X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=07fd4d68310a87eb29647b4807c87271b33c7216;hb=2b08c849bd54a0799ddf251f602a421d4696005e;hp=330919b8918be79901b0882980c27d992d18aed4;hpb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 330919b..07fd4d6 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,16 +20,25 @@ */ package jalview.bin; +import jalview.api.AlignViewportI; +import jalview.api.JalviewApp; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; import jalview.gui.Desktop; +import jalview.gui.Preferences; import jalview.gui.PromptUserConfig; +import jalview.gui.StructureViewer; 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.FileFormats; import jalview.io.FileLoader; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; @@ -85,41 +94,48 @@ import groovy.util.GroovyScriptEngine; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements ApplicationSingletonI { - // @formatter:off - /** - * find first query parameter (if any) that doesn't start with j2s - * and set as space-delimited arguments to Jalview main - * - * @j2sNative - * var hr = decodeURI(document.location.href); - * var pos = hr.indexOf("?"); - * if (pos > 0) - * { - * q = hr.substring(pos+1); - * args = q.split("&"); - * for (i = 0 ; i < args.length; i++) - * { - * arg1 = args[i]; - * if (!arg1.startsWith("j2s")) - * { - * thisApplet.__Info.args = arg1.split(" "); - * break; - * } - * } - * } - */ - // @formatter:on - /* - * singleton instance of this class - */ - private static Jalview instance; + public static Jalview getInstance() + { + return (Jalview) ApplicationSingletonProvider + .getInstance(Jalview.class); + } + + private Jalview() + { + } + + static + { + Platform.getURLCommandArguments(); + } + + private boolean headless; + + public static boolean isHeadlessMode() + { + return getInstance().headless; + } private Desktop desktop; - public static AlignFrame currentAlignFrame; + private AlignFrame currentAlignFrame; + + public boolean isJavaAppletTag; + + public String appletResourcePath; + + public static AlignFrame getCurrentAlignFrame() + { + return getInstance().currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + getInstance().currentAlignFrame = currentAlignFrame; + } static { @@ -127,25 +143,25 @@ public class Jalview /** * Java only * - * @j2sNative + * @j2sIgnore */ { // grab all the rights we can for the JVM - Policy.setPolicy(new Policy() - { - @Override - public PermissionCollection getPermissions(CodeSource codesource) - { - Permissions perms = new Permissions(); - perms.add(new AllPermission()); - return (perms); - } - - @Override - public void refresh() - { - } - }); + Policy.setPolicy(new Policy() + { + @Override + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + @Override + public void refresh() + { + } + }); } } @@ -208,11 +224,6 @@ public class Jalview } - public static Jalview getInstance() - { - return instance; - } - /** * main class for Jalview application * @@ -221,44 +232,49 @@ public class Jalview */ public static void main(String[] args) { -// setLogging(); // BH - for event debugging in JavaScript - instance = new Jalview(); - instance.doMain(args); -} + // setLogging(); // BH - for event debugging in JavaScript + getInstance().doMain(args); + } - private static void logClass(String name) - { - // BH - for event debugging in JavaScript - ConsoleHandler consoleHandler = new ConsoleHandler(); - consoleHandler.setLevel(Level.ALL); - Logger logger = Logger.getLogger(name); - logger.setLevel(Level.ALL); - logger.addHandler(consoleHandler); + private static void logClass(String name) + { + // BH - for event debugging in JavaScript + ConsoleHandler consoleHandler = new ConsoleHandler(); + consoleHandler.setLevel(Level.ALL); + Logger logger = Logger.getLogger(name); + logger.setLevel(Level.ALL); + logger.addHandler(consoleHandler); } @SuppressWarnings("unused") - private static void setLogging() + private static void setLogging() { - // BH - for event debugging in JavaScript (Java mode only) + + /** + * @j2sIgnore + * + */ + { + System.out.println("not in js"); + } + + // BH - for event debugging in JavaScript (Java mode only) if (!Platform.isJS()) /** * Java only * - * @j2sNative + * @j2sIgnore */ - { - Logger.getLogger("").setLevel(Level.ALL); - logClass("java.awt.EventDispatchThread"); - logClass("java.awt.EventQueue"); - logClass("java.awt.Component"); - logClass("java.awt.focus.Component"); - logClass("java.awt.focus.DefaultKeyboardFocusManager"); - } + { + Logger.getLogger("").setLevel(Level.ALL); + logClass("java.awt.EventDispatchThread"); + logClass("java.awt.EventQueue"); + logClass("java.awt.Component"); + logClass("java.awt.focus.Component"); + logClass("java.awt.focus.DefaultKeyboardFocusManager"); + } } - - - /** * @param