/* * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) * Copyright (C) 2009 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 /** * @return String list of selected sequence IDs, each terminated by "¬" * (¬) */ public String getSelectedSequences() { return getSelectedSequencesFrom(getDefaultTargetFrame()); } /** * @param sep * separator string or null for default * @return String list of selected sequence IDs, each terminated by sep or * ("¬" as default) */ public String getSelectedSequences(String sep) { return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); } /** * @param alf * alignframe containing selection * @return String list of selected sequence IDs, each terminated by "¬" * */ public String getSelectedSequencesFrom(AlignFrame alf) { return getSelectedSequencesFrom(alf, "¬"); } /** * get list of selected sequence IDs separated by given separator * * @param alf * window containing selection * @param sep * separator string to use - default is "¬" * @return String list of selected sequence IDs, each terminated by the given * separator */ public String getSelectedSequencesFrom(AlignFrame alf, String sep) { StringBuffer result = new StringBuffer(""); if (sep == null || sep.length() == 0) { sep = "¬"; } if (alf.viewport.getSelectionGroup() != null) { SequenceI[] seqs = alf.viewport.getSelectionGroup() .getSequencesInOrder(alf.viewport.getAlignment()); for (int i = 0; i < seqs.length; i++) { result.append(seqs[i].getName()); result.append(sep); } } return result.toString(); } /** * get sequences selected in current alignFrame and return their alignment in * format 'format' either with or without suffix * * @param alf - * where selection is * @param format - * format of alignment file * @param suffix - * "true" to append /start-end string to each sequence ID * @return selected sequences as flat file or empty string if there was no * current selection */ public String getSelectedSequencesAsAlignment(String format, String suffix) { return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format, suffix); } /** * get sequences selected in alf and return their alignment in format 'format' * either with or without suffix * * @param alf - * where selection is * @param format - * format of alignment file * @param suffix - * "true" to append /start-end string to each sequence ID * @return selected sequences as flat file or empty string if there was no * current selection */ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix) { try { boolean seqlimits = suffix.equalsIgnoreCase("true"); if (alf.viewport.getSelectionGroup() != null) { String reply = new AppletFormatAdapter().formatSequences(format, new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits); return reply; } } catch (Exception ex) { ex.printStackTrace(); return "Error retrieving alignment in " + format + " format. "; } return ""; } public String getAlignment(String format) { return getAlignmentFrom(getDefaultTargetFrame(), format, "true"); } public String getAlignmentFrom(AlignFrame alf, String format) { return getAlignmentFrom(alf, format, "true"); } public String getAlignment(String format, String suffix) { return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); } public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { try { boolean seqlimits = suffix.equalsIgnoreCase("true"); String reply = new AppletFormatAdapter().formatSequences(format, alf.viewport.getAlignment(), seqlimits); return reply; } catch (Exception ex) { ex.printStackTrace(); return "Error retrieving alignment in " + format + " format. "; } } public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); } public void loadAnnotationFrom(AlignFrame alf, String annotation) { if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport() .getAlignment(), annotation, AppletFormatAdapter.PASTE)) { alf.alignPanel.fontChanged(); alf.alignPanel.setScrollValues(0, 0); } else { alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); } } public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); } public String getFeaturesFrom(AlignFrame alf, String format) { return alf.outputFeatures(false, format); } public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); } public String getAnnotationFrom(AlignFrame alf) { return alf.outputAnnotations(false); } public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); } public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); } public AlignFrame newViewFrom(AlignFrame alf) { return alf.newView(null); } public AlignFrame newViewFrom(AlignFrame alf, String name) { return alf.newView(name); } /** * * @param text * alignment file as a string * @param title * window title * @return null or new alignment frame */ public AlignFrame 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) { return new AlignFrame(al, this, title, false); } } catch (java.io.IOException ex) { ex.printStackTrace(); } return