X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=28e2ced1d2ccde94fa027564eb09efc4d786f359;hb=418006c3714eb8da78234660698231597eb90fb1;hp=607193317fb359e82ed041342c5ee71581e1be88;hpb=fbb0bb25258ea06802fd971ef94a89687a382996;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 6071933..28e2ced 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -20,11 +20,11 @@
  */
 package jalview.javascript;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
+import jalview.api.JalviewApp;
 import jalview.api.SequenceRenderer;
 import jalview.appletgui.AlignFrame;
-import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolCommands;
 import jalview.structure.AtomSpec;
@@ -76,12 +76,12 @@ public class MouseOverStructureListener extends JSFunctionExec
 
   String _listenerfn;
 
-  String[] modelSet;
+  public String[] modelSet;
 
-  public MouseOverStructureListener(JalviewLite jalviewLite,
-          String listener, String[] modelList)
+  public MouseOverStructureListener(JalviewApp app, String listener,
+          String[] modelList, boolean debug)
   {
-    super(jalviewLite);
+    super(app, debug);
     _listenerfn = listener;
     modelSet = modelList;
     if (modelSet != null)
@@ -165,21 +165,22 @@ public class MouseOverStructureListener extends JSFunctionExec
   }
 
   @Override
-  public synchronized void updateColours(Object srce)
+  public synchronized void updateColours(Object source)
   {
-    final Object source = srce;
     StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(jvlite);
+            .getStructureSelectionManager(
+                    jvlite.getStructureSelectionManagerProvider());
 
-    if (JalviewLite.debug)
+    if (debug)
     {
       System.err.println(
               this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
       ssm.reportMapping();
     }
 
-    if (source instanceof jalview.api.AlignmentViewPanel)
+    if (source instanceof AlignmentViewPanel)
     {
+      AlignmentViewPanel panel = (AlignmentViewPanel) source;
       SequenceI[][] sequence = new SequenceI[modelSet.length][];
       for (int m = 0; m < modelSet.length; m++)
       {
@@ -203,25 +204,20 @@ public class MouseOverStructureListener extends JSFunctionExec
         // }
       }
 
-      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
-              .getSequenceRenderer();
-      FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
-              .isShowSequenceFeatures()
-                      ? new jalview.appletgui.FeatureRenderer(
-                              ((jalview.appletgui.AlignmentPanel) source).av)
-                      : null;
+      SequenceRenderer sr = panel.getSequenceRenderer();
+      AlignViewportI vp = panel.getAlignViewport();
+      jalview.renderer.seqfeatures.FeatureRenderer fr = vp
+              .isShowSequenceFeatures() ? jvlite.getNewFeatureRenderer(vp)
+              : null;
       if (fr != null)
       {
-        ((jalview.appletgui.FeatureRenderer) fr).transferSettings(
-                ((jalview.appletgui.AlignmentPanel) source)
-                        .getFeatureRenderer());
+        fr.transferSettings(panel.getFeatureRenderer());
       }
-      ;
 
       // Form a colour command from the given alignment panel for each distinct
       // structure
-      ArrayList<String[]> ccomands = new ArrayList<String[]>();
-      ArrayList<String> pdbfn = new ArrayList<String>();
+      ArrayList<String[]> ccomands = new ArrayList<>();
+      ArrayList<String> pdbfn = new ArrayList<>();
       StructureMappingcommandSet[] colcommands = JmolCommands
               .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
                       (AlignmentViewPanel) source);
@@ -237,7 +233,6 @@ public class MouseOverStructureListener extends JSFunctionExec
         pdbfn.add(ccset.mapping);
       }
 
-      String mclass, mhandle;
       String ccomandset[] = new String[sz];
       sz = 0;
       for (String[] ccset : ccomands)
@@ -245,28 +240,16 @@ public class MouseOverStructureListener extends JSFunctionExec
         System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
         sz += ccset.length;
       }
-      if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
-              mhandle = ((jalview.appletgui.AlignmentPanel) source).av
-                      .getViewId(),
-              ccomandset))
+      String mclass = "colourstruct";
+      String mhandle = vp.getViewId();
+      if (isJsMessageSetChanged(mclass, mhandle, ccomandset, jvlite))
       {
-        jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
+        setJsMessageSet(mclass, mhandle, ccomandset, jvlite);
         // and notify javascript handler
-        String st[] = new String[] { "colourstruct",
-            "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
+        String st[] = new String[] { mclass, mhandle,
             "" + ccomandset.length, jvlite.arrayToSeparatorList(
                     pdbfn.toArray(new String[pdbfn.size()])) };
-        try
-        {
-          executeJavascriptFunction(true, _listenerfn, st);
-        } catch (Exception ex)
-        {
-          System.err.println("Couldn't execute callback with " + _listenerfn
-                  + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
-                  + "," + st[3] + "}"); // + ","+st[4]+"\n");
-          ex.printStackTrace();
-
-        }
+        executeJavascriptFunction(true, st);
       }
       /*
        * new Thread(new Runnable() { public void run() { // and send to
@@ -283,6 +266,7 @@ public class MouseOverStructureListener extends JSFunctionExec
        */
     }
 
+    jvlite.updateColoursFromMouseOver(source, this);
   }
 
   @Override
@@ -312,4 +296,19 @@ public class MouseOverStructureListener extends JSFunctionExec
     return true;
   }
 
+  public void executeJavascriptFunction(boolean b, String[] st)
+  {
+    try
+    {
+      executeJavascriptFunction(true, _listenerfn, st);
+    } catch (Exception ex)
+    {
+      System.err.println("Couldn't execute callback with " + _listenerfn
+              + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + ","
+              + st[3] + "}"); // + ","+st[4]+"\n");
+      ex.printStackTrace();
+
+    }
+  }
+
 }