JAL-3446 JavaScript interface

- testing with two apps on a page
- now requires Jalview1.getApp().xxxx, not just Jalview1.app, because a
call is needed to ensure that ThreadGroup is set correctly.

- still working on this...

diff --git a/doc/JalviewJS-API.md b/doc/JalviewJS-API.md
index 3386b2a..1302021 100644 (file)
--- a/doc/JalviewJS-API.md
+++ b/doc/JalviewJS-API.md
@@ -1,6 +1,6 @@
-## public interface JalviewJSApi
+# public interface JalviewJSApi
 
-# full list of available methods (from JalviewLiteJsApi):
+## full list of available methods (from JalviewLiteJsApi):
 
   public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
   public String getAlignment(String format);
@@ -67,7 +67,7 @@
   public void showOverview();
   public void updateForAnnotations();
 
-# addition available methods (from JalviewLite):
+## addition available methods (from JalviewLite):
 
   public static String getBuildDate()
   public static String getInstallation()
@@ -75,7 +75,7 @@
 
 
 
-# proposed alias list:
+## proposed alias list:
  
 - remove overloaded methods
 - indicate null options

diff --git a/doc/JalviewJS-startupParams.md b/doc/JalviewJS-startupParams.md
new file mode 100644 (file)
index 0000000..9ff3352
--- /dev/null
+++ b/doc/JalviewJS-startupParams.md
@@ -0,0 +1,92 @@
+## JalviewJS startup parameters
+
+TODO -- go through these
+
+# parameters -- from jalview.bin.AppletParams
+
+  private final static String[] params = { 
+      "alignpdbfiles",
+      "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN",
+      "annotations",
+      "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
+      "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
+      "embedded", "enableSplitFrame", "externalstructureviewer", "features",
+      "file", "file2", "format", "heightScale", "hidefeaturegroups",
+      "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
+      "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
+      "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
+      "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
+      "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
+      "showConsensus", "showConsensusHistogram", "showConservation",
+      "showfeaturegroups", "showFeatureSettings", "showFullId",
+      "showGroupConsensus", "showGroupConservation", "showOccupancy",
+      "showQuality", "showSequenceLogo", "showTreeBootstraps",
+      "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
+      "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
+      "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
+      "wrap", };
+
+
+
+
+# arguments -- from jalview.bin.ArgsParser
+
+  public static final String NOCALCULATION = "nocalculation";
+
+  public static final String NOMENUBAR = "nomenubar";
+
+  public static final String NOSTATUS = "nostatus";
+
+  public static final String SHOWOVERVIEW = "showoverview";
+
+  //
+  public static final String ANNOTATIONS = "annotations";
+
+  public static final String COLOUR = "colour";
+
+  public static final String FEATURES = "features";
+
+  public static final String GROOVY = "groovy";
+
+  public static final String GROUPS = "groups";
+
+  public static final String HEADLESS = "headless";
+
+  public static final String JABAWS = "jabaws";
+
+  public static final String NOANNOTATION = "no-annotation";
+
+  public static final String NOANNOTATION2 = "noannotation"; // BH 2019.05.07
+
+  public static final String NODISPLAY = "nodisplay";
+
+  public static final String NOGUI = "nogui";
+
+  public static final String NONEWS = "nonews";
+
+  public static final String NOQUESTIONNAIRE = "noquestionnaire";
+
+  public static final String NOSORTBYTREE = "nosortbytree";
+
+  public static final String NOUSAGESTATS = "nousagestats";
+
+  public static final String OPEN = "open";
+
+  public static final String OPEN2 = "open2"; // BH added -- for applet
+                                              // compatibility; not fully
+                                              // implemented
+
+  public static final String PROPS = "props";
+
+  public static final String QUESTIONNAIRE = "questionnaire";
+
+  public static final String SETPROP = "setprop";
+
+  public static final String SORTBYTREE = "sortbytree";
+
+  public static final String TREE = "tree";
+
+  public static final String VDOC = "vdoc";
+
+  public static final String VSESS = "vsess";
+

diff --git a/src/jalview/api/JalviewJSApp.java b/src/jalview/api/JalviewJSApp.java
index d6c2ec6..5641295 100644 (file)
--- a/src/jalview/api/JalviewJSApp.java
+++ b/src/jalview/api/JalviewJSApp.java
@@ -65,9 +65,17 @@ public class JalviewJSApp implements JalviewJSApi
                                        // be '|', but many sequence IDS include
                                        // pipes.
 
