X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e98ea638a5b8d0cc0844d8beca81dcd1612c6d79;hb=564c47bdd60cf84046269e45d2f85f39408e4441;hp=7cbbd7df24f2594286bb297f925675ba64d8cbce;hpb=d9f0a24d9662a0b530fd79b51108dd074d03d6e0;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 7cbbd7d..e98ea63 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,27 +20,6 @@ */ 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.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -58,17 +37,58 @@ import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; import java.util.HashMap; +import java.util.Hashtable; import java.util.Map; import java.util.Vector; -import java.util.logging.ConsoleHandler; -import java.util.logging.Level; -import java.util.logging.Logger; import javax.swing.LookAndFeel; import javax.swing.UIManager; +import com.threerings.getdown.util.LaunchUtil; + import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; +import jalview.api.AlignCalcWorkerI; +import jalview.api.AlignViewportI; +import jalview.api.JalviewApp; +import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.ext.so.SequenceOntology; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.AlignmentPanel; +import jalview.gui.CalculationChooser; +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; +import jalview.io.NewickFile; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.javascript.JSFunctionExec; +import jalview.javascript.MouseOverStructureListener; +import jalview.renderer.seqfeatures.FeatureRenderer; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.structure.SelectionSource; +import jalview.structure.VamsasSource; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; +import netscape.javascript.JSObject; /** * Main class for Jalview Application
@@ -85,55 +105,80 @@ import groovy.util.GroovyScriptEngine; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements JalviewJSApi { - /** - * // 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; } } } - */ + static + { + Platform.getURLCommandArguments(); + } + + private boolean headless; + + // singleton instance of this class - /* - * singleton instance of this class - */ private static Jalview instance; private Desktop desktop; public static AlignFrame currentAlignFrame; + public boolean isJavaAppletTag; + + public String appletResourcePath; + + JalviewAppLoader appLoader; + + protected JSFunctionExec jsFunctionExec; + + private boolean noCalculation, noMenuBar, noStatus; + + private boolean noAnnotation; + + public boolean getStartCalculations() + { + return !noCalculation; + } + + public boolean getAllowMenuBar() + { + return !noMenuBar; + } + + public boolean getShowStatus() + { + return !noStatus; + } + + public boolean getShowAnnotation() + { + return !noAnnotation; + } + static { if (!Platform.isJS()) /** * 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() + { + } + }); } } @@ -146,8 +191,8 @@ public class Jalview class FeatureFetcher { /* - * TODO: generalise to track all jalview events to orchestrate batch - * processing events. + * TODO: generalise to track all jalview events to orchestrate batch processing + * events. */ private int queued = 0; @@ -200,6 +245,9 @@ public class Jalview { return instance; } + + + private final static boolean doPlatformLogging = false; /** * main class for Jalview application @@ -209,44 +257,14 @@ public class Jalview */ public static void main(String[] args) { -// setLogging(); // BH - for event debugging in JavaScript + if (doPlatformLogging) + { + Platform.startJavaLogging(); + } + instance = new Jalview(); instance.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); - } - - @SuppressWarnings("unused") - private static void setLogging() - { - // BH - for event debugging in JavaScript (Java mode only) - if (!Platform.isJS())// !(/** @j2sNative true ||*/false)) - /** - * Java only - * - * @j2sNative - */ - { - 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 @@ -254,49 +272,91 @@ public class Jalview void doMain(String[] args) { - if (!Platform.isJS()) + boolean isJS = Platform.isJS(); + if (isJS) + { + Platform.setAppClass(this); + } + else { System.setSecurityManager(null); } System.out .println("Java version: " + System.getProperty("java.version")); + System.out.println("Java Home: " + System.getProperty("java.home")); System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); + String val = System.getProperty("sys.install4jVersion"); + if (val != null) + { + System.out.println("Install4j version: " + val); + } + val = System.getProperty("installer_template_version"); + if (val != null) + { + System.out.println("Install4j template version: " + val); + } + val = System.getProperty("launcher_version"); + if (val != null) + { + System.out.println("Launcher version: " + val); + } + + // report Jalview version + Cache.loadBuildProperties(true); ArgsParser aparser = new ArgsParser(args); - boolean headless = false; + headless = false; String usrPropsFile = aparser.getValue("props"); + Cache.loadProperties(usrPropsFile); // must do this before - if (usrPropsFile != null) + + 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 /** - * ignore in JavaScript + * 