/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\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
-* 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
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
import java.applet.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-import jalview.appletgui.FeatureSettings;\r
\r
+import jalview.appletgui.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
\r
/**\r
* Jalview Applet. Runs in Java 1.18 runtime\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class JalviewLite extends Applet\r
+public class JalviewLite\r
+ extends Applet\r
{\r
\r
///////////////////////////////////////////\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
- StringBuffer result = new StringBuffer("");\r
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
+ getSequencesInOrder(\r
+ initialAlignFrame.viewport.getAlignment());\r
\r
- if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
+ for (int i = 0; i < seqs.length; i++)\r
{\r
- SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
- getSequencesInOrder(\r
- initialAlignFrame.viewport.getAlignment());\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- result.append(seqs[i].getName() + "¬");\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
- return result.toString();\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 String getAlignment(String format)\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
- return getAlignment(format, "true");\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
- public String getAlignment(String format, String suffix)\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
- boolean seqlimits = suffix.equalsIgnoreCase("true");\r
-\r
- String reply = new AppletFormatAdapter().formatSequences(format,\r
- currentAlignFrame.viewport.getAlignment(), seqlimits);\r
- return reply;\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
- ex.printStackTrace();\r
- return "Error retrieving alignment in " + format + " format. ";\r
+ r = 255;\r
+ g = 255;\r
+ b = 255;\r
}\r
}\r
\r
- public void loadAnnotation(String annotation)\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
- if (new AnnotationFile().readAnnotationFile(\r
- currentAlignFrame.getAlignViewport().getAlignment(), annotation,\r
- AppletFormatAdapter.PASTE))\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
- currentAlignFrame.alignPanel.fontChanged();\r
- currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ data.append(file.toString() + "\n");\r
+ i++;\r
}\r
- else\r
+ if (data.length() > 5)\r
{\r
- currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+ file = data.toString();\r
}\r
}\r
\r
- public String getFeatures(String format)\r
+ final JalviewLite applet = this;\r
+ if (getParameter("embedded") != null\r
+ && getParameter("embedded").equalsIgnoreCase("true"))\r
{\r
- return currentAlignFrame.outputFeatures(false, format);\r
+ embedded = true;\r
+ LoadingThread loader = new LoadingThread(file, applet);\r
+ loader.start();\r
}\r
-\r
- public String getAnnotation()\r
+ else if (file != null)\r
{\r
- return currentAlignFrame.outputAnnotations(false);\r
- }\r
+ add(launcher);\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
- al = new AppletFormatAdapter().readFile(text,\r
- AppletFormatAdapter.PASTE,\r
- format);\r
- if (al.getHeight() > 0)\r
- new AlignFrame(al, this, title, false);\r
- }catch(java.io.IOException ex)\r
+ launcher.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
{\r
- ex.printStackTrace();\r
+ LoadingThread loader = new LoadingThread(file,\r
+ applet);\r
+ loader.start();\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
+ }\r
+ else\r
+ {\r
+ file = "NO FILE";\r
+ fileFound = false;\r
+ }\r
+ }\r
\r
- boolean embedded = false;\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
- /**\r
- * init method for Jalview Applet\r
- */\r
- public void init()\r
+ Alignment al = null;\r
+ try\r
{\r
- int r = 255;\r
- int g = 255;\r
- int b = 255;\r
- String param = getParameter("RGB");\r
-\r
- if (param != null)\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
- 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
+ ( (AlignFrame) frame).closeMenuItem_actionPerformed();\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
- if(file==null)\r
+ if (currentAlignFrame == frame)\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
- file = data.toString();\r
+ currentAlignFrame = null;\r
}\r
+ lastFrameX -= 40;\r
+ lastFrameY -= 40;\r
+ frame.setMenuBar(null);\r
+ frame.dispose();\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
+ public void windowActivated(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
{\r
- file = "NO FILE";\r
- fileFound = false;\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 static void main(String [] args)\r
+ public LoadingThread(String _file,\r
+ JalviewLite _applet)\r
{\r
- if(args.length!=1)\r
+ file = _file;\r
+ if (file.startsWith("PASTE"))\r
{\r
- System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");\r
- System.exit(1);\r
+ file = file.substring(5);\r
+ protocol = AppletFormatAdapter.PASTE;\r
}\r
-\r
- String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);\r
-\r
- Alignment al = null;\r
- try{\r
- al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);\r
- }catch(java.io.IOException ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- if ( (al != null) && (al.getHeight() > 0))\r
+ else if (inArchive(file))\r
{\r
