X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ca2a5845fa306051b2c33f2980045444970d51b8;hb=6f812eb434553c97cccaaaefa35da54afc72bb79;hp=229c6c21b72186693913518278d77343a48692da;hpb=2d3d981f9d654c6804612c9058dc607a7b7fb0bc;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 229c6c2..ca2a584 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,27 +20,38 @@ */ package jalview.bin; +import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.PromptUserConfig; +import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileLoader; import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.NewickFile; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.jws2.Jws2Discoverer; -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.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; -import java.lang.reflect.Constructor; import java.net.MalformedURLException; import java.net.URI; +import java.net.URISyntaxException; import java.net.URL; -import java.net.URLDecoder; import java.security.AllPermission; import java.security.CodeSource; import java.security.PermissionCollection; @@ -50,19 +61,40 @@ import java.util.HashMap; import java.util.Map; import java.util.Vector; +import javax.swing.LookAndFeel; import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; + +import com.threerings.getdown.util.LaunchUtil; + +import groovy.lang.Binding; +import groovy.util.GroovyScriptEngine; /** * Main class for Jalview Application
*
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview + * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \ + * jalview.bin.Jalview + * + * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \ + * jalview.bin.Jalview jalview.bin.Jalview + * + * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not + * embellish '*' to e.g. '*.jar') * * @author $author$ * @version $Revision$ */ public class Jalview { + /* + * singleton instance of this class + */ + private static Jalview instance; + + private Desktop desktop; + + public static AlignFrame currentAlignFrame; + static { // grab all the rights we can the JVM @@ -84,19 +116,94 @@ public class Jalview } /** + * 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() + { + + @Override + public void run() + { + synchronized (us) + { + queued--; + running++; + } + + af.setProgressBar(MessageManager + .getString("status.das_features_being_retrived"), id); + af.featureSettings_actionPerformed(null); + af.setProgressBar(null, id); + synchronized (us) + { + running--; + } + } + }).start(); + } + + public synchronized boolean allFinished() + { + return queued == 0 && running == 0; + } + + } + + public static Jalview getInstance() + { + return instance; + } + + /** * main class for Jalview application * * @param args - * open filename + * open filename */ public static void main(String[] args) { + instance = new Jalview(); + instance.doMain(args); + } + + /** + * @param args + */ + void doMain(String[] args) + { System.setSecurityManager(null); - System.out.println("Java version: " - + System.getProperty("java.version")); + System.out + .println("Java version: " + System.getProperty("java.version")); System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); + // report Jalview version + Cache.loadBuildProperties(true); ArgsParser aparser = new ArgsParser(args); boolean headless = false; @@ -116,8 +223,8 @@ public class Jalview Cache.loadProperties(usrPropsFile); // must do this before if (usrPropsFile != null) { - System.out.println("CMD [-props " + usrPropsFile - + "] executed successfully!"); + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); } // anything else! @@ -128,12 +235,12 @@ public class Jalview try { Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); - System.out.println("CMD [-jabaws " + jabawsUrl - + "] executed successfully!"); + System.out.println( + "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); } catch (MalformedURLException e) { - System.err.println("Invalid jabaws parameter: " + jabawsUrl - + " ignored"); + System.err.println( + "Invalid jabaws parameter: " + jabawsUrl + " ignored"); } } @@ -164,43 +271,89 @@ public class Jalview try { Cache.initLogger(); - } catch (java.lang.NoClassDefFoundError error) + } catch (NoClassDefFoundError error) { error.printStackTrace(); - System.out - .println("\nEssential logging libraries not found." - + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview"); + System.out.println("\nEssential logging libraries not found." + + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"); System.exit(0); } - Desktop desktop = null; + desktop = null; try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception ex) { + System.err.println("Unexpected Look and Feel Exception"); + ex.printStackTrace(); } - if (new Platform().isAMac()) + if (Platform.isAMac()) { + + LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel(); System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview"); System.setProperty("apple.laf.useScreenMenuBar", "true"); - try + if (lookAndFeel != null) { - UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager - .getLookAndFeel()); - } catch (UnsupportedLookAndFeelException e) + try + { + UIManager.setLookAndFeel(lookAndFeel); + } catch (Throwable e) + { + System.err.println( + "Failed to set QuaQua look and feel: " + e.toString()); + } + } + if (lookAndFeel == null + || !