread loader = new LoadingThread(file, applet);\r
+ loader.start();\r
+ }\r
+ else if (file != null)\r
+ {\r
+ add(launcher);\r
+\r
+ launcher.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file,\r
+ applet);\r
+ loader.start();\r
+ }\r
+ });\r
+ }\r
+ else\r
+ {\r
+ file = "NO FILE";\r
+ fileFound = false;\r
+ }\r
+ }\r
+\r
+ public static void main(String[] args)\r
+ {\r
+ if (args.length != 1)\r
+ {\r
+ System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");\r
+ System.exit(1);\r
+ }\r
+\r
+ String format = new jalview.io.IdentifyFile().Identify(args[0],\r
+ AppletFormatAdapter.FILE);\r
+\r
+ Alignment al = null;\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE,\r
+ format);\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ if ( (al != null) && (al.getHeight() > 0))\r
+ {\r
+ AlignFrame af = new AlignFrame(al, null, args[0], false);\r
+ af.statusBar.setText("Successfully loaded file " + args[0]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Initialises and displays a new java.awt.Frame\r
+ *\r
+ * @param frame java.awt.Frame to be displayed\r
+ * @param title title of new frame\r
+ * @param width width if new frame\r
+ * @param height height of new frame\r
+ */\r
+ public static void addFrame(final Frame frame, String title, int width,\r
+ int height)\r
+ {\r
+ frame.setLocation(lastFrameX, lastFrameY);\r
+ lastFrameX += 40;\r
+ lastFrameY += 40;\r
+ frame.setSize(width, height);\r
+ frame.setTitle(title);\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
+ {\r
+ ( (AlignFrame) frame).closeMenuItem_actionPerformed();\r
+ }\r
+ if (currentAlignFrame == frame)\r
+ {\r
+ currentAlignFrame = null;\r
+ }\r
+ lastFrameX -= 40;\r
+ lastFrameY -= 40;\r
+ frame.setMenuBar(null);\r
+ frame.dispose();\r
+ }\r
+\r
+ public void windowActivated(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
+ {\r
+ currentAlignFrame = (AlignFrame) frame;\r
+ }\r
+ }\r
+\r
+ });\r
+ frame.setVisible(true);\r
+ }\r
+\r
+ /**\r
+ * This paints the background surrounding the "Launch Jalview button"\r
+ * <br>\r
+ * <br>If file given in parameter not found, displays error message\r
+ *\r
+ * @param g graphics context\r
+ */\r
+ public void paint(Graphics g)\r
+ {\r
+ if (!fileFound)\r
+ {\r
+ g.setColor(new Color(200, 200, 200));\r
+ g.setColor(Color.cyan);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.red);\r
+ g.drawString("Jalview can't open file", 5, 15);\r
+ g.drawString("\"" + file + "\"", 5, 30);\r
+ }\r
+ else if (embedded)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Arial", Font.BOLD, 24));\r
+ g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);\r
+ g.drawString("Loading Data...", 50, this.getSize().height / 2);\r
+ }\r
+\r
+ }\r
+\r
+ class LoadingThread\r
+ extends Thread\r
+ {\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+ JalviewLite applet;\r
+\r
+ public LoadingThread(String _file,\r
+ JalviewLite _applet)\r
+ {\r
+ file = _file;\r
+ if (file.startsWith("PASTE"))\r
+ {\r
+ file = file.substring(5);\r
+ protocol = AppletFormatAdapter.PASTE;\r
+ }\r
+ else if (inArchive(file))\r
+ {\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ }\r
+ else\r
+ {\r
+ file = addProtocol(file);\r
+ protocol = AppletFormatAdapter.URL;\r
+ }\r
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
+ applet = _applet;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ Alignment al = null;\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(file, protocol,\r
+ format);\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ if ( (al != null) && (al.getHeight() > 0))\r
+ {\r
+ currentAlignFrame = new AlignFrame(al,\r
+ applet,\r
+ file,\r
+ embedded);\r
+\r
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
+ {\r
+ currentAlignFrame.setTitle("Sequences from " + getDocumentBase());\r
+ }\r
\r
+ initialAlignFrame = currentAlignFrame;\r
\r
-public class JalviewLite extends Applet {\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
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
\r
- public void init() {\r
- applet = this;\r
+ String treeFile = applet.getParameter("tree");\r
+ if (treeFile == null)\r
+ {\r
+ treeFile = applet.getParameter("treeFile");\r
+ }\r
\r
- int r=255,g=255,b=255;\r
- String param = getParameter("RGB");\r
- if(param!=null)\r
+ if (treeFile != null)\r
{\r
try\r
{\r
- r = Integer.parseInt(param.substring(0,2),16);\r
- g = Integer.parseInt(param.substring(2,4),16);\r
- b = Integer.parseInt(param.substring(4,6),16);\r
+ if (inArchive(treeFile))\r
+ {\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ }\r
+ else\r
+ {\r
+ protocol = AppletFormatAdapter.URL;\r
+ treeFile = addProtocol(treeFile);\r
+ }\r
+\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,\r
+ protocol);\r
+\r
+ fin.parse();\r
+\r
+ if (fin.getTree() != null)\r
+ {\r
+ currentAlignFrame.loadTree(fin, treeFile);\r
+ }\r
}\r