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")) { System.setProperty("java.awt.headless", "true"); headless = true; } + // < 0) { - 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 + final File appdir = new File(appdirString); + new Thread() { - if (desktop.joinVamsasSession(vamsasSession)) + @Override + public void run() { - System.out.println( - "Successfully joined vamsas session " + vamsasSession); - } - else - { - System.err.println("WARNING: Failed to join vamsas session " - + vamsasSession); + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); } - } 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(); - } + }.start(); } + + // completed one way or another + // extract groovy argument and execute if necessary + groovyscript = aparser.getValue("groovy", true); + + } + + String file = aparser.getValue("open", true); + + if (file == null && desktop == null) + { + System.out.println("No files to open!"); + System.exit(1); } + long progress = -1; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + FileFormatI format = null; // Finally, deal with the remaining input data. if (file != null) { @@ -594,11 +632,11 @@ public class Jalview System.out.println("CMD [-open " + file + "] executed successfully!"); if (!Platform.isJS()) - /** - * ignore in JavaScript -- can't just file existence - could load it? - * - * @j2sNative - */ + /** + * ignore in JavaScript -- can't just file existence - could load it? + * + * @j2sIgnore + */ { if (!file.startsWith("http://") && !file.startsWith("https://")) // BH 2019 added https check for Java @@ -613,45 +651,106 @@ public class Jalview } } } - - protocol = AppletFormatAdapter.checkProtocol(file); - + String fileFormat = (isJavaAppletTag + ? aparser.getAppletValue("format", null) + : null); + protocol = AppletFormatAdapter.checkProtocol(file); try { + format = (isJavaAppletTag && fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } format = new IdentifyFile().identify(file, protocol); } catch (FileFormatException e1) { // TODO ? } - AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, - format); + if (aparser.contains(ArgsParser.NOMENUBAR)) + { + noMenuBar = true; + System.out.println("CMD [nomenu] executed successfully!"); + } + + if (aparser.contains(ArgsParser.NOSTATUS)) + { + noStatus = true; + System.out.println("CMD [nostatus] executed successfully!"); + } + + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) + { + noAnnotation = true; + System.out.println("CMD no-annotation executed successfully!"); + } + if (aparser.contains(ArgsParser.NOCALCULATION)) + { + noCalculation = true; + System.out.println("CMD [nocalculation] executed successfully!"); + } + + AlignFrame af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, + protocol, format); if (af == null) { System.out.println("error"); } else { - setCurrentAlignFrame(af); - data = aparser.getValue("colour", true); - if (data != null) - { - data.replaceAll("%20", " "); - ColourSchemeI cs = ColourSchemeProperty - .getColourScheme(af.getViewport(), - af.getViewport().getAlignment(), data); - - if (cs != null) + // JalviewLite interface for JavaScript allows second file open + String file2 = aparser.getValue(ArgsParser.OPEN2, true); + if (file2 != null) + { + protocol = AppletFormatAdapter.checkProtocol(file2); + try { - System.out.println( - "CMD [-color " + data + "] executed successfully!"); + 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); + System.out.println( + "CMD [-open2 " + file2 + "] executed successfully!"); + } + } + setCurrentAlignFrame(af); + + String data = aparser.getValue(ArgsParser.COLOUR, true); + if (data != null) + { + data.replaceAll("%20", " "); + + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); + + if (cs != null) + { + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } af.changeColour(cs); } // 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, @@ -660,7 +759,7 @@ 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, @@ -669,8 +768,7 @@ public class Jalview System.out.println( "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); @@ -678,8 +776,17 @@ public class Jalview System.out.println( "CMD [-annotations " + data + "] executed successfully!"); } + + // JavaScript feature + + if (aparser.contains(ArgsParser.SHOWOVERVIEW)) + { + af.overviewMenuItem_actionPerformed(null); + System.out.println("CMD [showoverview] 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()) @@ -687,24 +794,50 @@ public class Jalview System.out.println("CMD [-sortbytree] executed successfully!"); } } - if (aparser.contains("no-annotation")) + + boolean doUpdateAnnotation = false; + /** + * we do this earlier in JalviewJS because of a complication with + * SHOWOVERVIEW + * + * For now, just fixing this in JalviewJS. + * + * + * @j2sIgnore + * + */ { - af.getViewport().setShowAnnotation(false); - if (!af.getViewport().isShowAnnotation()) + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) { - System.out.println("CMD no-annotation executed successfully!"); + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + doUpdateAnnotation = true; + 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()) { + doUpdateAnnotation = true; System.out .println("CMD [-nosortbytree] executed