-/*\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
-\r
-package jalview.bin;\r
-\r
-import java.applet.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.appletgui.AlignFrame;\r
-\r
-public class JalviewLite extends Applet\r
-{\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
- public void init()\r
- {\r
- applet = this;\r
- this.setBackground(Color.white);\r
-\r
- file = getParameter("file");\r
- if (file != null)\r
- {\r
- add(launcher);\r
- file = applet.getCodeBase() + file;\r
- launcher.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- String format = jalview.io.IdentifyFile.Identify( file, "URL");\r
- LoadFile(file, "URL", format);\r
- }\r
- });\r
- }\r
- else\r
- {\r
- file = "NO FILE";\r
- fileFound = false;\r
- }\r
- }\r
-\r
-\r
- public static void showURL(String url)\r
- {\r
- try{\r
- applet.getAppletContext().showDocument(new java.net.URL(url), "HELP_WINDOW");\r
- }catch(Exception ex){}\r
- }\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
- public static void addFrame(final Frame frame, String title, int width, int height)\r
- {\r
- frame.setLocation(lastFrameX,lastFrameY);\r
- lastFrameX+=40; 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
- frame.dispose();\r
- }\r
- });\r
- frame.setVisible(true);\r
- }\r
-\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
- }\r
-\r
- class LoadingThread extends Thread\r
- {\r
- String file, protocol, format;\r
- JalviewLite jlapplet;\r
-\r
- public LoadingThread(String file, String protocol, String format, JalviewLite applet)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- this.jlapplet = applet;\r
- }\r
- public void run()\r
- {\r
- SequenceI [] sequences = null;\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if (sequences != null && sequences.length>0)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), jlapplet );\r
- addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
- }\r
- else\r
- {\r
- fileFound = false;\r
- remove(launcher);\r
- repaint();\r
- }\r
- }\r
- }\r
-}\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.bin;
+
+import java.applet.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.*;
+
+import jalview.appletgui.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JalviewLite
+ extends Applet
+{
+
+
+
+ ///////////////////////////////////////////
+ //The following public methods maybe called
+ //externally, eg via javascript in HTML page
+
+ public String getSelectedSequences()
+ {
+ StringBuffer result = new StringBuffer("");
+
+ if (initialAlignFrame.viewport.getSelectionGroup() != null)
+ {
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
+ getSequencesInOrder(
+ initialAlignFrame.viewport.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ result.append(seqs[i].getName() + "¬");
+ }
+ }
+
+ return result.toString();
+ }
+
+ public String getAlignment(String format)
+ {
+ return getAlignment(format, "true");
+ }
+
+ public String getAlignment(String format, String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ currentAlignFrame.viewport.getAlignment(), seqlimits);
+ return reply;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+
+ public void loadAnnotation(String annotation)
+ {
+ if (new AnnotationFile().readAnnotationFile(
+ currentAlignFrame.getAlignViewport().getAlignment(), annotation,
+ AppletFormatAdapter.PASTE))
+ {
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ }
+ }
+
+ public String getFeatures(String format)
+ {
+ return currentAlignFrame.outputFeatures(false, format);
+ }
+
+ public String getAnnotation()
+ {
+ return currentAlignFrame.outputAnnotations(false);
+ }
+
+ public void loadAlignment(String text, String title)
+ {
+ Alignment al = null;
+ String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
+ try
+ {
+ al = new AppletFormatAdapter().readFile(text,
+ AppletFormatAdapter.PASTE,
+ format);
+ if (al.getHeight() > 0)
+ {
+ new AlignFrame(al, this, title, false);
+ }
+ }
+ catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ ////////////////////////////////////////////////
+ ////////////////////////////////////////////////
+
+
+
+ static int lastFrameX = 200;
+ static int lastFrameY = 200;
+ boolean fileFound = true;
+ String file = "No file";
+ Button launcher = new Button("Start Jalview");
+
+ //The currentAlignFrame is static, it will change