catch (Exception ex)\r
- { r=255;g=255;b=255; }\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
- this.setBackground(new Color(r,g,b));\r
-\r
- file = getParameter("file");\r
-\r
- if (file != null) {\r
- add(launcher);\r
- file = applet.getCodeBase() + file;\r
- launcher.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- String format = jalview.io.IdentifyFile.Identify(file,\r
- "URL");\r
- LoadFile(file, "URL", format);\r
- }\r
- });\r
- } else {\r
- file = "NO FILE";\r
- fileFound = false;\r
- }\r
- }\r
+ String param = getParameter("features");\r
+ if (param != null)\r
+ {\r
+ if (!inArchive(param))\r
+ {\r
+ param = addProtocol(param);\r
+ }\r
\r
- public static void showURL(String url) {\r
- try {\r
- applet.getAppletContext().showDocument(new java.net.URL(url),\r
- "HELP_WINDOW");\r
- } catch (Exception ex) {\r
+ currentAlignFrame.parseFeaturesFile(param, protocol);\r
}\r
- }\r
\r
- public void LoadFile(String file, String protocol, String format) {\r
- LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
- loader.start();\r
- }\r
-\r
- public static void addFrame(final Frame frame, String title, int width,\r
- int height) {\r
- frame.setLocation(lastFrameX, lastFrameY);\r
- lastFrameX += 40;\r
- lastFrameY += 40;\r
- frame.setSize(width, height);\r
- frame.setTitle(title);\r
- frame.addWindowListener(new WindowAdapter() {\r
- public void windowClosing(WindowEvent e) {\r
- frame.dispose();\r
- }\r
- });\r
- frame.setVisible(true);\r
- }\r
-\r
- public void paint(Graphics g) {\r
- if (!fileFound) {\r
- g.setColor(new Color(200, 200, 200));\r
- g.setColor(Color.cyan);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.red);\r
- g.drawString("Jalview can't open file", 5, 15);\r
- g.drawString("\"" + file + "\"", 5, 30);\r
+ param = getParameter("showFeatureSettings");\r
+ if (param != null && param.equalsIgnoreCase("true"))\r
+ {\r
+ currentAlignFrame.viewport.showSequenceFeatures(true);\r
+ new FeatureSettings(currentAlignFrame.alignPanel);\r
}\r
- }\r
\r
- class LoadingThread extends Thread {\r
- String file;\r
- String protocol;\r
- String format;\r
- JalviewLite jlapplet;\r
+ param = getParameter("annotations");\r
+ if (param != null)\r
+ {\r
+ if (!inArchive(param))\r
+ {\r
+ param = addProtocol(param);\r
+ }\r
+\r
+ new AnnotationFile().readAnnotationFile(\r
+ currentAlignFrame.viewport.getAlignment(),\r
+ param,\r
+ protocol);\r
+\r
+ currentAlignFrame.alignPanel.fontChanged();\r
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
\r
- public LoadingThread(String file, String protocol, String format,\r
- JalviewLite applet) {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- this.jlapplet = applet;\r
}\r
\r
- public void run() {\r
- SequenceI[] sequences = null;\r
- 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
- fileFound = false;\r
- remove(launcher);\r
- repaint();\r
+ param = getParameter("jnetfile");\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ if (inArchive(param))\r
+ {\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ }\r
+ else\r
+ {\r
+ protocol = AppletFormatAdapter.URL;\r
+ param = addProtocol(param);\r
}\r
+\r
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+ param, protocol);\r
+ new JnetAnnotationMaker().add_annotation(predictions,\r
+ currentAlignFrame.viewport.getAlignment(),\r
+ 0, false); // do not add sequence profile from concise output\r
+ currentAlignFrame.alignPanel.fontChanged();\r
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
+\r
+ param = getParameter("PDBFILE");\r
+ if (param != null)\r
+ {\r
+ if (inArchive(param))\r
+ {\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ }\r
+ else\r
+ {\r
+ protocol = AppletFormatAdapter.URL;\r
+ param = addProtocol(param);\r
+ }\r
+\r
+ String sequence = applet.getParameter("PDBSEQ");\r
+\r
+ if (sequence != null)\r
+ {\r
+ new MCview.AppletPDBViewer(param, protocol,\r
+ (Sequence) currentAlignFrame.\r
+ getAlignViewport().getAlignment().\r
+ findName(sequence),\r
+ currentAlignFrame.getSeqcanvas());\r
+ }\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ fileFound = false;\r
+ remove(launcher);\r
+ repaint();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Discovers whether the given file is in the Applet Archive\r
+ * @param file String\r
+ * @return boolean\r
+ */\r
+ boolean inArchive(String file)\r
+ {\r
+ //This might throw a security exception in certain browsers\r
+ //Netscape Communicator for instance.\r
+ try\r
+ {\r
+ return (getClass().getResourceAsStream("/" + file) != null);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Exception checking resources: " + file + " " + ex);\r
+ return false;\r
+ }\r
}\r
+\r
+ String addProtocol(String file)\r
+ {\r
+ if (file.indexOf("://") == -1)\r
+ {\r
+ file = getCodeBase() + file;\r
+ }\r
+\r
+ return file;\r
+ }\r
+\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff