X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalview.java;h=9da666bf4e78b80f45dadefe516fd580b68b97b3;hb=0eb1ca5fbc6e21ae91e8d80a1bfa2b95f2957bd3;hp=cd7d1af2e82009f1f5e52137250b4facab8bc9bf;hpb=1cb8662ae0ce8b7c29fa510809a6e883c769dcdc;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cd7d1af..9da666b 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,10 +20,17 @@
  */
 package jalview.bin;
 
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.ext.ensembl.EnsemblInfo;
 import jalview.ext.so.SequenceOntology;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.uniprot.UniProtFTSRestClient;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
+import jalview.httpserver.HttpServer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
@@ -35,12 +42,23 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.rest.RestHandler;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
+import jalview.ws.rest.RestClient;
+import jalview.ws.sifts.SiftsSettings;
 
+import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -58,8 +76,12 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
+import java.util.IdentityHashMap;
 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;
@@ -84,33 +106,100 @@ import groovy.util.GroovyScriptEngine;
  */
 public class Jalview
 {
-  /*
-   * singleton instance of this class
+
+  public Jalview()
+  {
+    setInstance(this);
+  }
+
+  static
+  {
+    Platform.getURLCommandArguments();
+  }
+
+  private boolean headless;
+
+  public static boolean isHeadlessMode()
+  {
+    return getInstance().headless;
+  }
+
+  /**
+   * singleton instance of this class in Java only
    */
+
   private static Jalview instance;
 
+  public static Jalview getInstance()
+  {
+    if (instance == null)
+    {
+      instance = new Jalview();
+    }
+    Jalview j;
+    @SuppressWarnings("unused")
+    ThreadGroup g = Thread.currentThread().getThreadGroup();
+    /**
+     * @j2sNative j = g._jalviewInstance;
+     */
+    {
+      j = instance;
+    }
+    return j;
+  }
+
+  private static void setInstance(Jalview j)
+  {
+    @SuppressWarnings("unused")
+    ThreadGroup g = Thread.currentThread().getThreadGroup();
+    /**
+     * @j2sNative g._jalviewInstance = j;
+     */
+    {
+      instance = j;
+    }
+  }
+
   private Desktop desktop;
 
-  public static AlignFrame currentAlignFrame;
+  private AlignFrame currentAlignFrame;
+
+  public static AlignFrame getCurrentAlignFrame()
+  {
+    return getInstance().currentAlignFrame;
+  }
+
+  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  {
+    getInstance().currentAlignFrame = currentAlignFrame;
+  }
 
   static
   {
-    // grab all the rights we can the JVM
-    Policy.setPolicy(new Policy()
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      @Override
-      public PermissionCollection getPermissions(CodeSource codesource)
+      // grab all the rights we can for the JVM
+      Policy.setPolicy(new Policy()
       {
-        Permissions perms = new Permissions();
-        perms.add(new AllPermission());
-        return (perms);
-      }
+        @Override
+        public PermissionCollection getPermissions(CodeSource codesource)
+        {
+          Permissions perms = new Permissions();
+          perms.add(new AllPermission());
+          return (perms);
+        }
 
-      @Override
-      public void refresh()
-      {
-      }
-    });
+        @Override
+        public void refresh()
+        {
+        }
+      });
+    }
   }
 
   /**
@@ -172,11 +261,6 @@ public class Jalview
 
   }
 
-  public static Jalview getInstance()
-  {
-    return instance;
-  }
-
   /**
    * main class for Jalview application
    * 
@@ -185,8 +269,49 @@ public class Jalview
    */
   public static void main(String[] args)
   {
-    instance = new Jalview();
-    instance.doMain(args);
+    // setLogging(); // BH - for event debugging in JavaScript
+    new Jalview();
+    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);
+  }
+
+  @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");
+    }
+
   }
 
   /**
@@ -194,7 +319,12 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-    System.setSecurityManager(null);
+
+    if (!Platform.isJS())
+    {
+      System.setSecurityManager(null);
+    }
+
     System.out
             .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
@@ -202,45 +332,55 @@ public class Jalview
             + System.getProperty("os.version"));
 
     ArgsParser aparser = new ArgsParser(args);
-    boolean headless = false;
 
-    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;
-    }
-    String usrPropsFile = aparser.getValue("props");
-    Cache.loadProperties(usrPropsFile); // must do this before
+    String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
+    Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
       System.out.println(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
 
-    // anything else!
-
-    final String jabawsUrl = aparser.getValue("jabaws");
-    if (jabawsUrl != null)
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      try
+      if (aparser.contains("help") || aparser.contains("h"))
       {
-        Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-        System.out.println(
-                "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
-      } catch (MalformedURLException e)
+        showUsage();
+        System.exit(0);
+      }
+      if (aparser.contains(ArgsParser.NODISPLAY)
+              || aparser.contains(ArgsParser.NOGUI)
+              || aparser.contains(ArgsParser.HEADLESS)
+              || "true".equals(System.getProperty("java.awt.headless")))
       {
-        System.err.println(
-                "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        headless = true;
       }
-    }
 
-    String defs = aparser.getValue("setprop");
+      // anything else!
+
+      final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
+      if (jabawsUrl != null)
+      {
+        try
+        {
+          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          System.out.println(
+                  "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+        } catch (MalformedURLException e)
+        {
+          System.err.println(
+                  "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        }
+      }
+
+    }
+    // check for property setting
+    String defs = aparser.getValue(ArgsParser.SETPROP);
     while (defs != null)
     {
       int p = defs.indexOf('=');
@@ -251,16 +391,12 @@ 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");
-    }
-    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"));
@@ -285,7 +421,7 @@ 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
@@ -304,8 +440,9 @@ 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"))
       {
@@ -336,75 +473,85 @@ public class Jalview
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
-      desktop.startServiceDiscovery();
-      if (!aparser.contains("nousagestats"))
-      {
-        startUsageStats(desktop);
-      }
-      else
-      {
-        System.err.println("CMD [-nousagestats] executed successfully!");
-      }
 