successfully!"); } } - data = aparser.getValue("tree", true); + if (doUpdateAnnotation) + { // BH 2019.07.24 + af.setMenusForViewport(); + af.alignPanel.updateLayout(); + } + + data = aparser.getValue(ArgsParser.TREE, true); if (data != null) { try @@ -724,120 +857,53 @@ 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")) - { - 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 (groovyscript != null) { - 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!!"); + // 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; } - } - + createOutputFiles(aparser, af, format); while (aparser.getSize() > 0) { System.out.println("Unknown arg: " + aparser.nextValue()); } } } + + AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user // //////////////////// - if (!Platform.isJS() && // /** @j2sNative false && */ // BH 2018 - !headless && file == null && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + if (!isJS && !headless && file == null + && Cache.getDefault("SHOW_STARTUP_FILE", true)) /** * Java only * - * @j2sNative + * @j2sIgnore */ { - file = jalview.bin.Cache.getDefault("STARTUP_FILE", - jalview.bin.Cache.getDefault("www.jalview.org", - "http://www.jalview.org") + file = Cache.getDefault("STARTUP_FILE", + 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")) @@ -845,7 +911,7 @@ public class Jalview // hardwire upgrade of the startup file file.replace("_2_3.jar", "_2_7.jar"); // and remove the stale setting - jalview.bin.Cache.removeProperty("STARTUP_FILE"); + Cache.removeProperty("STARTUP_FILE"); } protocol = DataSourceType.FILE; @@ -872,9 +938,10 @@ public class Jalview startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); - // extract groovy arguments before anything else. - } + } + + // extract groovy arguments before anything else. // Once all other stuff is done, execute any groovy scripts (in order) if (groovyscript != null) { @@ -890,6 +957,7 @@ public class Jalview + groovyscript); } } + // and finally, turn off batch mode indicator - if the desktop still exists if (desktop != null) { @@ -901,6 +969,109 @@ public class Jalview } } + /** + * Writes an output file for each format (if any) specified in the + * command-line arguments. Supported formats are currently + * + * A format parameter should be followed by a parameter specifying the output + * file name. {@code imgMap} parameters should follow those for the + * corresponding alignment image output. + * + * @param aparser + * @param af + * @param format + */ + private void createOutputFiles(ArgsParser aparser, AlignFrame af, + FileFormatI format) + { + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + 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( @@ -938,10 +1109,6 @@ public class Jalview // passed in correctly)" + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\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"); } @@ -1071,7 +1238,7 @@ public class Jalview } try { - Map vbinding = new HashMap<>(); + Map vbinding = new HashMap<>(); vbinding.put("Jalview", this); if (af != null) { @@ -1137,4 +1304,806 @@ public class Jalview { Jalview.currentAlignFrame = currentAlignFrame; } + + /** + * 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) + { + String id = Cache.getProperty("Info.j2sAppletID"); + if (id == null) + { + id = "jalview"; + } + return id + (frameType == null ? "" : "-" + frameType); + } + + /** + * Handle all JalviewLite applet parameters + * + * @param aparser + * @param af + */ + private void loadAppletParams(ArgsParser aparser, AlignFrame af) + { + JalviewApp app = new JalviewApp() + { + + // TODO BH 2019 + // + // These are methods that are in JalviewLite that various classes call + // but are not in JalviewLiteJsApi. Or, even if they are, other classes + // call + // them to JalviewLite directly. Some may not be necessary, but they have + // to + // be at least mentioned here, or the classes calling them should + // reference + // JalviewLite itself. + + private boolean alignPDBStructures; // From JalviewLite; not implemented + + private Hashtable> jsmessages; + + private Hashtable jshashes; + + @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"); + } + + private Vector jsExecQueue; + + @Override + public Vector getJsExecQueue(JSFunctionExec exec) + { + jsFunctionExec = exec; + return (jsExecQueue == null ? (jsExecQueue = new Vector<>()) + : jsExecQueue); + } + +// AppletContext deprecated +// +// @Override +// public AppletContext getAppletContext() +// { +// // TODO Auto-generated method stub +// return null; +// } +// + @Override + public boolean isJsfallbackEnabled() + { + // TODO Auto-generated method stub + return false; + } + + @Override + public JSObject getJSObject() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public StructureSelectionManagerProvider getStructureSelectionManagerProvider() + { + // TODO Q: what exactly is this? BH + return null; + } + + @Override + public void updateColoursFromMouseOver(Object source, + MouseOverStructureListener mouseOverStructureListener) + { + // TODO Auto-generated method stub + + } + + @Override + public Object[] getSelectionForListener(SequenceGroup seqsel, + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source, Object