X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=dfd092491d058527ca31061c3030c908d2d06825;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=bfd6d70eb6611f36b896e8833210241e54b3058a;hpb=87185978c81d7d07f683f0c1a1bac5f080e88192;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index bfd6d70..dfd0924 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,30 +1,57 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview 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 3 * 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. - * + * + * Jalview 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; -import java.io.IOException; -import java.util.*; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.io.BioJsHTMLOutput; +import jalview.io.HtmlSvgOutput; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; -import javax.swing.*; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +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.MalformedURLException; +import java.net.URI; +import java.net.URL; +import java.net.URLDecoder; +import java.security.AllPermission; +import java.security.CodeSource; +import java.security.PermissionCollection; +import java.security.Permissions; +import java.security.Policy; +import java.util.HashMap; +import java.util.Map; +import java.util.Vector; -import jalview.gui.*; -import jalview.io.AppletFormatAdapter; +import javax.swing.UIManager; +import javax.swing.UnsupportedLookAndFeelException; /** * Main class for Jalview Application
@@ -36,12 +63,29 @@ import jalview.io.AppletFormatAdapter; */ public class Jalview { + static + { + // grab all the rights we can the JVM + Policy.setPolicy(new Policy() + { + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + public void refresh() + { + } + }); + } /** * main class for Jalview application * * @param args - * open filename + * open filename */ public static void main(String[] args) { @@ -56,45 +100,64 @@ public class Jalview 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." - + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + showUsage(); System.exit(0); } + if (aparser.contains("nodisplay") || aparser.contains("nogui") + || aparser.contains("headless")) + { + System.setProperty("java.awt.headless", "true"); + headless = true; + } + String usrPropsFile = aparser.getValue("props"); + Cache.loadProperties(usrPropsFile); // must do this before + if (usrPropsFile != null) + { + System.out.println("CMD [-props " + usrPropsFile + + "] executed successfully!"); + } - Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! - if (aparser.contains("nodisplay")) + final String jabawsUrl = aparser.getValue("jabaws"); + if (jabawsUrl != null) { - System.setProperty("java.awt.headless", "true"); + try + { + Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + System.out.println("CMD [-jabaws " + jabawsUrl + + "] executed successfully!"); + } catch (MalformedURLException e) + { + System.err.println("Invalid jabaws parameter: " + jabawsUrl + + " ignored"); + } + } + + String defs = aparser.getValue("setprop"); + while (defs != null) + { + int p = defs.indexOf('='); + if (p == -1) + { + System.err.println("Ignoring invalid setprop argument : " + defs); + } + else + { + System.out.println("Executing setprop argument: " + defs); + // DISABLED FOR SECURITY REASONS + // TODO: add a property to allow properties to be overriden by cli args + // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + } + defs = aparser.getValue("setprop"); } if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { headless = true; } - + System.setProperty("http.agent", + "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); try { Cache.initLogger(); @@ -111,22 +174,41 @@ public class Jalview 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" - - ); + UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception ex) { } + if (new Platform().isAMac()) + { + System.setProperty("com.apple.mrj.application.apple.menu.about.name", + "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); + try + { + UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel()); + } catch (UnsupportedLookAndFeelException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + if (!headless) { desktop = new Desktop(); + desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); - desktop.discoverer.start(); + desktop.startServiceDiscovery(); + if (!aparser.contains("nousagestats")) + { + startUsageStats(desktop); + } + else + { + System.err.println("CMD [-nousagestats] executed successfully!"); + } + if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); @@ -136,6 +218,8 @@ public class Jalview // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); } else { @@ -154,23 +238,130 @@ public class Jalview } } } + else + { + System.err.println("CMD [-noquestionnaire] executed successfully!"); + } + desktop.checkForNews(); + } + + if (!isHeadlessMode()) + { + BioJsHTMLOutput.updateBioJS(); } 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 + jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless); + Vector getFeatures = null; // vector of das source nicknames to fetch + // features from // loading is done. - file = aparser.getValue("open"); + 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", true); + file = aparser.getValue("open", true); if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } + String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser + .getValue("vsess"); + if (vamsasImport != null || vamsasSession != null) + { + if (desktop == null || headless) + { + System.out + .println("Headless vamsas sessions not yet supported. Sorry."); + System.exit(1); + } + // if we have a file, start a new session and import it. + boolean inSession = false; + if (vamsasImport != null) + { + try + { + String viprotocol = jalview.io.AppletFormatAdapter + .checkProtocol(vamsasImport); + if (viprotocol == jalview.io.FormatAdapter.FILE) + { + inSession = desktop.vamsasImport(new File(vamsasImport)); + } + else if (viprotocol == jalview.io.FormatAdapter.URL) + { + inSession = desktop.vamsasImport(new URL(vamsasImport)); + } + } catch (Exception e) + { + System.err.println("Exeption when importing " + vamsasImport + + " as a vamsas document."); + e.printStackTrace(); + } + if (!inSession) + { + System.err.println("Failed to import " + vamsasImport + + " as a vamsas document."); + } + else + { + System.out.println("Imported Successfully into new session " + + desktop.getVamsasApplication().getCurrentSession()); + } + } + if (vamsasSession != null) + { + if (vamsasImport != null) + { + // close the newly imported session and import the Jalview specific + // remnants into the new session later on. + desktop.vamsasStop_actionPerformed(null); + } + // now join the new session + try + { + if (desktop.joinVamsasSession(vamsasSession)) + { + System.out.println("Successfully joined vamsas session " + + vamsasSession); + } + else + { + System.err.println("WARNING: Failed to join vamsas session " + + vamsasSession); + } + } catch (Exception e) + { + System.err.println("ERROR: Failed to join vamsas session " + + vamsasSession); + e.printStackTrace(); + } + if (vamsasImport != null) + { + // the Jalview specific remnants can now be imported into the new + // session at the user's leisure. + Cache.log + .info("Skipping Push for import of data into existing vamsas session."); // TODO: + // enable + // this + // when + // debugged + // desktop.getVamsasApplication().push_update(); + } + } + } + long progress = -1; + // Finally, deal with the remaining input data. if (file != null) { - System.out.println("Opening file: " + file); + if (!headless) + { + desktop.setProgressBar(MessageManager + .getString("status.processing_commandline_args"), + progress = System.currentTimeMillis()); + } + System.out.println("CMD [-open " + file + "] executed successfully!"); if (!file.startsWith("http://")) { @@ -184,147 +375,244 @@ public class Jalview } } - protocol = checkProtocol(file); + protocol = jalview.io.AppletFormatAdapter.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) + else { - data.replaceAll("%20", " "); - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); - - if (cs == null) + data = aparser.getValue("colour", true); + if (data != null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(data); - cs = ucs; - } - - System.out.println("colour is " + data); - af.changeColour(cs); - } + data.replaceAll("%20", " "); - // 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); - } + jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty + .getColour(af.getViewport().getAlignment(), 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) + if (cs == null) { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( + "white"); + ucs.parseAppletParameter(data); + cs = ucs; } - } catch (IOException ex) + else + { + System.out.println("CMD [-color " + data + + "] executed successfully!"); + } + af.changeColour(cs); + } + + // Must maintain ability to use the groups flag + data = aparser.getValue("groups", true); + if (data != null) { - System.err.println("Couldn't add tree " + data); - ex.printStackTrace(System.err); + af.parseFeaturesFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println("CMD groups[-" + data + + "] executed successfully!"); } - } - getFeatures = checkDasArguments(aparser); - if (af != null && getFeatures!