+ //if and when the user selects a new window
+ public static AlignFrame currentAlignFrame;
+
+ //This is the first frame to be displayed, and does not change
+ AlignFrame initialAlignFrame;
+
+ boolean embedded = false;
+
+ public boolean jmolAvailable = false;
+
+ /**
+ * init method for Jalview Applet
+ */
+ public void init()
+ {
+ try
+ {
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+ jmolAvailable = true;
+ }
+ }
+ catch (java.lang.ClassNotFoundException ex)
+ {
+ System.out.println("Jmol not available - Using MCview for structures");
+ }
+
+ int r = 255;
+ int g = 255;
+ int b = 255;
+ String param = getParameter("RGB");
+
+ if (param != null)
+ {
+ try
+ {
+ r = Integer.parseInt(param.substring(0, 2), 16);
+ g = Integer.parseInt(param.substring(2, 4), 16);
+ b = Integer.parseInt(param.substring(4, 6), 16);
+ }
+ catch (Exception ex)
+ {
+ r = 255;
+ g = 255;
+ b = 255;
+ }
+ }
+
+ param = getParameter("label");
+ if (param != null)
+ {
+ launcher.setLabel(param);
+ }
+
+ this.setBackground(new Color(r, g, b));
+
+ file = getParameter("file");
+
+ if (file == null)
+ {
+ //Maybe the sequences are added as parameters
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ while ( (file = getParameter("sequence" + i)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ }
+
+ final JalviewLite applet = this;
+ if (getParameter("embedded") != null
+ && getParameter("embedded").equalsIgnoreCase("true"))
+ {
+ embedded = true;
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
+ else if (file != null)
+ {
+ add(launcher);
+
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file,
+ applet);
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ file = "NO FILE";
+ fileFound = false;
+ }
+ }
+
+ public static void main(String[] args)
+ {
+ if (args.length != 1)
+ {
+ System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+ System.exit(1);
+ }
+
+ String format = new jalview.io.IdentifyFile().Identify(args[0],
+ AppletFormatAdapter.FILE);
+
+ Alignment al = null;
+ try
+ {
+ al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE,
+ format);
+ }
+ catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ if ( (al != null) && (al.getHeight() > 0))
+ {
+ AlignFrame af = new AlignFrame(al, null, args[0], false);
+ af.statusBar.setText("Successfully loaded file " + args[0]);
+ }
+ }
+
+ /**
+ * Initialises and displays a new java.awt.Frame
+ *
+ * @param frame java.awt.Frame to be displayed
+ * @param title title of new frame
+ * @param width width if new frame
+ * @param height height of new frame
+ */
+ public static void addFrame(final Frame frame, String title, int width,
+ int height)
+ {
+ frame.setLocation(lastFrameX, lastFrameY);
+ lastFrameX += 40;
+ lastFrameY += 40;
+ frame.setSize(width, height);
+ frame.setTitle(title);
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ if (frame instanceof AlignFrame)
+ {
+ ( (AlignFrame) frame).closeMenuItem_actionPerformed();
+ }
+ if (currentAlignFrame == frame)
+ {
+ currentAlignFrame = null;
+ }
+ lastFrameX -= 40;
+ lastFrameY -= 40;
+ frame.setMenuBar(null);
+ frame.dispose();
+ }
+
+ public void windowActivated(WindowEvent e)
+ {
+ if (frame instanceof AlignFrame)
+ {
+ currentAlignFrame = (AlignFrame) frame;
+ }
+ }
+
+ });
+ frame.setVisible(true);
+ }
+
+ /**
+ * This paints the background surrounding the "Launch Jalview button"
+ * <br>
+ * <br>If file given in parameter not found, displays error message
+ *
+ * @param g graphics context
+ */
+ public void paint(Graphics g)
+ {
+ if (!fileFound)
+ {
+ g.setColor(new Color(200, 200, 200));
+ g.setColor(Color.cyan);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setColor(Color.red);
+ g.drawString("Jalview can't open file", 5, 15);
+ g.drawString("\"" + file + "\"", 5, 30);
+ }
+ else if (embedded)
+ {
+ g.setColor(Color.black);
+ g.setFont(new Font("Arial", Font.BOLD, 24));
+ g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
+ g.drawString("Loading Data...", 50, this.getSize().height / 2);
+ }
+
+ }
+
+ class LoadingThread
+ extends Thread
+ {
+ String file;
+ String protocol;
+ String format;
+ JalviewLite applet;
+
+ public LoadingThread(String _file,
+ JalviewLite _applet)
+ {
+ file = _file;
+ if (file.startsWith("PASTE"))
+ {
+ file = file.substring(5);
+ protocol = AppletFormatAdapter.PASTE;