(lookAndFeel.getClass().isAssignableFrom( + UIManager.getLookAndFeel().getClass())) + || !UIManager.getLookAndFeel().getClass().toString() + .toLowerCase().contains("quaqua")) { - // TODO Auto-generated catch block - e.printStackTrace(); + try + { + System.err.println( + "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976"); + UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel"); + } catch (Throwable e) + { + System.err.println( + "Failed to reset look and feel: " + e.toString()); + } } } + /* + * configure 'full' SO model if preferences say to, else use the default (SO + * Lite) + */ + if (Cache.getDefault("USE_FULL_SO", true)) + { + SequenceOntologyFactory.setInstance(new SequenceOntology()); + } + if (!headless) { desktop = new Desktop(); desktop.setInBatchMode(true); // indicate we are starting up + + try + { + JalviewTaskbar.setTaskbar(this); + } catch (Exception e) + { + System.out.println("Cannot set Taskbar"); + // e.printStackTrace(); + } catch (Throwable t) + { + System.out.println("Cannot set Taskbar"); + // t.printStackTrace(); + } + desktop.setVisible(true); desktop.startServiceDiscovery(); if (!aparser.contains("nousagestats")) @@ -221,8 +374,8 @@ public class Jalview // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); - System.out.println("CMD questionnaire[-" + url - + "] executed successfully!"); + System.out.println( + "CMD questionnaire[-" + url + "] executed successfully!"); } else { @@ -234,10 +387,9 @@ public class Jalview // "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); + Cache.log.debug( + "Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); - } } } @@ -245,19 +397,39 @@ public class Jalview { System.err.println("CMD [-noquestionnaire] executed successfully!"); } - desktop.checkForNews(); + + if (!aparser.contains("nonews")) + { + desktop.checkForNews(); + } + + BioJsHTMLOutput.updateBioJS(); } - if (!isHeadlessMode()) + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 0) { - BioJsHTMLOutput.updateBioJS(); + final File appdir = new File(appdirString); + new Thread() + { + @Override + public void run() + { + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); } - String file = null, protocol = null, format = null, data = null; - jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless); - Vector getFeatures = null; // vector of das source nicknames to fetch - // features from - // loading is done. + String file = null, data = null; + FileFormatI format = null; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + String groovyscript = null; // script to execute after all loading is // completed one way or another // extract groovy argument and execute if necessary @@ -269,106 +441,22 @@ public class Jalview 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) { if (!headless) { - desktop.setProgressBar(MessageManager - .getString("status.processing_commandline_args"), + desktop.setProgressBar( + MessageManager + .getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } System.out.println("CMD [-open " + file + "] executed successfully!"); if (!file.startsWith("http://")) { - if (!(new java.io.File(file)).exists()) + if (!(new File(file)).exists()) { System.out.println("Can't find " + file); if (headless) @@ -378,9 +466,15 @@ public class Jalview } } - protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); + protocol = AppletFormatAdapter.checkProtocol(file); - format = new jalview.io.IdentifyFile().identify(file, protocol); + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); @@ -390,26 +484,19 @@ public class Jalview } else { - Desktop.setCurrentAlignFrame(af); + setCurrentAlignFrame(af); data = aparser.getValue("colour", true); if (data != null) { data.replaceAll("%20", " "); - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); - if (cs == null) + if (cs != null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(data); - cs = ucs; - } - else - { - System.out.println("CMD [-color " + data - + "] executed successfully!"); + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } af.changeColour(cs); } @@ -419,19 +506,19 @@ public class Jalview if (data != null) { af.parseFeaturesFile(data, - jalview.io.AppletFormatAdapter.checkProtocol(data)); + AppletFormatAdapter.checkProtocol(data)); // System.out.println("Added " + data); - System.out.println("CMD groups[-" + data - + "] executed successfully!"); + System.out.println( + "CMD groups[-" + data + "] executed successfully!"); } data = aparser.getValue("features", true); if (data != null) { af.parseFeaturesFile(data, - jalview.io.AppletFormatAdapter.checkProtocol(data)); + AppletFormatAdapter.checkProtocol(data)); // System.out.println("Added " + data); - System.out.println("CMD [-features " + data - + "] executed successfully!"); + System.out.println( + "CMD [-features " + data + "] executed successfully!"); } data = aparser.getValue("annotations", true); @@ -439,8 +526,8 @@ public class Jalview { af.loadJalviewDataFile(data, null, null, null); // System.out.println("Added " + data); - System.out.println("CMD [-annotations " + data - + "] executed successfully!"); + System.out.println( + "CMD [-annotations " + data + "] executed successfully!"); } // set or clear the sortbytree flag. if (aparser.contains("sortbytree")) @@ -471,18 +558,14 @@ public class Jalview data = aparser.getValue("tree", true); if (data != null) { - 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()); - } + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + NewickFile nf = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); } catch (IOException ex) { System.err.println("Couldn't add tree " + data); @@ -492,87 +575,79 @@ public class Jalview // 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) - { - 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) { // 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); - } + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); groovyscript = null; } String imageName = "unnamed.png"; while (aparser.getSize() > 1) { - format = aparser.nextValue(); + String outputFormat = aparser.nextValue(); file = aparser.nextValue(); - if (format.equalsIgnoreCase("png")) + if (outputFormat.equalsIgnoreCase("png")) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); + af.createPNG(new File(file)); + imageName = (new File(file)).getName(); System.out.println("Creating PNG image: " + file); continue; } - else if (format.equalsIgnoreCase("svg")) + else if (outputFormat.equalsIgnoreCase("svg")) { - File imageFile = new java.io.File(file); + File imageFile = new File(file); imageName = imageFile.getName(); af.createSVG(imageFile); System.out.println("Creating SVG image: " + file); continue; } - else if (format.equalsIgnoreCase("html")) + else if (outputFormat.equalsIgnoreCase("html")) { - File imageFile = new java.io.File(file); + File imageFile = new File(file); imageName = imageFile.getName(); - new HtmlSvgOutput(new java.io.File(file), af.alignPanel); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(file); + System.out.println("Creating HTML image: " + file); continue; } - else if (format.equalsIgnoreCase("imgMap")) + else if (outputFormat.equalsIgnoreCase("biojsmsa")) + { + if (file == null) + { + System.err.println("The output html file must not be null"); + return; + } + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(file); + System.out + .println("Creating BioJS MSA Viwer HTML file: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("imgMap")) { - af.createImageMap(new java.io.File(file), imageName); + af.createImageMap(new File(file), imageName); System.out.println("Creating image map: " + file); continue; } - else if (format.equalsIgnoreCase("eps")) + else if (outputFormat.equalsIgnoreCase("eps")) { - File outputFile = new java.io.File(file); - System.out.println("Creating EPS file: " - + outputFile.getAbsolutePath()); + File outputFile = new File(file); + System.out.println( + "Creating EPS file: " + outputFile.getAbsolutePath()); af.createEPS(outputFile); continue; } @@ -601,15 +676,15 @@ public class Jalview // And the user // //////////////////// - if (!headless && file == null && vamsasImport == null + if (!headless && file == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { - file = jalview.bin.Cache.getDefault( - "STARTUP_FILE", + 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")) + 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"); @@ -617,51 +692,45 @@ public class Jalview jalview.bin.Cache.removeProperty("STARTUP_FILE"); } - protocol = "File"; + protocol = DataSourceType.FILE; if (file.indexOf("http:") > -1) { - protocol = "URL"; + protocol = DataSourceType.URL; } if (file.endsWith(".jar")) { - format = "Jalview"; + format = FileFormat.Jalview; } else { - format = new jalview.io.IdentifyFile().identify(file, protocol); + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e) + { + // TODO what? + } } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); - getFeatures = checkDasArguments(aparser); // extract groovy arguments before anything else. } - // 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) - { - startFeatureFetching(getFeatures); - } - } + // Once all other stuff is done, execute any groovy scripts (in order) if (groovyscript != null) { - if (jalview.bin.Cache.groovyJarsPresent()) + if (Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] { desktop, - startUpAlframe }); + executeGroovyScript(groovyscript, startUpAlframe); } else { - System.err - .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + System.err.println( + "Sorry. Groovy Support is not available, so ignoring the provided groovy script " + groovyscript); } } @@ -678,8 +747,8 @@ public class Jalview private static void showUsage() { - System.out - .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" + 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" @@ -698,22 +767,21 @@ public class Jalview + "-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" + + "-biojsMSA FILE\tCreate BioJS MSA Viewer 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" + + "-nonews\tTurn off check for Jalview news.