X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=84fec4569df2aad30c78c0ea9171e28f16861235;hp=ac6fcd666b8c8168915f461fea6dcbb8334d40b9;hb=418006c3714eb8da78234660698231597eb90fb1;hpb=fbb0bb25258ea06802fd971ef94a89687a382996

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ac6fcd6..84fec45 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,14 +20,20 @@
  */
 package jalview.bin;
 
+import jalview.api.AlignFrameI;
 import jalview.api.AlignViewportI;
 import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+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.Desktop;
 import jalview.gui.Preferences;
 import jalview.gui.PromptUserConfig;
@@ -44,13 +50,19 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
+import jalview.javascript.JSFunctionExec;
 import jalview.javascript.JalviewLiteJsApi;
+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 java.applet.AppletContext;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -68,6 +80,7 @@ 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;
@@ -79,6 +92,7 @@ import javax.swing.UIManager;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
 
 /**
  * Main class for Jalview Application <br>
@@ -128,6 +142,10 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 
   public String appletResourcePath;
 
+  private JalviewAppLoader appLoader;
+
+  protected JSFunctionExec jsFunctionExec;
+
   public static AlignFrame getCurrentAlignFrame()
   {
     return getInstance().currentAlignFrame;
@@ -1226,6 +1244,12 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
    */
   public void quit()
   {
+    if (jsFunctionExec != null)
+    {
+      jsFunctionExec.tidyUp();
+      jsFunctionExec = null;
+    }
+
     if (desktop != null)
     {
       desktop.quit();
@@ -1266,6 +1290,10 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 
       private boolean alignPDBStructures; // From JalviewLite; not implemented
 
+      private Hashtable<String, Hashtable<String, String[]>> jsmessages;
+
+      private Hashtable<String, int[]> jshashes;
+
       @Override
       public String getParameter(String name)
       {
@@ -1377,9 +1405,112 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
                 "Jalview applet interface newFeatureSettings not implemented");
       }
 
+      private Vector<Runnable> jsExecQueue;
+
+      @Override
+      public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
+      {
+        jsFunctionExec = exec;
+        return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
+                : jsExecQueue);
+      }
+
+      @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 Auto-generated method stub
+        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)
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      public String arrayToSeparatorList(String[] array)
+      {
+        return appLoader.arrayToSeparatorList(array);
+      }
+
+      @Override
+      public Hashtable<String, int[]> getJSHashes()
+      {
+        return (jshashes == null
+                ? (jshashes = new Hashtable<>())
+                : jshashes);
+      }
+
+      @Override
+      public Hashtable<String, Hashtable<String, String[]>> 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);
+      }
+
     };
 
-    new JalviewAppLoader(true).load(app);
+    appLoader = new JalviewAppLoader(true);
+    appLoader.load(app);
   }
 
