X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=6a59093047939cc74d559162723d223133918ca2;hb=c13784724ba3826e6cc3faeb85571cf30776592d;hp=7e70bf4f94c554db9cbb9be321871bd8277e48f8;hpb=86938ab0eb804fd939b0c0ec08f464fba8d5b7f3;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 7e70bf4..6a59093 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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 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. * - * 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 + * 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 Jalview. If not, see . */ package jalview.bin; @@ -26,12 +25,18 @@ import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; 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.*; import javax.swing.*; import jalview.gui.*; -import jalview.io.AppletFormatAdapter; +import jalview.util.Platform; /** * Main class for Jalview Application
@@ -43,12 +48,29 @@ 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) { @@ -57,6 +79,11 @@ public class Jalview System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); + if (new Platform().isAMac()) + { + System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); + } ArgsParser aparser = new ArgsParser(args); boolean headless = false; @@ -67,6 +94,7 @@ public class Jalview .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" @@ -83,12 +111,17 @@ public class Jalview + "-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)" - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n" - +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" - +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\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)" + + "-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"); System.exit(0); @@ -96,16 +129,19 @@ public class Jalview Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! String defs = aparser.getValue("setprop"); - while (defs!=null) + while (defs != null) { int p = defs.indexOf('='); - if ( p==-1 ) + if (p == -1) + { + System.err.println("Ignoring invalid setprop argument : " + defs); + } + else { - System.err.println("Ignoring invalid setprop argument : "+defs); - } else { - System.out.println("Executing setprop argument: "+defs); + System.out.println("Executing setprop argument: " + defs); // DISABLED FOR SECURITY REASONS - // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + // 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"); } @@ -135,23 +171,21 @@ 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 (!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); + } if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); @@ -184,20 +218,104 @@ public class Jalview 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 + // features from // loading is done. String groovyscript = null; // script to execute after all loading is - // completed one way or another + // completed one way or another // extract groovy argument and execute if necessary - groovyscript = aparser.getValue("groovy"); - file = aparser.getValue("open"); + 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.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(); + } + } + } + // Finally, deal with the remaining input data. if (file != null) { System.out.println("Opening file: " + file); @@ -220,14 +338,13 @@ public class Jalview AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); - if (af == null) { System.out.println("error"); return; } - data = aparser.getValue("colour"); + data = aparser.getValue("colour", true); if (data != null) { data.replaceAll("%20", " "); @@ -248,20 +365,20 @@ public class Jalview } // Must maintain ability to use the groups flag - data = aparser.getValue("groups"); + data = aparser.getValue("groups", true); if (data != null) { af.parseFeaturesFile(data, checkProtocol(data)); System.out.println("Added " + data); } - data = aparser.getValue("features"); + data = aparser.getValue("features", true); if (data != null) { af.parseFeaturesFile(data, checkProtocol(data)); System.out.println("Added " + data); } - data = aparser.getValue("annotations"); + data = aparser.getValue("annotations", true); if (data != null) { af.loadJalviewDataFile(data); @@ -276,7 +393,7 @@ public class Jalview { af.getViewport().setSortByTree(false); } - data = aparser.getValue("tree"); + data = aparser.getValue("tree", true); if (data != null) { jalview.io.NewickFile fin = null; @@ -295,22 +412,27 @@ public class Jalview ex.printStackTrace(System.err); } } + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) + 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 + FeatureFetcher ff = startFeatureFetching(getFeatures); + if (ff != null) + while (!ff.allFinished() || af.operationInProgress()) { - Thread.sleep(10); - } catch (Exception e) - { - + // wait around until fetching is finished. + try + { + Thread.sleep(100); + } catch (Exception e) + { + + } } - } + getFeatures = null; // have retrieved features - forget them now. } if (groovyscript != null) { @@ -377,7 +499,7 @@ public class Jalview // 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", @@ -404,7 +526,10 @@ public class Jalview getFeatures = checkDasArguments(aparser); // extract groovy arguments before anything else. } - // Once all loading is done. Retrieve features. + // 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) @@ -412,6 +537,7 @@ public class Jalview startFeatureFetching(getFeatures); } } + // Once all other stuff is done, execute any groovy scripts (in order) if (groovyscript != null) { if (jalview.bin.Cache.groovyJarsPresent()) @@ -426,18 +552,52 @@ public class Jalview + groovyscript); } } + // and finally, turn off batch mode indicator - if the desktop still exists + if (desktop!=null) + { + desktop.setInBatchMode(false); + } + } - // Once all other stuff is done, execute any groovy scripts (in order) + 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 + .info("Initialising googletracker for usage stats."); + Cache.initGoogleTracker(); + Cache.log.debug("Tracking enabled."); + } + }, new Runnable() + { + public void run() + { + Cache.log.info("Not enabling Google Tracking."); + } + }, null, true); + SwingUtilities.invokeLater(prompter); } /** * Locate the given string as a file and pass it to the groovy interpreter. * * @param groovyscript - * the script to execute + * the script to execute * @param jalviewContext - * the Jalview Desktop object passed in to the groovy binding - * as the 'Jalview' object. + * the Jalview Desktop object passed in to the groovy binding as the + * 'Jalview' object. */ private static void executeGroovyScript(String groovyscript, Object jalviewContext) @@ -505,8 +665,8 @@ public class Jalview * 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"); + * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding + * = new Binding(); binding.setVariable("input", "world"); * gse.run("hello.groovy", binding); */ ClassLoader cl = jalviewContext.getClass().getClassLoader(); @@ -554,11 +714,11 @@ public class Jalview 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; + boolean seq = false, feat = true; int pos = data.indexOf('='); // determine capabilities if (pos > 0) @@ -566,7 +726,9 @@ public class Jalview nickname = data.substring(0, pos); } url = data.substring(pos + 1); - if (url != null && (url.startsWith("http:") || url.startsWith("sequence:http:"))) + if (url != null + && (url.startsWith("http:") || url + .startsWith("sequence:http:"))) { if (nickname == null) { @@ -597,7 +759,7 @@ public class Jalview + 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) @@ -614,26 +776,19 @@ public class Jalview * * @param dasSources */ - private static void startFeatureFetching(final Vector dasSources) + private static FeatureFetcher startFeatureFetching(final Vector dasSources) { + FeatureFetcher ff = new FeatureFetcher(); AlignFrame afs[] = Desktop.getAlignframes(); if (afs == null || afs.length == 0) { - return; + return null; } 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); - } - }); + ff.addFetcher(afs[i], dasSources); } + return ff; } private static String checkProtocol(String file) @@ -683,13 +838,29 @@ class ArgsParser */ 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; } @@ -724,3 +895,59 @@ 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("DAS features being retrieved...", 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; + } +};