=null) - { - startFeatureFetching(getFeatures); - // need to block until fetching is complete. - while (af.operationInProgress()) + data = aparser.getValue("features", true); + if (data != null) + { + af.parseFeaturesFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println("CMD [-features " + data + + "] executed successfully!"); + } + + data = aparser.getValue("annotations", true); + if (data != null) { - // wait around until fetching is finished. - try { - Thread.sleep(10); - } catch (Exception e) + af.loadJalviewDataFile(data, null, null, null); + // System.out.println("Added " + data); + System.out.println("CMD [-annotations " + data + + "] executed successfully!"); + } + // set or clear the sortbytree flag. + if (aparser.contains("sortbytree")) + { + af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) { - + System.out.println("CMD [-sortbytree] executed successfully!"); } } - } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - format = aparser.nextValue(); - file = aparser.nextValue(); - - if (format.equalsIgnoreCase("png")) + if (aparser.contains("no-annotation")) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + System.out.println("CMD no-annotation executed successfully!"); + } } - else if (format.equalsIgnoreCase("imgMap")) + if (aparser.contains("nosortbytree")) { - af.createImageMap(new java.io.File(file), imageName); - System.out.println("Creating image map: " + file); - continue; + af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } } - else if (format.equalsIgnoreCase("eps")) + data = aparser.getValue("tree", true); + if (data != null) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); - continue; + jalview.io.NewickFile fin = null; + try + { + System.out.println("CMD [-tree " + data + + "] executed successfully!"); + fin = new jalview.io.NewickFile(data, + jalview.io.AppletFormatAdapter.checkProtocol(data)); + if (fin != null) + { + af.getViewport().setCurrentTree( + af.ShowNewickTree(fin, data).getTree()); + } + } catch (IOException ex) + { + System.err.println("Couldn't add tree " + data); + ex.printStackTrace(System.err); + } } + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) - if (af.saveAlignment(file, format)) + getFeatures = checkDasArguments(aparser); + if (af != null && getFeatures != null) { - System.out.println("Written alignment in " + format - + " format to " + file); + FeatureFetcher ff = startFeatureFetching(getFeatures); + if (ff != null) + { + while (!ff.allFinished() || af.operationInProgress()) + { + // wait around until fetching is finished. + try + { + Thread.sleep(100); + } catch (Exception e) + { + + } + } + } + getFeatures = null; // have retrieved features - forget them now. } - else + if (groovyscript != null) { - System.out.println("Error writing file " + file + " in " + format - + " format!!"); + // 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, new Object[] { desktop, af }); + + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + } + 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("svg")) + { + File imageFile = new java.io.File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG image: " + file); + continue; + } + else if (format.equalsIgnoreCase("html")) + { + File imageFile = new java.io.File(file); + imageName = imageFile.getName(); + new HtmlSvgOutput(new java.io.File(file), af.alignPanel); + System.out.println("Creating HTML 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")) + { + File outputFile = new java.io.File(file); + System.out.println("Creating EPS file: " + + outputFile.getAbsolutePath()); + af.createEPS(outputFile); + continue; + } - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); + 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 + + if (!headless && file == null && vamsasImport == 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"); + file = jalview.bin.Cache.getDefault( + "STARTUP_FILE", + jalview.bin.Cache.getDefault("www.jalview.org", + "http://www.jalview.org") + + "/examples/exampleFile_2_7.jar"); + if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")) + { + // hardwire upgrade of the startup file + file.replace("_2_3.jar", "_2_7.jar"); + // and remove the stale setting + jalview.bin.Cache.removeProperty("STARTUP_FILE"); + } protocol = "File"; @@ -345,67 +633,362 @@ public class Jalview 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 the user has specified features to be retrieved, + // or a groovy script to be executed, do them if they + // haven't been done already + // fetch features for the default alignment + if (getFeatures != null) { - if (startUpAlframe!=null) + if (startUpAlframe != null) { startFeatureFetching(getFeatures); } } + // Once all other stuff is done, execute any groovy scripts (in order) + if (groovyscript != null) + { + if (jalview.bin.Cache.groovyJarsPresent()) + { + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, new Object[] { desktop, + startUpAlframe }); + } + else + { + System.err + .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); + } + } + // and finally, turn off batch mode indicator - if the desktop still exists + if (desktop != null) + { + if (progress != -1) + { + desktop.setProgressBar(null, progress); + } + desktop.setInBatchMode(false); + } + } + + private static void showUsage() + { + 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" + + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\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" + + "-json FILE\tCreate alignment file FILE in JSON format.