X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=2b935ed9590fdd1c9e19724337a8d1b3864c0e3b;hb=af1471fa3d7d3cb32d203e81d394838608dd1c96;hp=4f383a0b22dea2bac633d13893306cd04086526e;hpb=30bc1314d4206cafea412dcd9decdea7e318481f;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 4f383a0..2b935ed 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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. + * + * 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 +79,12 @@ 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 +95,7 @@ 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" @@ -80,19 +109,43 @@ public class Jalview + "-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"); + + "-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\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); } - Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! - + 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 (aparser.contains("nodisplay")) { System.setProperty("java.awt.headless", "true"); @@ -119,22 +172,21 @@ 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"); @@ -166,19 +218,105 @@ 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 + 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 + 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"); + 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(); + } + } + } + // Finally, deal with the remaining input data. if (file != null) { System.out.println("Opening file: " + file); @@ -195,20 +333,19 @@ 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"); + data = aparser.getValue("colour", true); if (data != null) { data.replaceAll("%20", " "); @@ -229,32 +366,41 @@ 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)); + af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); System.out.println("Added " + data); } - data = aparser.getValue("features"); + data = aparser.getValue("features", true); if (data != null) { - af.parseFeaturesFile(data, checkProtocol(data)); + af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); System.out.println("Added " + data); } - data = aparser.getValue("annotations"); + data = aparser.getValue("annotations", true); if (data != null) { - af.loadJalviewDataFile(data); + af.loadJalviewDataFile(data, null, null, null); System.out.println("Added " + data); } - data = aparser.getValue("tree"); + // set or clear the sortbytree flag. + if (aparser.contains("sortbytree")) + { + af.getViewport().setSortByTree(true); + } + if (aparser.contains("nosortbytree")) + { + af.getViewport().setSortByTree(false); + } + data = aparser.getValue("tree", true); if (data != null) { jalview.io.NewickFile fin = null; try { - fin = new jalview.io.NewickFile(data, checkProtocol(data)); + fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); if (fin != null) { af.getViewport().setCurrentTree( @@ -267,32 +413,42 @@ 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) + 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) + 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. } - if (groovyscript!=null) + if (groovyscript != null) { - // Execute the groovy script after we've done all the rendering stuff + // 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); + 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); + } + else + { + System.err + .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); } groovyscript = null; } @@ -344,7 +500,7 @@ 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", @@ -371,170 +527,243 @@ public class Jalview 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); } } - if (groovyscript!=null) + // 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); + 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); } + 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) + { + 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 - * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object. + * + * @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) + private static void executeGroovyScript(String groovyscript, + Object jalviewContext) { - if (jalviewContext==null) + if (jalviewContext == null) { - System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); + 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 { + 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) + 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"); + 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())); + System.err.println("Failed to read from STDIN into tempfile " + + ((sfile == null) ? "(tempfile wasn't created)" : sfile + .toString())); ex.printStackTrace(); return; } - } else { + } + else + { sfile = new File(groovyscript); } if (!sfile.exists()) { - System.err.println("File '"+groovyscript+"' does not exist."); + System.err.println("File '" + groovyscript + "' does not exist."); return; } if (!sfile.canRead()) { - System.err.println("File '"+groovyscript+"' cannot be read."); + System.err.println("File '" + groovyscript + "' cannot be read."); return; } - if (sfile.length()<1) + if (sfile.length() < 1) { - System.err.println("File '"+groovyscript+"' is empty."); + 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; + 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."); + 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 + // 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; + 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); } } // 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(); } @@ -542,50 +771,36 @@ 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) { + FeatureFetcher ff = new FeatureFetcher(); AlignFrame afs[] = Desktop.getAlignframes(); - if (afs==null || afs.length==0) + if (afs == null || afs.length == 0) { - return; - } - for (int i = 0; i -1 || file.indexOf("file:") > -1) + for (int i = 0; i < afs.length; i++) { - protocol = jalview.io.FormatAdapter.URL; + ff.addFetcher(afs[i], dasSources); } - return protocol; + return ff; } } /** * 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 ArgsParser { @@ -604,25 +819,45 @@ 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. */ @@ -650,3 +885,59 @@ 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; + } +};