   @Override
@@ -1397,14 +1528,14 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf)
+  public String getSelectedSequencesFrom(AlignFrameI alf)
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf,
+  public String getSelectedSequencesFrom(AlignFrameI alf,
           String sep)
   {
     // TODO Auto-generated method stub
@@ -1420,7 +1551,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void highlightIn(jalview.appletgui.AlignFrame alf,
+  public void highlightIn(AlignFrameI alf,
           String sequenceId, String position, String alignedPosition)
   {
     // TODO Auto-generated method stub
@@ -1442,7 +1573,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
+  public void selectIn(AlignFrameI alf, String sequenceIds,
           String columns)
   {
     // TODO Auto-generated method stub
@@ -1450,7 +1581,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
+  public void selectIn(AlignFrameI alf, String sequenceIds,
           String columns, String sep)
   {
     // TODO Auto-generated method stub
@@ -1467,7 +1598,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 
   @Override
   public String getSelectedSequencesAsAlignmentFrom(
-          jalview.appletgui.AlignFrame alf, String format, String suffix)
+          AlignFrameI alf, String format, String suffix)
   {
     // TODO Auto-generated method stub
     return null;
@@ -1481,14 +1612,14 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf)
+  public String getAlignmentOrderFrom(AlignFrameI alf)
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf,
+  public String getAlignmentOrderFrom(AlignFrameI alf,
           String sep)
   {
     // TODO Auto-generated method stub
@@ -1510,7 +1641,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String orderAlignmentBy(jalview.appletgui.AlignFrame alf,
+  public String orderAlignmentBy(AlignFrameI alf,
           String order, String undoName, String sep)
   {
     // TODO Auto-generated method stub
@@ -1525,7 +1656,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
+  public String getAlignmentFrom(AlignFrameI alf,
           String format)
   {
     // TODO Auto-generated method stub
@@ -1540,7 +1671,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
+  public String getAlignmentFrom(AlignFrameI alf,
           String format, String suffix)
   {
     // TODO Auto-generated method stub
@@ -1555,7 +1686,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void loadAnnotationFrom(jalview.appletgui.AlignFrame alf,
+  public void loadAnnotationFrom(AlignFrameI alf,
           String annotation)
   {
     // TODO Auto-generated method stub
@@ -1570,7 +1701,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public boolean loadFeaturesFrom(jalview.appletgui.AlignFrame alf,
+  public boolean loadFeaturesFrom(AlignFrameI alf,
           String features, boolean autoenabledisplay)
   {
     // TODO Auto-generated method stub
@@ -1585,7 +1716,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getFeaturesFrom(jalview.appletgui.AlignFrame alf,
+  public String getFeaturesFrom(AlignFrameI alf,
           String format)
   {
     // TODO Auto-generated method stub
@@ -1600,44 +1731,42 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getAnnotationFrom(jalview.appletgui.AlignFrame alf)
+  public String getAnnotationFrom(AlignFrameI alf)
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newView()
+  public AlignFrameI newView()
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newView(String name)
+  public AlignFrameI newView(String name)
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newViewFrom(
-          jalview.appletgui.AlignFrame alf)
+  public AlignFrameI newViewFrom(AlignFrameI alf)
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newViewFrom(
-          jalview.appletgui.AlignFrame alf, String name)
+  public AlignFrameI newViewFrom(AlignFrameI alf, String name)
   {
     // TODO Auto-generated method stub
     return null;
   }
 
   @Override
-  public jalview.appletgui.AlignFrame loadAlignment(String text,
+  public AlignFrameI loadAlignment(String text,
           String title)
   {
     // TODO Auto-generated method stub
@@ -1652,7 +1781,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void setMouseoverListener(jalview.appletgui.AlignFrame af,
+  public void setMouseoverListener(AlignFrameI af,
           String listener)
   {
     // TODO Auto-generated method stub
@@ -1667,7 +1796,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void setSelectionListener(jalview.appletgui.AlignFrame af,
+  public void setSelectionListener(AlignFrameI af,
           String listener)
   {
     // TODO Auto-generated method stub
@@ -1682,7 +1811,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void removeJavascriptListener(jalview.appletgui.AlignFrame af,
+  public void removeJavascriptListener(AlignFrameI af,
           String listener)
   {
     // TODO Auto-generated method stub
@@ -1698,7 +1827,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public boolean addPdbFile(jalview.appletgui.AlignFrame alFrame,
+  public boolean addPdbFile(AlignFrameI alFrame,
           String sequenceId, String pdbEntryString, String pdbFile)
   {
     // TODO Auto-generated method stub
@@ -1706,7 +1835,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void scrollViewToIn(jalview.appletgui.AlignFrame alf,
+  public void scrollViewToIn(AlignFrameI alf,
           String topRow, String leftHandColumn)
   {
     // TODO Auto-generated method stub
@@ -1714,7 +1843,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void scrollViewToRowIn(jalview.appletgui.AlignFrame alf,
+  public void scrollViewToRowIn(AlignFrameI alf,
           String topRow)
   {
     // TODO Auto-generated method stub
@@ -1722,7 +1851,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void scrollViewToColumnIn(jalview.appletgui.AlignFrame alf,
+  public void scrollViewToColumnIn(AlignFrameI alf,
           String leftHandColumn)
   {
     // TODO Auto-generated method stub
@@ -1737,7 +1866,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getFeatureGroupsOn(jalview.appletgui.AlignFrame alf)
+  public String getFeatureGroupsOn(AlignFrameI alf)
   {
     // TODO Auto-generated method stub
     return null;
@@ -1751,7 +1880,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public String getFeatureGroupsOfStateOn(jalview.appletgui.AlignFrame alf,
+  public String getFeatureGroupsOfStateOn(AlignFrameI alf,
           boolean visible)
   {
     // TODO Auto-generated method stub
@@ -1759,7 +1888,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   }
 
   @Override
-  public void setFeatureGroupStateOn(jalview.appletgui.AlignFrame alf,
+  public void setFeatureGroupStateOn(AlignFrameI alf,
           String groups, boolean state)
   {
     // TODO Auto-generated method stub