args @@ -266,7 +282,8 @@ public class Jalview void doMain(String[] args) { - if (!Platform.isJS()) + boolean isJS = Platform.isJS(); + if (!isJS) { System.setSecurityManager(null); } @@ -278,42 +295,56 @@ public class Jalview + System.getProperty("os.version")); ArgsParser aparser = new ArgsParser(args); - boolean headless = false; - String usrPropsFile = aparser.getValue("props"); - Cache.loadProperties(usrPropsFile); // must do this before - if (usrPropsFile != null) + String usrPropsFile = aparser.getValue(ArgsParser.PROPS); + Cache.loadProperties(usrPropsFile); + if (isJS) { + isJavaAppletTag = aparser.isApplet(); + if (isJavaAppletTag) + { + Preferences.setAppletDefaults(); + Cache.loadProperties(usrPropsFile); // again, because we + // might be changing defaults here? + } System.out.println( - "CMD [-props " + usrPropsFile + "] executed successfully!"); + " found: " + aparser.getValue("Info.j2sAppletID")); + appletResourcePath = aparser.getValue("Info.resourcePath"); } - - if (!Platform.isJS()) + else /** * Java only * - * @j2sNative + * @j2sIgnore */ { + if (usrPropsFile != null) + { + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); + } + if (aparser.contains("help") || aparser.contains("h")) { showUsage(); System.exit(0); } - if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) + if (aparser.contains(ArgsParser.NODISPLAY) + || aparser.contains(ArgsParser.NOGUI) + || aparser.contains(ArgsParser.HEADLESS) + || "true".equals(System.getProperty("java.awt.headless"))) { - System.setProperty("java.awt.headless", "true"); headless = true; } + // anything else! - final String jabawsUrl = aparser.getValue("jabaws"); + final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS); if (jabawsUrl != null) { try { - Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl); System.out.println( "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); } catch (MalformedURLException e) @@ -324,7 +355,8 @@ public class Jalview } } - String defs = aparser.getValue("setprop"); + // check for property setting + String defs = aparser.getValue(ArgsParser.SETPROP); while (defs != null) { int p = defs.indexOf('='); @@ -335,17 +367,12 @@ public class Jalview else { System.out.println("Executing setprop argument: " + defs); - if (Platform.isJS()) + if (isJS) { - Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + 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; + defs = aparser.getValue(ArgsParser.SETPROP); } System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); @@ -389,8 +416,9 @@ public class Jalview "Failed to set QuaQua look and feel: " + e.toString()); } } - if (lookAndFeel == null || !(lookAndFeel.getClass() - .isAssignableFrom(UIManager.getLookAndFeel().getClass())) + if (lookAndFeel == null + || !(lookAndFeel.getClass().isAssignableFrom( + UIManager.getLookAndFeel().getClass())) || !UIManager.getLookAndFeel().getClass().toString() .toLowerCase().contains("quaqua")) { @@ -413,33 +441,24 @@ public class Jalview */ if (Cache.getDefault("USE_FULL_SO", false)) { - SequenceOntologyFactory.setInstance(new SequenceOntology()); + SequenceOntologyFactory.setSequenceOntology(new SequenceOntology()); } if (!headless) { - desktop = new Desktop() -// { -// // BH testing -// @Override -// protected void processEvent(AWTEvent e) { -// System.out.println("Jalview.java " + e); -// super.processEvent(e); -// } -// } - ; + desktop = Desktop.getInstance(); desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); - if (!Platform.isJS()) + if (!isJS) /** * Java only * - * @j2sNative + * @j2sIgnore */ { desktop.startServiceDiscovery(); - if (!aparser.contains("nousagestats")) + if (!aparser.contains(ArgsParser.NOUSAGESTATS)) { startUsageStats(desktop); } @@ -448,9 +467,9 @@ public class Jalview System.err.println("CMD [-nousagestats] executed successfully!"); } - if (!aparser.contains("noquestionnaire")) + if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE)) { - String url = aparser.getValue("questionnaire"); + String url = aparser.getValue(ArgsParser.QUESTIONNAIRE); if (url != null) { // Start the desktop questionnaire prompter with the specified @@ -462,7 +481,7 @@ public class Jalview } else { - if (Cache.getProperty("NOQUESTIONNAIRES") == null) + if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null) { // Start the desktop questionnaire prompter with the specified // questionnaire @@ -482,7 +501,7 @@ public class Jalview .println("CMD [-noquestionnaire] executed successfully!"); } - if (!aparser.contains("nonews")) + if (!aparser.contains(ArgsParser.NONEWS)) { desktop.checkForNews(); } @@ -491,109 +510,29 @@ public class Jalview } } - 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 + // 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); + String