- AlignFrame af = new AlignFrame(al, null, args[0], false);\r
- af.statusBar.setText("Successfully loaded file " + args[0]);\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
-\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
+ public void run()\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
- ((AlignFrame)frame).closeMenuItem_actionPerformed();\r
- if(currentAlignFrame == frame)\r
- {\r
- currentAlignFrame = null;\r
- }\r
- lastFrameX -=40;\r
- lastFrameY -=40;\r
- frame.setMenuBar(null);\r
- frame.dispose();\r
- }\r
- public void windowActivated(WindowEvent e)\r
- {\r
- if(frame instanceof AlignFrame)\r
- currentAlignFrame = (AlignFrame)frame;\r
- }\r
-\r
- });\r
- frame.setVisible(true);\r
- }\r
-\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
- /**\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
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)\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
+ currentAlignFrame.setTitle("Sequences from " + getDocumentBase());\r
}\r
\r
+ initialAlignFrame = currentAlignFrame;\r
\r
- }\r
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
\r
- class LoadingThread extends Thread\r
- {\r
- String file;\r
- String protocol;\r
- String format;\r
- JalviewLite applet;\r
+ String treeFile = applet.getParameter("tree");\r
+ if (treeFile == null)\r
+ {\r
+ treeFile = applet.getParameter("treeFile");\r
+ }\r
\r
- public LoadingThread(String _file,\r
- JalviewLite _applet)\r
+ if (treeFile != null)\r
{\r
- file = _file;\r
- if(file.startsWith("PASTE"))\r
+ try\r
+ {\r
+ if (inArchive(treeFile))\r
{\r
- file = file.substring(5);\r
- protocol = AppletFormatAdapter.PASTE;\r
- }\r
- else if(inArchive(file))\r
protocol = AppletFormatAdapter.CLASSLOADER;\r
+ }\r
else\r
{\r
- file = addProtocol(file);\r
protocol = AppletFormatAdapter.URL;\r
+ treeFile = addProtocol(treeFile);\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
- al = new AppletFormatAdapter().readFile(file, protocol,\r
- format);\r
- }catch(java.io.IOException ex)\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,\r
+ protocol);\r
+\r
+ fin.parse();\r
+\r
+ if (fin.getTree() != null)\r
{\r
- ex.printStackTrace();\r
+ currentAlignFrame.loadTree(fin, treeFile);\r
}\r
- if ((al != null) && (al.getHeight() > 0))\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ String param = getParameter("features");\r
+ if (param != null)\r
+ {\r
+ if (!inArchive(param))\r
+ {\r
+ param = addProtocol(param);\r
+ }\r
+\r
+ currentAlignFrame.parseFeaturesFile(param, protocol);\r
+ }\r
+\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
+ 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
+ }\r
+\r
+ param = getParameter("jnetfile");\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ if (inArchive(param))\r
{\r
- currentAlignFrame = new AlignFrame(al,\r
- applet,\r
- file,\r
- embedded);\r
-\r
- if(protocol==jalview.io.AppletFormatAdapter.PASTE)\r
- currentAlignFrame.setTitle("Sequences from "+getDocumentBase());\r
-\r
- initialAlignFrame = currentAlignFrame;\r
-\r
- currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
-\r
-\r
- String treeFile = applet.getParameter("tree");\r
- if(treeFile==null)\r
- treeFile = applet.getParameter("treeFile");\r
-\r
- if (treeFile != null)\r
- {\r
- try\r
- {\r
- if(inArchive(treeFile))\r
- protocol = AppletFormatAdapter.CLASSLOADER;\r
- else\r
- {\r
- protocol = AppletFormatAdapter.URL;\r
- treeFile = addProtocol(treeFile);\r
- }\r
-\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, 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
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- String param = getParameter("features");\r
- if (param != null)\r
- {\r
- if( !inArchive(param) )\r
- param = addProtocol( param );\r
-\r
- currentAlignFrame.parseFeaturesFile(param, protocol);\r
- }\r
-\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
- param = getParameter("annotations");\r
- if (param != null)\r
- {\r
- if( !inArchive(param) )\r
- param = addProtocol( param );\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
- }\r
-\r
- param = getParameter("jnetfile");\r
- if (param != null)\r
- {\r
- try\r
- {\r
- if (inArchive(param))\r
- protocol = AppletFormatAdapter.CLASSLOADER;\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
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
-\r
- param = getParameter("PDBFILE");\r
- if(param!=null)\r
- {\r
- if( inArchive(param) )\r
- protocol = AppletFormatAdapter.CLASSLOADER;\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.getAlignViewport().getAlignment().findName(sequence),\r
- currentAlignFrame.getSeqcanvas());\r
- }\r
-\r
- }\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
}\r
else\r
{\r
- fileFound = false;\r
- remove(launcher);\r
- repaint();\r
+ protocol = AppletFormatAdapter.URL;\r
+ param = addProtocol(param);\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
- return (getClass().getResourceAsStream("/" + file) != null);\r
- }catch(Exception ex)\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
- System.out.println("Exception checking resources: "+file+" "+ex);\r
- return false;\r
+ ex.printStackTrace();\r
}\r
}\r
\r
- String addProtocol(String file)\r
+ param = getParameter("PDBFILE");\r
+ if (param != null)\r
{\r
- if (file.indexOf("://") == -1)\r
- file = getCodeBase() + file;\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
- return file;\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