alignFrame) + { + return appLoader.getSelectionForListener(getCurrentAlignFrame(), + seqsel, colsel, hidden, source, alignFrame); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public Hashtable getJSHashes() + { + return (jshashes == null ? (jshashes = new Hashtable<>()) + : jshashes); + } + + @Override + public Hashtable> getJSMessages() + { + return (jsmessages == null ? (jsmessages = new Hashtable<>()) + : jsmessages); + } + + @Override + public Object getFrameForSource(VamsasSource source) + { + if (source != null) + { + AlignFrame af; + if (source instanceof jalview.gui.AlignViewport + && source == (af = getCurrentAlignFrame()).getViewport()) + { + // should be valid if it just generated an event! + return af; + } + // TODO: ensure that if '_af' is specified along with a handler + // function, then only events from that alignFrame are sent to that + // function + } + return null; + } + + @Override + public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp) + { + return new jalview.gui.FeatureRenderer((AlignmentPanel) vp); + } + + }; + + appLoader = new JalviewAppLoader(true); + appLoader.load(app); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() + */ + @Override + public String getSelectedSequences() + { + return getSelectedSequencesFrom(getCurrentAlignFrame()); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) + */ + @Override + public String getSelectedSequences(String sep) + { + return getSelectedSequencesFrom(getCurrentAlignFrame(), sep); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame) + */ + @Override + public String getSelectedSequencesFrom(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return getSelectedSequencesFrom(alf, null); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + @Override + public String getSelectedSequencesFrom(AlignFrame alf, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesFrom(alf, sep); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + @Override + public void highlight(String sequenceId, String position, + String alignedPosition) + { + highlightIn(null, sequenceId, position, alignedPosition); + } + + @Override + public void highlightIn(AlignFrame alf, String sequenceId, + String position, String alignedPosition) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.highlightIn(alf, sequenceId, position, alignedPosition); + } + + @Override + public void select(String sequenceIds, String columns) + { + selectIn(getCurrentAlignFrame(), sequenceIds, columns, null); + } + + @Override + public void select(String sequenceIds, String columns, String sep) + { + selectIn(null, sequenceIds, columns, sep); + } + + @Override + public void selectIn(AlignFrame alf, String sequenceIds, String columns) + { + selectIn(alf, sequenceIds, columns, null); + } + + @Override + public void selectIn(AlignFrame alf, String sequenceIds, String columns, + String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.selectIn(alf, sequenceIds, columns, sep); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); + } + + @Override + public String getAlignmentOrder() + { + return getAlignmentFrom(getCurrentAlignFrame(), null); + } + + @Override + public String getAlignmentOrderFrom(AlignFrame alf) + { + return getAlignmentFrom(alf, null); + } + + @Override + public String getAlignmentOrderFrom(AlignFrame alf, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAlignmentOrderFrom(alf, sep); + } + + @Override + public String orderBy(String order, String undoName) + { + return orderBy(order, undoName, null); + } + + @Override + public String orderBy(String order, String undoName, String sep) + { + return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep); + } + + @Override + public String orderAlignmentBy(AlignFrame alf, String order, + String undoName, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.orderAlignmentBy(alf, order, undoName, sep); + } + + @Override + public String getAlignment(String format) + { + return getAlignmentFrom(null, format, null); + } + + @Override + public String getAlignmentFrom(AlignFrame alf, String format) + { + return getAlignmentFrom(alf, format, null); + } + + @Override + public String getAlignment(String format, String suffix) + { + return getAlignmentFrom(getCurrentAlignFrame(), format, suffix); + } + + @Override + public String getAlignmentFrom(AlignFrame alf, String format, + String suffix) + { + return appLoader.getAlignmentFrom(alf, format, suffix); + } + + @Override + public void loadAnnotation(String annotation) + { + loadAnnotationFrom(getCurrentAlignFrame(), annotation); + } + + @Override + public void loadAnnotationFrom(AlignFrame alf, String annotation) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.loadAnnotationFrom(alf, annotation); + } + + @Override + public void loadFeatures(String features, boolean autoenabledisplay) + { + loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay); + } + + @Override + public boolean loadFeaturesFrom(AlignFrame alf, String features, + boolean autoenabledisplay) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay); + } + + @Override + public String getFeatures(String format) + { + return getFeaturesFrom(null, format); + } + + @Override + public String