X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=28e2ced1d2ccde94fa027564eb09efc4d786f359;hb=0b6324afbf67fd0fc672b60f4f4988e6e1f4390e;hp=e25f47c0a33166e0bc5d8987d84cd498c75c36c5;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index e25f47c..28e2ced 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -70,18 +70,18 @@ import java.util.List;
  * @author Jim Procter (jprocter)
  * 
  */
-public class MouseOverStructureListener extends JSFunctionExec implements
-        JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+        implements JsCallBack, StructureListener
 {
 
   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)
@@ -126,7 +126,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return modelSet;
   }
@@ -152,9 +152,9 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // JBPComment: yep - this is right! the Javascript harness uses the
         // absolute pdbFile URI to locate the PDB file in the external viewer
         executeJavascriptFunction(_listenerfn,
-                new String[] { "mouseover", "" + atom.getPdbFile(),
-                    "" + atom.getChain(), "" + (atom.getPdbResNum()),
-                    "" + atom.getAtomIndex() });
+                new String[]
+                { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
+                    "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
       } catch (Exception ex)
       {
         System.err.println("Couldn't execute callback with " + _listenerfn
@@ -165,21 +165,22 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @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]);
+      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++)
       {
@@ -203,26 +204,23 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // }
       }
 
-      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, fr,
-                      ((AlignmentViewPanel) source).getAlignment());
+              .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+                      (AlignmentViewPanel) source);
       if (colcommands == null)
       {
         return;
@@ -235,7 +233,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         pdbfn.add(ccset.mapping);
       }
 
-      String mclass, mhandle;
       String ccomandset[] = new String[sz];
       sz = 0;
       for (String[] ccset : ccomands)
@@ -243,30 +240,16 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         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(),
-            "" + 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();
-
-        }
+        String st[] = new String[] { mclass, mhandle,
+            "" + ccomandset.length, jvlite.arrayToSeparatorList(
+                    pdbfn.toArray(new String[pdbfn.size()])) };
+        executeJavascriptFunction(true, st);
       }
       /*
        * new Thread(new Runnable() { public void run() { // and send to
@@ -283,6 +266,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
        */
     }
 
+    jvlite.updateColoursFromMouseOver(source, this);
   }
 
   @Override
@@ -298,12 +282,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
-  {
-    jvlite = null;
-    super.finalize();
-  }
-
   @Override
   public void releaseReferences(Object svl)
   {
@@ -318,4 +296,19 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     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();
+
+    }
+  }
+
 }