\n" + + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" + + "-png FILE\tCreate PNG image FILE from alignment.\n" + + "-svg FILE\tCreate SVG image FILE from alignment.\n" + + "-html FILE\tCreate HTML 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.\n" + + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" + + "-noquestionnaire\tTurn off questionnaire check.\n" + + "-nousagestats\tTurn off google analytics tracking for this session.\n" + + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" + // + + // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" + + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" + + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" + + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" + + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" + + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" + // + + // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" + // + "-vses vamsas-session\tJoin session with given URN\n" + + "-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"); + } + + private static void startUsageStats(final Desktop desktop) + { + /** + * start a User Config prompt asking if we can log usage statistics. + */ + jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig( + desktop.desktop, + "USAGESTATS", + "Jalview Usage Statistics", + "Do you want to help make Jalview better by enabling " + + "the collection of usage statistics with Google Analytics ?" + + "\n\n(you can enable or disable usage tracking in the preferences)", + new Runnable() + { + public void run() + { + Cache.log + .debug("Initialising googletracker for usage stats."); + Cache.initGoogleTracker(); + Cache.log.debug("Tracking enabled."); + } + }, new Runnable() + { + public void run() + { + Cache.log.debug("Not enabling Google Tracking."); + } + }, null, true); + desktop.addDialogThread(prompter); + } + + /** + * 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."); + } + /** + * for scripts contained in files + */ + File tfile = null; + /** + * script's URI + */ + URL sfile = null; + if (groovyscript.trim().equals("STDIN")) + { + // read from stdin into a tempfile and execute it + try + { + tfile = File.createTempFile("jalview", "groovy"); + PrintWriter outfile = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(tfile))); + 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 " + + ((tfile == null) ? "(tempfile wasn't created)" : tfile + .toString())); + ex.printStackTrace(); + return; + } + try + { + sfile = tfile.toURI().toURL(); + } catch (Exception x) + { + System.err + .println("Unexpected Malformed URL Exception for temporary file created from STDIN: " + + tfile.toURI()); + x.printStackTrace(); + return; + } + } + else + { + try + { + sfile = new URI(groovyscript).toURL(); + } catch (Exception x) + { + tfile = new File(groovyscript); + if (!tfile.exists()) + { + System.err.println("File '" + groovyscript + "' does not exist."); + return; + } + if (!tfile.canRead()) + { + System.err.println("File '" + groovyscript + "' cannot be read."); + return; + } + if (tfile.length() < 1) + { + System.err.println("File '" + groovyscript + "' is empty."); + return; + } + try + { + sfile = tfile.getAbsoluteFile().toURI().toURL(); + } catch (Exception ex) + { + System.err.println("Failed to create a file URL for " + + tfile.getAbsoluteFile()); + 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); + */ + Class[] bspec; + Object[] binding; + int blen = ((jalviewContext[0] == null) ? 0 : 1) + + ((jalviewContext[1] == null) ? 0 : 1); + String cnames[] = new String[] { "Jalview", "currentAlFrame" }; + bspec = new Class[blen * 2]; + binding = new Object[blen * 2]; + blen = 0; + ClassLoader cl = null; + Map vbinding = new HashMap(); + for (int jc = 0; jc < jalviewContext.length; jc++) + { + if (jalviewContext[jc] != null) + { + if (cl == null) + { + cl = jalviewContext[jc].getClass().getClassLoader(); + } + bspec[blen * 2] = String.class; + bspec[blen * 2 + 1] = Object.class; + binding[blen * 2] = cnames[jc]; + binding[blen * 2 + 1] = jalviewContext[jc]; + vbinding.put(cnames[jc], jalviewContext[jc]); + blen++; + } + } + Class gbindingc = cl.loadClass("groovy.lang.Binding"); + Constructor gbcons; + Object gbinding; + try + { + gbcons = gbindingc.getConstructor(Map.class); + gbinding = gbcons.newInstance(vbinding); + } catch (NoSuchMethodException x) + { + // old style binding config - using series of string/object values to + // setVariable. + gbcons = gbindingc.getConstructor(); + gbinding = gbcons.newInstance(); + java.lang.reflect.Method setvar = gbindingc.getMethod( + "setVariable", bspec); + setvar.invoke(gbinding, binding); + } + + 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 } }); // .toString() + // } }); + java.lang.reflect.Method run = gsec.getMethod("run", new Class[] { + String.class, gbindingc }); + run.invoke(gse, new Object[] { sfile.toString(), 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 + tfile.