null; } // ////////////////////////////////////////////// // ////////////////////////////////////////////// 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. Note that it will *never* point back to the embedded * AlignFrame if the applet is started as embedded on the page and then * afterwards a new view is created. */ public static AlignFrame currentAlignFrame=null; /** * This is the first frame to be displayed, and does not change. API calls * will default to this instance if currentAlignFrame is null. */ AlignFrame initialAlignFrame=null; boolean embedded = false; private boolean checkForJmol = true; private boolean checkedForJmol = false; // ensure we don't check for jmol every time the app is re-inited public boolean jmolAvailable = false; public static boolean debug=false; /** * init method for Jalview Applet */ public void init() { /** * turn on extra applet debugging */ String dbg = getParameter("debug"); if (dbg != null) { debug = dbg.toLowerCase().equals("true"); } /** * if true disable the check for jmol */ String chkforJmol = getParameter("nojmol"); if (chkforJmol != null) { checkForJmol = !chkforJmol.equals("true"); } /** * get the separator parameter if present */ String sep = getParameter("separator"); if (sep != null) { if (sep.length() > 0) { separator = sep; if (debug) { System.err.println("Separator set to '" + separator + "'"); } } else { throw new Error( "Invalid separator parameter - must be non-zero length"); } } 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")) { // Launch as embedded applet in page embedded = true; LoadingThread loader = new LoadingThread(file, applet); loader.start(); } else if (file != null) { if (getParameter("showbutton") == null || !getParameter("showbutton").equalsIgnoreCase("false")) { // Add the JalviewLite 'Button' to the page add(launcher); launcher.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { LoadingThread loader = new LoadingThread(file, applet); loader.start(); } }); } else { // Open jalviewLite immediately. LoadingThread loader = new LoadingThread(file, applet); loader.start(); } } else { // jalview initialisation with no alignment. loadAlignment() method can // still be called to open new alignments. file = "NO FILE"; fileFound = false; } } /** * 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; if (frame instanceof EmbmenuFrame) { ((EmbmenuFrame) frame).destroyMenus(); } frame.setMenuBar(null); frame.dispose(); } public void windowActivated(WindowEvent e) { if (frame instanceof AlignFrame) { currentAlignFrame = (AlignFrame) frame; if (debug) { System.err.println("Activated window " + frame); } } // be good. super.windowActivated(e); } /* * Probably not necessary to do this - see TODO above. (non-Javadoc) * * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent) * * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame == * frame) { currentAlignFrame = null; if (debug) { * System.err.println("Deactivated window "+frame); } } * super.windowDeactivated(e); } */ }); frame.setVisible(true); } /** * This paints the background surrounding the "Launch Jalview button"
*
* 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 LoadJmolThread extends Thread { private boolean running=false; public void run() { if (running || checkedForJmol) { return; } running=true; if (checkForJmol) { try { if (!System.getProperty("java.version").startsWith("1.1")) { Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter"); jmolAvailable = true; } if (!jmolAvailable) { System.out .println("Jmol not available - Using MCview for structures"); } } catch (java.lang.ClassNotFoundException ex) { } } else { jmolAvailable = false; if (debug) { System.err .println("Skipping Jmol check. Will use MCView (probably)"); } } checkedForJmol=true; running=false; } public boolean notFinished() { return running || !checkedForJmol; } } class LoadingThread extends Thread { /** * State variable: File source */ String file; /** * State variable: protocol for access to file source */ String protocol; /** * State variable: format of file source */ String format; String _file; JalviewLite applet; private void dbgMsg(String msg) { if (applet.debug) { System.err.println(msg); } } /** * update the protocol state variable for accessing the datasource located * by file. * * @param file * @return possibly updated datasource string */ public String setProtocolState(String 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; } dbgMsg("Protocol identified as '" + protocol + "'"); return file; } public LoadingThread(String _file, JalviewLite _applet) { this._file=_file; applet = _applet; } public void run() { LoadJmolThread jmolchecker = new LoadJmolThread(); jmolchecker.start(); while (jmolchecker.notFinished()) { // wait around until the Jmol check is complete. try { Thread.sleep(2); } catch (Exception e) {}; } startLoading(); } private void startLoading() { AlignFrame newAlignFrame; dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); file = setProtocolState(_file); format = new jalview.io.IdentifyFile().Identify(file, protocol); dbgMsg("File identified as '" + format + "'"); dbgMsg("Loading started."); Alignment al = null; try { al = new AppletFormatAdapter().readFile(file, protocol, format); } catch (java.io.IOException ex) { dbgMsg("File load exception."); ex.printStackTrace(); if (debug) { try { FileParse fp = new FileParse(file, protocol); String ln = null; dbgMsg(">>>Dumping contents of '"+file+"' "+"("+protocol+")"); while ((ln=fp.nextLine())!