getFeaturesFrom(AlignFrame alf, String format) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeaturesFrom(alf, format); + } + + @Override + public String getAnnotation() + { + return getAnnotationFrom(null); + } + + @Override + public String getAnnotationFrom(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAnnotationFrom(alf); + } + + // @Override + // public AlignFrame newView() + // { + // return newViewFrom(null, null); + // } + // + // @Override + // public AlignFrame newView(String name) + // { + // return newViewFrom(null, name); + // } + // + // @Override + // public AlignFrame newViewFrom(AlignFrame alf) + // { + // return newViewFrom(alf, null); + // } + // + // @Override + // public AlignFrame newViewFrom(AlignFrame alf, String name) + // { + // if (alf == null) + // { + // alf = getCurrentAlignFrame(); + // } + // return appLoader.newViewFrom(alf, name); + // } + + @Override + public AlignFrame loadAlignment(String text, String title) + { + return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT, title); + } + + @Override + public boolean addPdbFile(AlignFrame alFrame, String sequenceId, + String pdbEntryString, String pdbFile) + { + if (alFrame == null) + { + alFrame = getCurrentAlignFrame(); + } + return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, + pdbFile); + } + + @Override + public void scrollViewToIn(AlignFrame alf, String topRow, + String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToIn(alf, topRow, leftHandColumn); + } + + @Override + public void scrollViewToRowIn(AlignFrame alf, String topRow) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToRowIn(alf, topRow); + } + + @Override + public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToColumnIn(alf, leftHandColumn); + } + + @Override + public String getFeatureGroups() + { + return getFeatureGroupsOn(null); + } + + @Override + public String getFeatureGroupsOn(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOn(alf); + } + + @Override + public String getFeatureGroupsOfState(boolean visible) + { + return getFeatureGroupsOfStateOn(null, visible); + } + + @Override + public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOfStateOn(alf, visible); + } + + @Override + public void setFeatureGroupState(String groups, boolean state) + { // JalviewLite API + setFeatureGroupStateOn(null, groups, state); + } + + @Override + public void setFeatureGroupStateOn(AlignFrame alf, String groups, + boolean state) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.setFeatureGroupStateOn(alf, groups, state); + } + + @Override + public String getSeparator() + { + return appLoader.getSeparator(); + } + + @Override + public void setSeparator(String separator) + { + appLoader.setSeparator(separator); + } + + @Override + public String getJsMessage(String messageclass, String viewId) + { + // see http://www.jalview.org/examples/jalviewLiteJs.html + return null; + } + + /** + * Open a new Tree panel on the desktop statically. Params are standard (not + * set by Groovy). No dialog is opened. + * + * @param af + * @param treeType + * @param modelName + * @return null, or the string "label.you_need_at_least_n_sequences" if number + * of sequences selected is inappropriate + */ + @Override + public Object openTreePanel(AlignFrame af, String treeType, + String modelName) + { // JalviewJS api + if (af == null) + { + af = getCurrentAlignFrame(); + } + return CalculationChooser.openTreePanel(af, treeType, modelName, null); + } + + /** + * public static method for JalviewJS API to open a PCAPanel without + * necessarily using a dialog. + * + * @param af + * @param modelName + * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences" + * if number of sequences selected is inappropriate + */ + @Override + public Object openPcaPanel(AlignFrame af, String modelName) + { + if (af == null) + { + af = getCurrentAlignFrame(); + } + return CalculationChooser.openPcaPanel(af, modelName, null); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + boolean suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, boolean suffix) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, + "" + suffix); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public String[] separatorListToArray(String list) + { + return appLoader.separatorListToArray(list); + } + + //// probably not needed in JalviewJS -- From when Jmol and Jalview did not + //// have a direct connection? + + @Override + public void setMouseoverListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setMouseoverListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setStructureListener(String listener, String modelSet) + { + // TODO Auto-generated method stub + + } + + @Override + public void removeJavascriptListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void mouseOverStructure(String pdbResNum, String chain, + String pdbfile) + { + // TODO Auto-generated method stub + + } + + @Override + public void showOverview() + { + currentAlignFrame.overviewMenuItem_actionPerformed(null); + } + + public void notifyWorker(AlignCalcWorkerI worker, String status) + { + // System.out.println("Jalview worker " + worker.getClass().getSimpleName() + // + " " + status); + } + }