groovyscript = (isJS ? null + : aparser.getValue(ArgsParser.GROOVY, true)); + String file = aparser.getValue(ArgsParser.OPEN, true); + String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null) + : null); + String fileFormat = (isJavaAppletTag + ? aparser.getAppletValue("format", null) + : null); + FileFormatI format = null; + DataSourceType protocol = null; if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } - String vamsasImport = aparser.getValue("vdoc"); - String 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 - { - DataSourceType viprotocol = AppletFormatAdapter - .checkProtocol(vamsasImport); - if (viprotocol == DataSourceType.FILE) - { - inSession = desktop.vamsasImport(new File(vamsasImport)); - } - else if (viprotocol == DataSourceType.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; + boolean haveImport = checkStartVamas(aparser); // Finally, deal with the remaining input data. + long progress = -1; if (file != null) { if (!headless) @@ -603,14 +542,14 @@ public class Jalview .getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } - System.out.println("CMD [-open " + file + "] executed successfully!"); - if (!Platform.isJS()) - /** - * ignore in JavaScript -- can't just file existence - could load it? - * - * @j2sNative - */ + if (!isJS) + /** + * ignore in JavaScript -- can't just check file existence - could load + * it? + * + * @j2sIgnore + */ { if (!file.startsWith("http://") && !file.startsWith("https://")) // BH 2019 added https check for Java @@ -626,17 +565,24 @@ public class Jalview } } - protocol = AppletFormatAdapter.checkProtocol(file); + protocol = AppletFormatAdapter.checkProtocol(file); try { - format = new IdentifyFile().identify(file, protocol); + format = (isJavaAppletTag && fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } } catch (FileFormatException e1) { // TODO ? } - AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, + AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file, + protocol, format); if (af == null) { @@ -644,15 +590,45 @@ public class Jalview } else { + System.out + .println("CMD [-open " + file + "] executed successfully!"); + if (file2 != null) + { + protocol = AppletFormatAdapter.checkProtocol(file2); + try + { + format = new IdentifyFile().identify(file2, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } + AlignFrame af2 = new FileLoader(!headless).loadFileWaitTillLoaded( + file2, + protocol, format); + if (af2 == null) + { + System.out.println("error"); + } + else + { + AlignViewport.openLinkedAlignmentAs(af, + af.getViewport().getAlignment(), + af2.getViewport().getAlignment(), "", + AlignViewport.SPLIT_FRAME); + } + } + setCurrentAlignFrame(af); - data = aparser.getValue("colour", true); + + // TODO: file2 How to implement file2 for the applet spit screen? + + String data = aparser.getValue(ArgsParser.COLOUR, true); if (data != null) { data.replaceAll("%20", " "); - ColourSchemeI cs = ColourSchemeProperty - .getColourScheme(af.getViewport(), - af.getViewport().getAlignment(), data); + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); if (cs != null) { @@ -663,7 +639,7 @@ public class Jalview } // Must maintain ability to use the groups flag - data = aparser.getValue("groups", true); + data = aparser.getValue(ArgsParser.GROUPS, true); if (data != null) { af.parseFeaturesFile(data, @@ -672,7 +648,7 @@ public class Jalview System.out.println( "CMD groups[-" + data + "] executed successfully!"); } - data = aparser.getValue("features", true); + data = aparser.getValue(ArgsParser.FEATURES, true); if (data != null) { af.parseFeaturesFile(data, @@ -682,7 +658,7 @@ public class Jalview "CMD [-features " + data + "] executed successfully!"); } - data = aparser.getValue("annotations", true); + data = aparser.getValue(ArgsParser.ANNOTATIONS, true); if (data != null) { af.loadJalviewDataFile(data, null, null, null); @@ -691,7 +667,7 @@ public class Jalview "CMD [-annotations " + data + "] executed successfully!"); } // set or clear the sortbytree flag. - if (aparser.contains("sortbytree")) + if (aparser.contains(ArgsParser.SORTBYTREE)) { af.getViewport().setSortByTree(true); if (af.getViewport().getSortByTree()) @@ -699,7 +675,8 @@ public class Jalview System.out.println("CMD [-sortbytree] executed successfully!"); } } - if (aparser.contains("no-annotation")) + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) { af.getViewport().setShowAnnotation(false); if (!af.getViewport().isShowAnnotation()) @@ -707,7 +684,7 @@ public class Jalview System.out.println("CMD no-annotation executed successfully!"); } } - if (aparser.contains("nosortbytree")) + if (aparser.contains(ArgsParser.NOSORTBYTREE)) { af.getViewport().setSortByTree(false); if (!af.getViewport().getSortByTree()) @@ -716,7 +693,7 @@ public class Jalview .println("CMD [-nosortbytree] executed successfully!"); } } - data = aparser.getValue("tree", true); + data = aparser.getValue(ArgsParser.TREE, true); if (data != null) { try @@ -736,100 +713,33 @@ public class Jalview // TODO - load PDB structure(s) to alignment JAL-629 // (associate with identical sequence in alignment, or a specified // sequence) - if (groovyscript != null) + if (isJavaAppletTag) { - // Execute the groovy script after we've done all the rendering stuff - // and before any images or figures are generated. - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, af); - System.out.println("CMD groovy[" + groovyscript - + "] executed successfully!"); - groovyscript = null; + loadAppletParams(aparser, af); } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) + else if (!isJS) + /** + * Java only + * + * @j2sIgnore + */ { - String outputFormat = aparser.nextValue(); - file = aparser.nextValue(); - - if (outputFormat.equalsIgnoreCase("png")) - { - af.createPNG(new File(file)); - imageName = (new File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("svg")) + if (groovyscript != null) { - File imageFile = new File(file); - imageName = imageFile.getName(); - af.createSVG(imageFile); - System.out.println("Creating SVG image: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("html")) - { - File imageFile = new File(file); - imageName = imageFile.getName(); - HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); - htmlSVG.exportHTML(file); - - System.out.println("Creating HTML image: " + file); - continue; - } - 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 File(file), imageName); - System.out.println("Creating image map: " + file); - continue; - } - else if (outputFormat.equalsIgnoreCase("eps")) - { - File outputFile = new File(file); - System.out.println( - "Creating EPS file: " + outputFile.getAbsolutePath()); - af.createEPS(outputFile); - continue; - } - - af.saveAlignment(file, format); - if (af.isSaveAlignmentSuccessful()) - { - System.out.println("Written alignment in " + format - + " format to " + file); + // Execute the groovy script after we've done all the rendering + // stuff + // and before any images or figures are generated. + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + groovyscript = null; } - else + checkOutputFile(aparser, af, format); + while (aparser.getSize() > 0) { - System.out.println("Error writing file " + file + " in " - + format + " format!!"); + System.out.println("Unknown arg: " + aparser.nextValue()); } - - } - - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); } } } @@ -838,13 +748,12 @@ public class Jalview // And the user // //////////////////// - if (!Platform.isJS() && !headless && file == null - && vamsasImport == null + if (!isJS && !headless && file == null && !haveImport && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) /** * Java only * - * @j2sNative + * @j2sIgnore */ { file = jalview.bin.Cache.getDefault("STARTUP_FILE", @@ -882,7 +791,8 @@ public class Jalview } } - startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, + startUpAlframe = new FileLoader(!headless) + .loadFileWaitTillLoaded(file, protocol, format); // extract groovy arguments before anything else. } @@ -913,6 +823,185 @@ public class Jalview } } + private boolean checkStartVamas(ArgsParser aparser) + { + String vamsasImport = aparser.getValue(ArgsParser.VDOC); + String vamsasSession = aparser.getValue(ArgsParser.VSESS); + if (vamsasImport == null && vamsasSession == null) + { + return false; + } + if (desktop == null || headless) + { + System.out.println( + "Headless vamsas sessions not yet supported. Sorry."); + System.exit(1); + } + boolean haveImport = (vamsasImport != null); + if (haveImport) + { + // if we have a file, start a new session and import it. + boolean inSession = false; + try + { + DataSourceType viprotocol = AppletFormatAdapter + .checkProtocol(vamsasImport); + if (viprotocol == DataSourceType.FILE) + { + inSession = desktop.vamsasImport(new File(vamsasImport)); + } + else if (viprotocol == DataSourceType.