-      if (!aparser.contains("noquestionnaire"))
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
       {
-        String url = aparser.getValue("questionnaire");
-        if (url != null)
+        desktop.startServiceDiscovery();
+        if (!aparser.contains(ArgsParser.NOUSAGESTATS))
         {
-          // Start the desktop questionnaire prompter with the specified
-          // questionnaire
-          Cache.log.debug("Starting questionnaire url at " + url);
-          desktop.checkForQuestionnaire(url);
-          System.out.println(
-                  "CMD questionnaire[-" + url + "] executed successfully!");
+          startUsageStats(desktop);
         }
         else
         {
-          if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+          System.err.println("CMD [-nousagestats] executed successfully!");
+        }
+
+        if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+        {
+          String url = aparser.getValue(ArgsParser.QUESTIONNAIRE);
+          if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            // String defurl =
-            // "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);
-            desktop.checkForQuestionnaire(defurl);
+            Cache.log.debug("Starting questionnaire url at " + url);
+            desktop.checkForQuestionnaire(url);
+            System.out.println("CMD questionnaire[-" + url
+                    + "] executed successfully!");
+          }
+          else
+          {
+            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            {
+              // Start the desktop questionnaire prompter with the specified
+              // questionnaire
+              // String defurl =
+              // "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);
+              desktop.checkForQuestionnaire(defurl);
+            }
           }
         }
-      }
-      else
-      {
-        System.err.println("CMD [-noquestionnaire] executed successfully!");
-      }
+        else
+        {
+          System.err
+                  .println("CMD [-noquestionnaire] executed successfully!");
+        }
 
-      if (!aparser.contains("nonews"))
-      {
-        desktop.checkForNews();
-      }
+        if (!aparser.contains(ArgsParser.NONEWS))
+        {
+          desktop.checkForNews();
+        }
 
-      BioJsHTMLOutput.updateBioJS();
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
-    String file = null, data = null;
+    String 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 = aparser.getValue(ArgsParser.GROOVY, true);
+    String file = aparser.getValue(ArgsParser.OPEN, true);
 
     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");
+    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
+    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
     if (vamsasImport != null || vamsasSession != null)
     {
       if (desktop == null || headless)
@@ -501,14 +648,24 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!file.startsWith("http://"))
+      if (!Platform.isJS())
+      /**
+       * ignore in JavaScript -- can't just check 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);
+            }
           }
         }
       }
@@ -532,13 +689,13 @@ public class Jalview
       else
       {
         setCurrentAlignFrame(af);
-        data = aparser.getValue("colour", true);
+        data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport().getAlignment(), data);
+          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                  af.getViewport(), af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {
@@ -549,7 +706,7 @@ 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,
@@ -558,7 +715,7 @@ 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,
@@ -568,7 +725,7 @@ 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);
@@ -577,7 +734,7 @@ 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())
@@ -585,7 +742,8 @@ 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())
@@ -593,7 +751,7 @@ 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())
@@ -602,7 +760,7 @@ public class Jalview
                     .println("CMD [-nosortbytree] executed successfully!");
           }
         }
-        data = aparser.getValue("tree", true);
+        data = aparser.getValue(ArgsParser.TREE, true);
         if (data != null)
         {
           try
@@ -635,6 +793,10 @@ public class Jalview
         String imageName = "unnamed.png";
         while (aparser.getSize() > 1)
         {
+          // PNG filename
+          // SVG filename
+          // HTML filename
+          // biojsmsa filename
           String outputFormat = aparser.nextValue();
           file = aparser.nextValue();
 
@@ -699,7 +861,8 @@ public class Jalview
             continue;
           }
 
-          if (af.saveAlignment(file, format))
+          af.saveAlignment(file, format);
+          if (af.isSaveAlignmentSuccessful())
           {
             System.out.println("Written alignment in " + format
                     + " format to " + file);
@@ -723,8 +886,14 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!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",
@@ -828,9 +997,6 @@ 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
@@ -845,8 +1011,9 @@ 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)",
@@ -989,16 +1156,6 @@ 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() }
@@ -1022,13 +1179,46 @@ public class Jalview
     }
   }
 
-  public static AlignFrame getCurrentAlignFrame()
-  {
-    return Jalview.currentAlignFrame;
-  }
+  // singleton instances
+
+  public Cache cache;
+
+  public AlignmentSorter alignmentSorter;
+
+  public EnsemblInfo ensemblInfo;
+
+  public HttpServer httpServer;
+
+  public IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> structureSelections;
+
+  public PDBFTSRestClient pdbFTSRestClient;
+
+  public RestHandler restHandler;
+
+  public ScoreModels scoreModels;
+
+  public SequenceFetcher sequenceFetcher;
+
+  public SequenceOntologyI sequenceOntology;
+
+  public UniProtFTSRestClient uniprotFTSRestClient;
+
+  public StructureSelectionManager nullProvider;
+
+  public Color[] rnaHelices = null;
+
+  public StructureImportSettings structureImportSettings;
+
+  public IdOrgSettings idOrgSettings;
+
+  public SiftsSettings siftsSettings;
+
+  public RestClient restClient;
+
+  public Jws2Discoverer j2s2discoverer;
+
+  public Jws2InstanceFactory jws2InstanceFactory;
+
+  public Discoverer discoverer;
 
-  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
-  {
-    Jalview.currentAlignFrame = currentAlignFrame;
-  }
 }