+  /**
+   * We maintain a pointer to the jalview instance here, because only with that do we have a direct 
+   * connection from the JavaScript "applet" object to the proper instance of Jalview in case there
+   * are multiple applets on a page.
+   */
+  private Jalview jalview;
+
 
-  public JalviewJSApp(ArgsParser aparser)
+  public JalviewJSApp(Jalview jalview, ArgsParser aparser)
   {
+    this.jalview = jalview;
     this.aparser = aparser;
     Platform.setAppClass(this);
   }
@@ -1397,7 +1405,7 @@ public class JalviewJSApp implements JalviewJSApi
 
     try
     {
-      Jalview.getInstance().parseArguments(new ArgsParser(args), false);
+      jalview.parseArguments(new ArgsParser(args), false);
       return null;
     } catch (Throwable t)
     {
@@ -1852,7 +1860,7 @@ public class JalviewJSApp implements JalviewJSApi
    */
   public String doSendCallback(Object callback, Object[] data)
   {
-    Jalview me = Jalview.getInstance();
+    Jalview me = jalview;
 
     if (me != null && callback != null)
     {

diff --git a/src/jalview/bin/AppletParams.java b/src/jalview/bin/AppletParams.java
index a6c87b1..3abaf72 100644 (file)
--- a/src/jalview/bin/AppletParams.java
+++ b/src/jalview/bin/AppletParams.java
@@ -17,8 +17,9 @@ import jalview.gui.Preferences;
 public class AppletParams extends HashMap<String, Object>
 {
 
-  private final static String[] params = { "alignpdbfiles",
-      Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
+  private final static String[] params = { 
+      "alignpdbfiles",
+      "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN",
       "annotations",
       "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
       "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ac44bfe..4819d7a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -822,7 +822,7 @@ public class Jalview implements ApplicationSingletonI
 
         if (isJS)
         {
-          jsApp = new JalviewJSApp(aparser);
+          jsApp = new JalviewJSApp(this, aparser);
           jsApp.load(af);
         }
         else

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 0a6a5c9..b1b6697 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -808,17 +808,17 @@ public class Platform
   {
     if (isJS)
     {
-      jsutil.setAppletAttribute("app", j);
+      jsutil.setAppClass(j);
     }
   }
 
   /**
    *
-   * If this frame ia embedded in a web page, return a known type.
+   * If this frame is embedded in a web page, return a known type.
    * 
    * @param frame
    *          a JFrame or JInternalFrame
-   * @param type
+   * @param type "name", "node", "init", "dim", or any DOM attribute, such as "id"
    * @return null if frame is not embedded.
    */
   public static Object getEmbeddedAttribute(Component frame, String type)

diff --git a/src/swingjs/api/JSUtilI.java b/src/swingjs/api/JSUtilI.java
index cc4f8d4..322ec83 100644 (file)
--- a/src/swingjs/api/JSUtilI.java
+++ b/src/swingjs/api/JSUtilI.java
@@ -348,4 +348,7 @@ public interface JSUtilI {
         */
        Map<String, Object> getAppletInfoAsMap();
 
+       
+  void setAppClass(Object j);
+
 }

diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 2a6782d..90ec5a2 100644 (file)
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ

diff --git a/swingjs/timestamp b/swingjs/timestamp
index 05d031a..5cb9ccc 100644 (file)
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20200605004905 
+20200606223527 

diff --git a/swingjs/ver/3.2.9-j11/SwingJS-site.zip b/swingjs/ver/3.2.9-j11/SwingJS-site.zip
index ea5d1e0..2a6782d 100644 (file)
Binary files a/swingjs/ver/3.2.9-j11/SwingJS-site.zip and b/swingjs/ver/3.2.9-j11/SwingJS-site.zip differ

diff --git a/swingjs/ver/3.2.9-j11/timestamp b/swingjs/ver/3.2.9-j11/timestamp
index b21d6d8..129de41 100644 (file)
--- a/swingjs/ver/3.2.9-j11/timestamp
+++ b/swingjs/ver/3.2.9-j11/timestamp
@@ -1 +1 @@
-20200604081344 
+20200606151807 

diff --git a/swingjs/ver/3.2.9/SwingJS-site.zip b/swingjs/ver/3.2.9/SwingJS-site.zip
index 2a6782d..90ec5a2 100644 (file)
Binary files a/swingjs/ver/3.2.9/SwingJS-site.zip and b/swingjs/ver/3.2.9/SwingJS-site.zip differ

diff --git a/swingjs/ver/3.2.9/timestamp b/swingjs/ver/3.2.9/timestamp
index 05d031a..5cb9ccc 100644 (file)
--- a/swingjs/ver/3.2.9/timestamp
+++ b/swingjs/ver/3.2.9/timestamp
@@ -1 +1 @@
-20200605004905 
+20200606223527