=null) { dbgMsg(ln); } dbgMsg(">>>Dump finished."); } catch (Exception e) { System.err.println("Exception when trying to dump the content of the file parameter."); e.printStackTrace(); } } } if ((al != null) && (al.getHeight() > 0)) { dbgMsg("Successfully loaded file."); newAlignFrame = new AlignFrame(al, applet, file, embedded); if (initialAlignFrame==null) { initialAlignFrame = newAlignFrame; } // update the focus. currentAlignFrame = newAlignFrame; if (protocol == jalview.io.AppletFormatAdapter.PASTE) { newAlignFrame.setTitle("Sequences from " + getDocumentBase()); } newAlignFrame.statusBar.setText("Successfully loaded file " + file); String treeFile = applet.getParameter("tree"); if (treeFile == null) { treeFile = applet.getParameter("treeFile"); } if (treeFile != null) { try { treeFile = setProtocolState(treeFile); /* * 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) { newAlignFrame.loadTree(fin, treeFile); dbgMsg("Successfuly imported tree."); } else { dbgMsg("Tree parameter did not resolve to a valid tree."); } } catch (Exception ex) { ex.printStackTrace(); } } String param = getParameter("features"); if (param != null) { param = setProtocolState(param); newAlignFrame.parseFeaturesFile(param, protocol); } param = getParameter("showFeatureSettings"); if (param != null && param.equalsIgnoreCase("true")) { newAlignFrame.viewport.showSequenceFeatures(true); new FeatureSettings(newAlignFrame.alignPanel); } param = getParameter("annotations"); if (param != null) { param = setProtocolState(param); if (new AnnotationFile().readAnnotationFile( newAlignFrame.viewport.getAlignment(), param, protocol)) { newAlignFrame.alignPanel.fontChanged(); newAlignFrame.alignPanel.setScrollValues(0, 0); } else { System.err .println("Annotations were not added from annotation file '" + param + "'"); } } param = getParameter("jnetfile"); if (param != null) { try { param = setProtocolState(param); jalview.io.JPredFile predictions = new jalview.io.JPredFile( param, protocol); JnetAnnotationMaker.add_annotation(predictions, newAlignFrame.viewport.getAlignment(), 0, false); // false==do // not // add // sequence // profile // from // concise // output newAlignFrame.alignPanel.fontChanged(); newAlignFrame.alignPanel.setScrollValues(0, 0); } catch (Exception ex) { ex.printStackTrace(); } } /* * * * * * */ int pdbFileCount = 0; do { if (pdbFileCount > 0) param = getParameter("PDBFILE" + pdbFileCount); else param = getParameter("PDBFILE"); if (param != null) { PDBEntry pdb = new PDBEntry(); String seqstring; SequenceI[] seqs = null; String[] chains = null; StringTokenizer st = new StringTokenizer(param, " "); if (st.countTokens() < 2) { String sequence = applet.getParameter("PDBSEQ"); if (sequence != null) seqs = new SequenceI[] { (Sequence) newAlignFrame.getAlignViewport() .getAlignment().findName(sequence) }; } else { param = st.nextToken(); Vector tmp = new Vector(); Vector tmp2 = new Vector(); while (st.hasMoreTokens()) { seqstring = st.nextToken(); StringTokenizer st2 = new StringTokenizer(seqstring, "="); if (st2.countTokens() > 1) { // This is the chain tmp2.addElement(st2.nextToken()); seqstring = st2.nextToken(); } tmp.addElement((Sequence) newAlignFrame .getAlignViewport().getAlignment().findName( seqstring)); } seqs = new SequenceI[tmp.size()]; tmp.copyInto(seqs); if (tmp2.size() == tmp.size()) { chains = new String[tmp2.size()]; tmp2.copyInto(chains); } } param = setProtocolState(param); if (// !jmolAvailable // && protocol == AppletFormatAdapter.CLASSLOADER) { // TODO: verify this Re: // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 // This exception preserves the current behaviour where, even if // the local pdb file was identified in the class loader protocol = AppletFormatAdapter.URL; // this is probably NOT // CORRECT! param = addProtocol(param); // } pdb.setFile(param); if (seqs != null) { for (int i = 0; i < seqs.length; i++) { if (seqs[i] != null) { ((Sequence) seqs[i]).addPDBId(pdb); } else { if (JalviewLite.debug) { // this may not really be a problem but we give a warning // anyway System.err .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + i + ")"); } } } if (jmolAvailable) { new jalview.appletgui.AppletJmol(pdb, seqs, chains, newAlignFrame.alignPanel, protocol); lastFrameX += 40; lastFrameY += 40; } else new MCview.AppletPDBViewer(pdb, seqs, chains, newAlignFrame.alignPanel, protocol); } } pdbFileCount++; } while (pdbFileCount < 10); // /////////////////////////// // modify display of features // // hide specific groups param = getParameter("hidefeaturegroups"); if (param != null) { applet.setFeatureGroupStateOn(newAlignFrame,param, false); } // show specific groups param = getParameter("showfeaturegroups"); if (param != null) { applet.setFeatureGroupStateOn(newAlignFrame,param, true); } } 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 { boolean rtn = (getClass().getResourceAsStream("/" + file) != null); if (debug) { System.err.println("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader."); } return rtn; } catch (Exception ex) { System.out.println("Exception checking resources: " + file + " " + ex); return false; } } String addProtocol(String file) { if (file.indexOf("://") == -1) { file = getCodeBase() + file; if (debug) { System.err.println("Prepended codebase for resource: '" + file + "'"); } } return file; } } /** * @return the default alignFrame acted on by the public applet methods. May * return null with an error message on System.err indicating the * fact. */ protected AlignFrame getDefaultTargetFrame() { if (currentAlignFrame != null) { return currentAlignFrame; } if (initialAlignFrame != null) { return initialAlignFrame; } System.err .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); return null; } /** * separator used for separatorList */ protected String separator = "|"; // this is a safe(ish) separator - tabs // don't work for firefox /** * parse the string into a list * * @param list * @return elements separated by separator */ public String[] separatorListToArray(String list) { int seplen = separator.length(); if (list == null || list.equals("")) return null; java.util.Vector jv = new Vector(); int cp = 0, pos; while ((pos = list.indexOf(separator, cp)) > cp) { jv.addElement(list.substring(cp, pos)); cp = pos + seplen; } if (cp < list.length()) { jv.addElement(list.substring(cp)); } if (jv.size() > 0) { String[] v = new String[jv.size()]; for (int i = 0; i < v.length; i++) { v[i] = (String) jv.elementAt(i); } jv.removeAllElements(); if (debug) { System.err.println("Array from '" + separator + "' separated List:\n" + v.length); for (int i = 0; i < v.length; i++) { System.err.println("item " + i + " '" + v[i] + "'"); } } return v; } if (debug) { System.err.println("Empty Array from '" + separator + "' separated List"); } return null; } /** * concatenate the list with separator * * @param list * @return concatenated string */ public String arrayToSeparatorList(String[] list) { StringBuffer v = new StringBuffer(); if (list != null) { for (int i = 0, iSize = list.length - 1; i < iSize; i++) { if (list[i] != null) { v.append(list[i]); } v.append(separator); } if (list[list.length - 1] != null) { v.append(list[list.length - 1]); } if (debug) { System.err.println("Returning '" + separator + "' separated List:\n"); System.err.println(v); } return v.toString(); } if (debug) { System.err.println("Returning empty '" + separator + "' separated List\n"); } return ""; } /** * @return * @see jalview.appletgui.AlignFrame#getFeatureGroups() */ public String getFeatureGroups() { String lst = arrayToSeparatorList(getDefaultTargetFrame() .getFeatureGroups()); return lst; } /** * @param alf * alignframe to get feature groups on * @return * @see jalview.appletgui.AlignFrame#getFeatureGroups() */ public String getFeatureGroupsOn(AlignFrame alf) { String lst = arrayToSeparatorList(alf.getFeatureGroups()); return lst; } /** * @param visible * @return * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean) */ public String getFeatureGroupsOfState(boolean visible) { return arrayToSeparatorList(getDefaultTargetFrame() .getFeatureGroupsOfState(visible)); } /** * @param alf * align frame to get groups of state visible * @param visible * @return * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean) */ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) { return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible)); } /** * @param groups * tab separated list of group names * @param state * true or false * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], * boolean) */ public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state) { boolean st = state;// !(state==null || state.equals("") || // state.toLowerCase().equals("false")); alf.setFeatureGroupState(separatorListToArray(groups), st); } public void setFeatureGroupState(String groups, boolean state) { setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state); } /** * List separator string * * @return the separator */ public String getSeparator() { return separator; } /** * List separator string * * @param separator * the separator to set */ public void setSeparator(String separator) { this.separator = separator; } }