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; + Vector source = null; String data; String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); - while ((data = aparser.getValue("dasserver"))!=null) + while ((data = aparser.getValue("dasserver", true)) != null) { String nickname = null; String url = null; + boolean seq = false, feat = true; int pos = data.indexOf('='); + // determine capabilities if (pos > 0) { nickname = data.substring(0, pos); } url = data.substring(pos + 1); - if (url != null && url.startsWith("http:")) + if (url != null + && (url.startsWith("http:") || url + .startsWith("sequence:http:"))) { if (nickname == null) { nickname = url; } - if (locsources==null) + if (locsources == null) { - locsources=""; - } else { - locsources+="\t"; + locsources = ""; } - locsources=locsources+nickname+"|"+url; + 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) + if (source == null) { source = new Vector(); } source.addElement(nickname); } + System.out.println("CMD [-dasserver " + data + + "] executed successfully!"); } // loop until no more server entries are found. - if (locsources!=null && locsources.indexOf('|')>-1) + if (locsources != null && locsources.indexOf('|') > -1) { - Cache.log.debug("Setting local source list in properties file to:\n"+locsources); + 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) + while ((data = aparser.getValue("fetchfrom", true)) != null) { - System.out.println("adding source '"+data+"'"); - if (source==null) + System.out.println("adding source '" + data + "'"); + if (source == null) { source = new Vector(); } @@ -413,51 +996,65 @@ public class Jalview } return source; } + /** * start a feature fetcher for every alignment frame + * * @param dasSources */ - private static void startFeatureFetching(final Vector dasSources) + private static FeatureFetcher startFeatureFetching(final Vector dasSources) { - AlignFrame afs[] = Desktop.getAlignframes(); - if (afs==null || afs.length==0) + FeatureFetcher ff = new FeatureFetcher(); + AlignFrame afs[] = Desktop.getAlignFrames(); + if (afs == null || afs.length == 0) { - return; + return null; } - for (int i = 0; i -1 || file.indexOf("file:") > -1) + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) { - protocol = jalview.io.FormatAdapter.URL; + return true; } - return protocol; + return false; } } /** * 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). + * 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 rnabuttonlistener implements ActionListener +{ + public void actionPerformed(ActionEvent arg0) + { + System.out.println("Good idea ! "); + + } +} + +class pbuttonlistener implements ActionListener +{ + public void actionPerformed(ActionEvent arg0) + { + + } +} + class ArgsParser { Vector vargs = null; @@ -475,25 +1072,45 @@ class ArgsParser 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) { + return getValue(arg, false); + } + + public String getValue(String arg, boolean utf8decode) + { int index = vargs.indexOf(arg); - String ret = null; + String dc = null, ret = null; if (index != -1) { ret = vargs.elementAt(index + 1).toString(); vargs.removeElementAt(index); vargs.removeElementAt(index); + if (utf8decode && ret != null) + { + try + { + dc = URLDecoder.decode(ret, "UTF-8"); + ret = dc; + } catch (Exception e) + { + // TODO: log failure to decode + } + } } return ret; } + /** * check for and remove first occurence of arg in arglist. + * * @param arg * @return true if arg was present in argslist. */ @@ -521,3 +1138,61 @@ class ArgsParser } } + +/** + * keep track of feature fetching tasks. + * + * @author JimP + * + */ +class FeatureFetcher +{ + /* + * TODO: generalise to track all jalview events to orchestrate batch + * processing events. + */ + + private int queued = 0; + + private int running = 0; + + public FeatureFetcher() + { + + } + + public void addFetcher(final AlignFrame af, final Vector dasSources) + { + final long id = System.currentTimeMillis(); + queued++; + final FeatureFetcher us = this; + new Thread(new Runnable() + { + + public void run() + { + synchronized (us) + { + queued--; + running++; + } + + af.setProgressBar(MessageManager + .getString("status.das_features_being_retrived"), id); + af.featureSettings_actionPerformed(null); + af.featureSettings.fetchDasFeatures(dasSources, true); + af.setProgressBar(null, id); + synchronized (us) + { + running--; + } + } + }).start(); + } + + public synchronized boolean allFinished() + { + return queued == 0 && running == 0; + } + +}