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(); + } + } + return haveImport; + } + + private void checkOutputFile(ArgsParser aparser, AlignFrame af, + FileFormatI format) + { + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + // PNG filename + // SVG filename + // HTML filename + // biojsmsa filename + String outputFormat = aparser.nextValue(); + String file = aparser.nextValue(); + if (outputFormat.equalsIgnoreCase("png")) + { + af.createPNG(new File(file)); + imageName = (new File(file)).getName(); + System.out.println("Creating PNG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("svg")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("html")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(file); + + System.out.println("Creating HTML image: " + file); + continue; + } + 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 File(file), imageName); + System.out.println("Creating image map: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("eps")) + { + File outputFile = new File(file); + System.out.println( + "Creating EPS file: " + outputFile.getAbsolutePath()); + af.createEPS(outputFile); + continue; + } + + af.saveAlignment(file, format); + if (af.isSaveAlignmentSuccessful()) + { + System.out.println( + "Written alignment in " + format + " format to " + file); + } + else + { + System.out.println("Error writing file " + file + " in " + format + + " format!!"); + } + + } + } + private static void showUsage() { System.out.println( @@ -963,8 +1052,9 @@ public class Jalview /** * start a User Config prompt asking if we can log usage statistics. */ - PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop, - "USAGESTATS", "Jalview Usage Statistics", + PromptUserConfig prompter = new PromptUserConfig( + Desktop.getDesktopPane(), "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)", @@ -1107,16 +1197,6 @@ public class Jalview } } - public static boolean isHeadlessMode() - { - String isheadless = System.getProperty("java.awt.headless"); - if (isheadless != null && isheadless.equalsIgnoreCase("true")) - { - return true; - } - return false; - } - public AlignFrame[] getAlignFrames() { return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } @@ -1140,13 +1220,150 @@ public class Jalview } } - public static AlignFrame getCurrentAlignFrame() + /** + * Get the SwingJS applet ID and combine that with the frameType + * + * @param frameType + * "alignment", "desktop", etc., or null + * @return + */ + public static String getAppID(String frameType) { - return Jalview.currentAlignFrame; + String id = Cache.getProperty("Info.j2sAppletID"); + if (id == null) + { + id = "jalview"; + } + return id + (frameType == null ? "" : "-" + frameType); } - public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + /** + * Handle all JalviewLite applet parameters + * + * @param aparser + * @param af + */ + private void loadAppletParams(ArgsParser aparser, AlignFrame af) { - Jalview.currentAlignFrame = currentAlignFrame; + JalviewApp app = new JalviewApp() + { + + private boolean alignPDBStructures; // From JalviewLite; not implemented + + @Override + public String getParameter(String name) + { + return aparser.getAppletValue(name, null); + } + + @Override + public boolean getDefaultParameter(String name, boolean def) + { + String stn; + return ((stn = getParameter(name)) == null ? def + : "true".equalsIgnoreCase(stn)); + } + + /** + * Get the applet-like document base even though this is an application. + */ + @Override + public URL getDocumentBase() + { + return Platform.getDocumentBase(); + } + + /** + * Get the applet-like code base even though this is an application. + */ + @Override + public URL getCodeBase() + { + return Platform.getCodeBase(); + } + + @Override + public AlignViewportI getViewport() + { + return af.getViewport(); + } + + /** + * features + * + */ + @Override + public boolean parseFeaturesFile(String filename, + DataSourceType protocol) + { + return af.parseFeaturesFile(filename, protocol); + } + + /** + * scorefile + * + */ + @Override + public boolean loadScoreFile(String sScoreFile) throws IOException + { + af.loadJalviewDataFile(sScoreFile, null, null, null); + return true; + } + + /** + * annotations, jpredfile, jnetfile + * + */ + @Override + public void updateForAnnotations() + { + af.updateForAnnotations(); + } + + @Override + public void loadTree(NewickFile fin, String treeFile) + throws IOException + { + // n/a -- already done by standard Jalview command line processing + } + + @Override + public void setAlignPdbStructures(boolean defaultParameter) + { + alignPDBStructures = true; + } + + @Override + public void newStructureView(PDBEntry pdb, SequenceI[] seqs, + String[] chains, DataSourceType protocol) + { + StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs); + } + + @Override + public void setFeatureGroupState(String[] groups, boolean state) + { + af.setFeatureGroupState(groups, state); + } + + @Override + public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, + String[][] chains, String[] protocols) + { + System.err.println( + "Jalview applet interface alignedStructureView not implemented"); + } + + @Override + public void newFeatureSettings() + { + System.err.println( + "Jalview applet interface newFeatureSettings not implemented"); + } + + }; + + new JalviewAppLoader(true).load(app); } + }