X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=694fe00d15de7c5cd0faf2ded40e23c5dcfc714a;hb=27a73b75c2195a7406f55bb81c57a4e3b8cc0962;hp=37f396eb842d5d6a204ee8279559c200dba18460;hpb=fab0afc9e1e7a5ca460f0cbd48545536f989a435;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 37f396e..694fe00 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -60,6 +60,9 @@ import java.security.Policy; import java.util.HashMap; 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; @@ -84,51 +87,44 @@ import groovy.util.GroovyScriptEngine; */ public class Jalview { + static + { + Platform.getURLCommandArguments(); + } - // BH 6/19/2018 starting to work on JS version - just discovering issues + // singleton instance of this class - /* - * singleton instance of this class - */ private static Jalview instance; private Desktop desktop; public static AlignFrame currentAlignFrame; - /** - * Answers true if Jalview is running as Javascript, else false. The value is - * set at compile time. - * - * @return - */ - public static boolean isJS() - { - return /** @j2sNative true || */ - false; - } - static { - if (!isJS()) - { // BH 2018 - // grab all the rights we can the JVM - Policy.setPolicy(new Policy() + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - @Override - public PermissionCollection getPermissions(CodeSource codesource) - { - Permissions perms = new Permissions(); - perms.add(new AllPermission()); - return (perms); - } - - @Override - public void refresh() - { - } - }); - + // 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() + { + } + }); } } @@ -204,9 +200,53 @@ public class Jalview */ public static void main(String[] args) { +// setLogging(); // BH - for event debugging in JavaScript 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() + { + + /** + * @j2sIgnore + * + */ + { + System.out.println("not in js"); + } + + // BH - for event debugging in JavaScript (Java mode only) + if (!Platform.isJS()) + /** + * Java only + * + * @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"); + } + } + + + /** * @param args @@ -214,7 +254,7 @@ public class Jalview void doMain(String[] args) { - if (!isJS()) + if (!Platform.isJS()) { System.setSecurityManager(null); } @@ -236,10 +276,11 @@ public class Jalview "CMD [-props " + usrPropsFile + "] executed successfully!"); } + if (!Platform.isJS()) /** - * BH 2018 ignoring this section for JS + * Java only * - * @j2sNative + * @j2sIgnore */ { if (aparser.contains("help") || aparser.contains("h")) @@ -282,9 +323,10 @@ public class Jalview else { System.out.println("Executing setprop argument: " + defs); - // DISABLED FOR SECURITY REASONS - // TODO: add a property to allow properties to be overriden by cli args - // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + if (Platform.isJS()) + { + Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + } } defs = aparser.getValue("setprop"); } @@ -316,7 +358,7 @@ public class Jalview System.err.println("Unexpected Look and Feel Exception"); ex.printStackTrace(); } - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager @@ -364,15 +406,24 @@ public class Jalview if (!headless) { - desktop = new Desktop(); + desktop = new Desktop() +// { +// // BH testing +// @Override +// protected void processEvent(AWTEvent e) { +// System.out.println("Jalview.java " + e); +// super.processEvent(e); +// } +// } + ; desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); + if (!Platform.isJS()) /** - * BH 2018 JS bypass this section - * - * @j2sNative + * Java only * + * @j2sIgnore */ { desktop.startServiceDiscovery(); @@ -432,10 +483,7 @@ public class Jalview FileFormatI format = null; DataSourceType protocol = null; FileLoader fileLoader = new FileLoader(!headless); - Vector getFeatures = null; // vector of das source nicknames to - // fetch - // features from - // loading is done. + String groovyscript = null; // script to execute after all loading is // completed one way or another // extract groovy argument and execute if necessary @@ -545,14 +593,23 @@ public class Jalview } System.out.println("CMD [-open " + file + "] executed successfully!"); - if (!isJS() && !file.startsWith("http://")) + if (!Platform.isJS()) + /** + * ignore in JavaScript -- can't just file existence - could load it? + * + * @j2sIgnore + */ { - if (!(new File(file)).exists()) + if (!file.startsWith("http://") && !file.startsWith("https://")) + // BH 2019 added https check for Java { - System.out.println("Can't find " + file); - if (headless) + if (!(new File(file)).exists()) { - System.exit(1); + System.out.println("Can't find " + file); + if (headless) + { + System.exit(1); + } } } } @@ -582,7 +639,8 @@ public class Jalview data.replaceAll("%20", " "); ColourSchemeI cs = ColourSchemeProperty - .getColourScheme(af.getViewport().getAlignment(), data); + .getColourScheme(af.getViewport(), + af.getViewport().getAlignment(), data); if (cs != null) { @@ -666,27 +724,6 @@ 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 @@ -789,9 +826,14 @@ public class Jalview // And the user // //////////////////// - if (/** @j2sNative false && */ // BH 2018 - !headless && file == null && vamsasImport == null + if (!Platform.isJS() && !headless && file == null + && vamsasImport == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + /** + * Java only + * + * @j2sIgnore + */ { file = jalview.bin.Cache.getDefault("STARTUP_FILE", jalview.bin.Cache.getDefault("www.jalview.org", @@ -830,20 +872,9 @@ public class Jalview 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) { @@ -906,9 +937,6 @@ public class Jalview // (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 @@ -1067,94 +1095,6 @@ public class Jalview } } - /** - * 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; - 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 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() { String isheadless = System.getProperty("java.awt.headless");