\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)" + // "-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"); } @@ -723,10 +791,8 @@ public class Jalview /** * 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", + PromptUserConfig prompter = new 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)", @@ -735,8 +801,8 @@ public class Jalview @Override public void run() { - Cache.log - .debug("Initialising googletracker for usage stats."); + Cache.log.debug( + "Initialising googletracker for usage stats."); Cache.initGoogleTracker(); Cache.log.debug("Tracking enabled."); } @@ -755,19 +821,13 @@ public class Jalview * 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) + private void executeGroovyScript(String groovyscript, AlignFrame af) { - 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 */ @@ -782,10 +842,10 @@ public class Jalview try { tfile = File.createTempFile("jalview", "groovy"); - PrintWriter outfile = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(tfile))); + PrintWriter outfile = new PrintWriter( + new OutputStreamWriter(new FileOutputStream(tfile))); BufferedReader br = new BufferedReader( - new java.io.InputStreamReader(System.in)); + new InputStreamReader(System.in)); String line = null; while ((line = br.readLine()) != null) { @@ -798,8 +858,8 @@ public class Jalview } catch (Exception ex) { System.err.println("Failed to read from STDIN into tempfile " - + ((tfile == null) ? "(tempfile wasn't created)" : tfile - .toString())); + + ((tfile == null) ? "(tempfile wasn't created)" + : tfile.toString())); ex.printStackTrace(); return; } @@ -808,8 +868,8 @@ public class Jalview sfile = tfile.toURI().toURL(); } catch (Exception x) { - System.err - .println("Unexpected Malformed URL Exception for temporary file created from STDIN: " + System.err.println( + "Unexpected Malformed URL Exception for temporary file created from STDIN: " + tfile.toURI()); x.printStackTrace(); return; @@ -849,75 +909,23 @@ public class Jalview } } } - 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++) + Map vbinding = new HashMap<>(); + vbinding.put("Jalview", this); + if (af != null) { - 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++; - } + vbinding.put("currentAlFrame", af); } - Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons; - Object gbinding; - try + Binding gbinding = new Binding(vbinding); + GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile }); + gse.run(sfile.toString(), gbinding); + if ("STDIN".equals(groovyscript)) { - 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); + // delete temp file that we made - + // only if it was successfully executed + tfile.delete(); } - - 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 @@ -925,101 +933,6 @@ public class Jalview 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; - String data; - String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); - 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:") || url - .startsWith("sequence: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); - } - System.out.println("CMD [-dasserver " + data - + "] executed successfully!"); - } // 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", true)) != 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 FeatureFetcher startFeatureFetching(final Vector dasSources) - { - FeatureFetcher ff = new FeatureFetcher(); - AlignFrame afs[] = Desktop.getAlignFrames(); - if (afs == null || afs.length == 0) - { - return null; - } - for (int i = 0; i < afs.length; i++) - { - ff.addFetcher(afs[i], dasSources); - } - return ff; } public static boolean isHeadlessMode() @@ -1031,176 +944,37 @@ public class Jalview } 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). - * - * @author Andrew Waterhouse and JBP documented. - * - */ - -class rnabuttonlistener implements ActionListener -{ - @Override - public void actionPerformed(ActionEvent arg0) - { - System.out.println("Good idea ! "); - - } -} - -class pbuttonlistener implements ActionListener -{ - @Override - public void actionPerformed(ActionEvent arg0) - { - - } -} - -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) + public AlignFrame[] getAlignFrames() { - return getValue(arg, false); - } + return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } + : Desktop.getAlignFrames(); - public String getValue(String arg, boolean utf8decode) - { - int index = vargs.indexOf(arg); - 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. + * Quit method delegates to Desktop.quit - unless running in headless mode when + * it just ends the JVM */ - public boolean contains(String arg) + public void quit() { - if (vargs.contains(arg)) + if (desktop != null) { - vargs.removeElement(arg); - return true; + desktop.quit(); } else { - return false; + System.exit(0); } } - public String nextValue() - { - return vargs.remove(0).toString(); - } - - public int getSize() - { - return vargs.size(); - } - -} - -/** - * 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) + public static AlignFrame getCurrentAlignFrame() { - final long id = System.currentTimeMillis(); - queued++; - final FeatureFetcher us = this; - new Thread(new Runnable() - { - - @Override - 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(); + return Jalview.currentAlignFrame; } - public synchronized boolean allFinished() + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) { - return queued == 0 && running == 0; + Jalview.currentAlignFrame = currentAlignFrame; } - }