+ }
+ else if (inArchive(file))
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
+ else
+ {
+ file = addProtocol(file);
+ protocol = AppletFormatAdapter.URL;
+ }
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ applet = _applet;
+ }
+
+ public void run()
+ {
+ Alignment al = null;
+ try
+ {
+ al = new AppletFormatAdapter().readFile(file, protocol,
+ format);
+ }
+ catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ if ( (al != null) && (al.getHeight() > 0))
+ {
+ currentAlignFrame = new AlignFrame(al,
+ applet,
+ file,
+ embedded);
+
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ {
+ currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ }
+
+ initialAlignFrame = currentAlignFrame;
+
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+ String treeFile = applet.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = applet.getParameter("treeFile");
+ }
+
+ if (treeFile != null)
+ {
+ try
+ {
+ if (inArchive(treeFile))
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ treeFile = addProtocol(treeFile);
+ }
+
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
+ protocol);
+
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ currentAlignFrame.loadTree(fin, treeFile);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ String param = getParameter("features");
+ if (param != null)
+ {
+ if (!inArchive(param))
+ {
+ param = addProtocol(param);
+ }
+
+ currentAlignFrame.parseFeaturesFile(param, protocol);
+ }
+
+ param = getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ currentAlignFrame.viewport.showSequenceFeatures(true);
+ new FeatureSettings(currentAlignFrame.alignPanel);
+ }
+
+ param = getParameter("annotations");
+ if (param != null)
+ {
+ if (!inArchive(param))
+ {
+ param = addProtocol(param);
+ }
+
+ new AnnotationFile().readAnnotationFile(
+ currentAlignFrame.viewport.getAlignment(),
+ param,
+ protocol);
+
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);
+
+ }
+
+ param = getParameter("jnetfile");
+ if (param != null)
+ {
+ try
+ {
+ if (inArchive(param))
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ param = addProtocol(param);
+ }
+
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ param, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ currentAlignFrame.viewport.getAlignment(),
+ 0, false); // do not add sequence profile from concise output
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+
+ param = getParameter("PDBFILE");
+ if (param != null)
+ {
+
+ PDBEntry pdb = new PDBEntry();
+
+ String seqstring;
+ SequenceI [] seqs = null;
+
+ if(param.indexOf(" ")>-1)
+ {
+ seqstring = param.substring(param.indexOf(" ")+1);
+ param = param.substring(0, param.indexOf(" "));
+ StringTokenizer st = new StringTokenizer(seqstring);
+ Vector tmp = new Vector();
+ while(st.hasMoreTokens())
+ {
+ tmp.addElement((Sequence) currentAlignFrame.
+ getAlignViewport().getAlignment().
+ findName(st.nextToken()));
+ }
+
+ seqs = new SequenceI[tmp.size()];
+ tmp.copyInto(seqs);
+ }
+ else
+ {
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
+ seqs = new SequenceI[]
+ {
+ (Sequence) currentAlignFrame.
+ getAlignViewport().getAlignment().
+ findName(sequence)};
+ }
+
+ if (!inArchive(param) || jmolAvailable)
+ {
+ param = addProtocol(param);
+ }
+
+ pdb.setFile(param);
+
+ for(int i=0; i<seqs.length; i++)
+ {
+ ((Sequence)seqs[i]).addPDBId(pdb);
+ }
+
+ if (jmolAvailable)
+ new jalview.appletgui.AppletJmol(pdb,
+ seqs,
+ currentAlignFrame.alignPanel,
+ protocol);
+ else
+
+ new MCview.AppletPDBViewer(pdb,
+ seqs,
+ currentAlignFrame.alignPanel,
+ protocol);
+ }
+ }
+ else
+ {
+ fileFound = false;
+ remove(launcher);
+ repaint();
+ }
+ }
+
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ * @param file String
+ * @return boolean
+ */
+ boolean inArchive(String file)
+ {
+ //This might throw a security exception in certain browsers
+ //Netscape Communicator for instance.
+ try
+ {
+ return (getClass().getResourceAsStream("/" + file) != null);
+ }
+ catch (Exception ex)
+ {
+ System.out.println("Exception checking resources: " + file + " " + ex);
+ return false;
+ }
+ }
+
+ String addProtocol(String file)
+ {
+ if (file.indexOf("://") == -1)
+ {
+ file = getCodeBase() + file;
+ }
+
+ return file;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff