/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) * Copyright (C) 2008 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.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; import java.net.URL; import java.util.*; import javax.swing.*; import jalview.gui.*; import jalview.io.AppletFormatAdapter; /** * Main class for Jalview Application
*
* start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview * * @author $author$ * @version $Revision$ */ public class Jalview { /** * main class for Jalview application * * @param args * open filename */ public static void main(String[] args) { System.out.println("Java version: " + System.getProperty("java.version")); System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); ArgsParser aparser = new ArgsParser(args); boolean headless = false; if (aparser.contains("help") || aparser.contains("h")) { System.out .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" + "-nodisplay\tRun Jalview without User Interface.\n" + "-props FILE\tUse the given Jalview properties file instead of users default.\n" + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" + "-tree FILE\tLoad the given newick format tree file onto the alignment\n" + "-features FILE\tUse the given file to mark features on the alignment.\n" + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n" + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n" + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n" + "-msf FILE\tCreate alignment file FILE in MSF format.\n" + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" + "-pir FILE\tCreate alignment file FILE in PIR format.\n" + "-blc FILE\tCreate alignment file FILE in BLC format.\n" + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" + "-png FILE\tCreate PNG image FILE from alignment.\n" + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n" + "-eps FILE\tCreate EPS file FILE from alignment." + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires." + "-noquestionnaire\tTurn off questionnaire check." + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments." + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them." + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)" + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); System.exit(0); } Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! if (aparser.contains("nodisplay")) { System.setProperty("java.awt.headless", "true"); } if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { headless = true; } try { Cache.initLogger(); } catch (java.lang.NoClassDefFoundError error) { error.printStackTrace(); System.out .println("\nEssential logging libraries not found." + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview"); System.exit(0); } Desktop desktop = null; try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName() // UIManager.getCrossPlatformLookAndFeelClassName() // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel" // "javax.swing.plaf.metal.MetalLookAndFeel" // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel" // "com.sun.java.swing.plaf.motif.MotifLookAndFeel" ); } catch (Exception ex) { } if (!headless) { desktop = new Desktop(); desktop.setVisible(true); desktop.discoverer.start(); if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); if (url != null) { // Start the desktop questionnaire prompter with the specified // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); } else { if (Cache.getProperty("NOQUESTIONNAIRES") == null) { // Start the desktop questionnaire prompter with the specified // questionnaire // String defurl = // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // // String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; Cache.log.debug("Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); } } } } String file = null, protocol = null, format = null, data = null; jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); Vector getFeatures = null; // vector of das source nicknames to fetch // features from // loading is done. String groovyscript = null; // script to execute after all loading is // completed one way or another // extract groovy argument and execute if necessary groovyscript = aparser.getValue("groovy"); file = aparser.getValue("open"); if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } if (file != null) { System.out.println("Opening file: " + file); if (!file.startsWith("http://")) { if (!(new java.io.File(file)).exists()) { System.out.println("Can't find " + file); if (headless) { System.exit(1); } } } protocol = checkProtocol(file); format = new jalview.io.IdentifyFile().Identify(file, protocol); AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); if (af == null) { System.out.println("error"); return; } data = aparser.getValue("colour"); if (data != null) { data.replaceAll("%20", " "); jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty .getColour(af.getViewport().getAlignment(), data); if (cs == null) { jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( "white"); ucs.parseAppletParameter(data); cs = ucs; } System.out.println("colour is " + data); af.changeColour(cs); } // Must maintain ability to use the groups flag data = aparser.getValue("groups"); if (data != null) { af.parseFeaturesFile(data, checkProtocol(data)); System.out.println("Added " + data); } data = aparser.getValue("features"); if (data != null) { af.parseFeaturesFile(data, checkProtocol(data)); System.out.println("Added " + data); } data = aparser.getValue("annotations"); if (data != null) { af.loadJalviewDataFile(data); System.out.println("Added " + data); } data = aparser.getValue("tree"); if (data != null) { jalview.io.NewickFile fin = null; try { fin = new jalview.io.NewickFile(data, checkProtocol(data)); if (fin != null) { af.getViewport().setCurrentTree( af.ShowNewickTree(fin, data).getTree()); System.out.println("Added tree " + data); } } catch (IOException ex) { System.err.println("Couldn't add tree " + data); ex.printStackTrace(System.err); } } getFeatures = checkDasArguments(aparser); if (af != null && getFeatures != null) { startFeatureFetching(getFeatures); // need to block until fetching is complete. while (af.operationInProgress()) { // wait around until fetching is finished. try { Thread.sleep(10); } catch (Exception e) { } } } if (groovyscript != null) { // Execute the groovy script after we've done all the rendering stuff // and before any images or figures are generated. if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, desktop); } else { System.err .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + groovyscript); } groovyscript = null; } String imageName = "unnamed.png"; while (aparser.getSize() > 1) { format = aparser.nextValue(); file = aparser.nextValue(); if (format.equalsIgnoreCase("png")) { af.createPNG(new java.io.File(file)); imageName = (new java.io.File(file)).getName(); System.out.println("Creating PNG image: " + file); continue; } else if (format.equalsIgnoreCase("imgMap")) { af.createImageMap(new java.io.File(file), imageName); System.out.println("Creating image map: " + file); continue; } else if (format.equalsIgnoreCase("eps")) { System.out.println("Creating EPS file: " + file); af.createEPS(new java.io.File(file)); continue; } if (af.saveAlignment(file, format)) { System.out.println("Written alignment in " + format + " format to " + file); } else { System.out.println("Error writing file " + file + " in " + format + " format!!"); } } while (aparser.getSize() > 0) { System.out.println("Unknown arg: " + aparser.nextValue()); } } AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user // //////////////////// if (!headless && file == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault("STARTUP_FILE", "http://www.jalview.org/examples/exampleFile_2_3.jar"); protocol = "File"; if (file.indexOf("http:") > -1) { protocol = "URL"; } if (file.endsWith(".jar")) { format = "Jalview"; } else { format = new jalview.io.IdentifyFile().Identify(file, protocol); } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); getFeatures = checkDasArguments(aparser); // extract groovy arguments before anything else. } // Once all loading is done. Retrieve features. if (getFeatures != null) { if (startUpAlframe != null) { startFeatureFetching(getFeatures); } } if (groovyscript != null) { if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, desktop); } else { System.err .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + groovyscript); } } // Once all other stuff is done, execute any groovy scripts (in order) } /** * Locate the given string as a file and pass it to the groovy interpreter. * * @param groovyscript * the script to execute * @param jalviewContext * the Jalview Desktop object passed in to the groovy binding * as the 'Jalview' object. */ private static void executeGroovyScript(String groovyscript, Object jalviewContext) { if (jalviewContext == null) { System.err .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); } File sfile = null; if (groovyscript.trim().equals("STDIN")) { // read from stdin into a tempfile and execute it try { sfile = File.createTempFile("jalview", "groovy"); PrintWriter outfile = new PrintWriter(new OutputStreamWriter( new FileOutputStream(sfile))); BufferedReader br = new BufferedReader( new java.io.InputStreamReader(System.in)); String line = null; while ((line = br.readLine()) != null) { outfile.write(line + "\n"); } br.close(); outfile.flush(); outfile.close(); } catch (Exception ex) { System.err.println("Failed to read from STDIN into tempfile " + ((sfile == null) ? "(tempfile wasn't created)" : sfile .toString())); ex.printStackTrace(); return; } } else { sfile = new File(groovyscript); } if (!sfile.exists()) { System.err.println("File '" + groovyscript + "' does not exist."); return; } if (!sfile.canRead()) { System.err.println("File '" + groovyscript + "' cannot be read."); return; } if (sfile.length() < 1) { System.err.println("File '" + groovyscript + "' is empty."); return; } boolean success = false; try { /* * The following code performs the GroovyScriptEngine invocation using * reflection, and is equivalent to this fragment from the embedding * groovy documentation on the groovy site: import * groovy.lang.Binding; import groovy.util.GroovyScriptEngine; * * String[] roots = new String[] { "/my/groovy/script/path" }; * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding = * new Binding(); binding.setVariable("input", "world"); * gse.run("hello.groovy", binding); */ ClassLoader cl = jalviewContext.getClass().getClassLoader(); Class gbindingc = cl.loadClass("groovy.lang.Binding"); Constructor gbcons = gbindingc.getConstructor(null); Object gbinding = gbcons.newInstance(null); java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class }); setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext }); Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class }); // String[].class }); Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } }); java.lang.reflect.Method run = gsec.getMethod("run", new Class[] { String.class, gbindingc }); run.invoke(gse, new Object[] { sfile.getName(), gbinding }); success = true; } catch (Exception e) { System.err.println("Exception Whilst trying to execute file " + sfile + " as a groovy script."); e.printStackTrace(System.err); } if (success && groovyscript.equals("STDIN")) { // delete temp file that we made - but only if it was successfully // executed sfile.delete(); } } /** * Check commandline for any das server definitions or any fetchfrom switches * * @return vector of DAS source nicknames to retrieve from */ private static Vector checkDasArguments(ArgsParser aparser) { Vector source = null; String data; String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); while ((data = aparser.getValue("dasserver")) != null) { String nickname = null; String url = null; int pos = data.indexOf('='); if (pos > 0) { nickname = data.substring(0, pos); } url = data.substring(pos + 1); if (url != null && url.startsWith("http:")) { if (nickname == null) { nickname = url; } if (locsources == null) { locsources = ""; } else { locsources += "\t"; } locsources = locsources + nickname + "|" + url; System.err .println("NOTE! dasserver parameter not yet really supported (got args of " + nickname + "|" + url); if (source == null) { source = new Vector(); } source.addElement(nickname); } } // loop until no more server entries are found. if (locsources != null && locsources.indexOf('|') > -1) { Cache.log.debug("Setting local source list in properties file to:\n" + locsources); Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources); } while ((data = aparser.getValue("fetchfrom")) != null) { System.out.println("adding source '" + data + "'"); if (source == null) { source = new Vector(); } source.addElement(data); } return source; } /** * start a feature fetcher for every alignment frame * * @param dasSources */ private static void startFeatureFetching(final Vector dasSources) { AlignFrame afs[] = Desktop.getAlignframes(); if (afs == null || afs.length == 0) { return; } for (int i = 0; i < afs.length; i++) { final AlignFrame af = afs[i]; SwingUtilities.invokeLater(new Runnable() { public void run() { af.featureSettings_actionPerformed(null); af.featureSettings.fetchDasFeatures(dasSources); } }); } } private static String checkProtocol(String file) { String protocol = jalview.io.FormatAdapter.FILE; if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) { protocol = jalview.io.FormatAdapter.URL; } return protocol; } } /** * Notes: this argParser does not distinguish between parameter switches, * parameter values and argument text. If an argument happens to be identical to * a parameter, it will be taken as such (even though it didn't have a '-' * prefixing it). * * @author Andrew Waterhouse and JBP documented. * */ class ArgsParser { Vector vargs = null; public ArgsParser(String[] args) { vargs = new Vector(); for (int i = 0; i < args.length; i++) { String arg = args[i].trim(); if (arg.charAt(0) == '-') { arg = arg.substring(1); } vargs.addElement(arg); } } /** * check for and remove first occurence of arg+parameter in arglist. * * @param arg * @return return the argument following the given arg if arg was in list. */ public String getValue(String arg) { int index = vargs.indexOf(arg); String ret = null; if (index != -1) { ret = vargs.elementAt(index + 1).toString(); vargs.removeElementAt(index); vargs.removeElementAt(index); } return ret; } /** * check for and remove first occurence of arg in arglist. * * @param arg * @return true if arg was present in argslist. */ public boolean contains(String arg) { if (vargs.contains(arg)) { vargs.removeElement(arg); return true; } else { return false; } } public String nextValue() { return vargs.remove(0).toString(); } public int getSize() { return vargs.size(); } }