JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / javascript / MouseOverStructureListener.java

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 28e2ced..6071933 100644 (file)
--- 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.JalviewApp;
+import jalview.api.FeatureRenderer;
 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;
 
-  public String[] modelSet;
+  String[] modelSet;
 
-  public MouseOverStructureListener(JalviewApp app, String listener,
-          String[] modelList, boolean debug)
+  public MouseOverStructureListener(JalviewLite jalviewLite,
+          String listener, String[] modelList)
   {
-    super(app, debug);
+    super(jalviewLite);
     _listenerfn = listener;
     modelSet = modelList;
     if (modelSet != null)
@@ -165,22 +165,21 @@ public class MouseOverStructureListener extends JSFunctionExec
   }
 
   @Override
-  public synchronized void updateColours(Object source)
+  public synchronized void updateColours(Object srce)
   {
+    final Object source = srce;
     StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(
-                    jvlite.getStructureSelectionManagerProvider());
+            .getStructureSelectionManager(jvlite);
 
-    if (debug)
+    if (JalviewLite.debug)
     {
       System.err.println(
               this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
       ssm.reportMapping();
     }
 
-    if (source instanceof AlignmentViewPanel)
+    if (source instanceof jalview.api.AlignmentViewPanel)
     {
-      AlignmentViewPanel panel = (AlignmentViewPanel) source;
       SequenceI[][] sequence = new SequenceI[modelSet.length][];
       for (int m = 0; m < modelSet.length; m++)
       {
@@ -204,20 +203,25 @@ public class MouseOverStructureListener extends JSFunctionExec
         // }
       }
 
-      SequenceRenderer sr = panel.getSequenceRenderer();
-      AlignViewportI vp = panel.getAlignViewport();
-      jalview.renderer.seqfeatures.FeatureRenderer fr = vp
-              .isShowSequenceFeatures() ? jvlite.getNewFeatureRenderer(vp)
-              : null;
+      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;
       if (fr != null)
       {
-        fr.transferSettings(panel.getFeatureRenderer());
+        ((jalview.appletgui.FeatureRenderer) fr).transferSettings(
+                ((jalview.appletgui.AlignmentPanel) source)
+                        .getFeatureRenderer());
       }
+      ;
 
       // Form a colour command from the given alignment panel for each distinct
       // structure
-      ArrayList<String[]> ccomands = new ArrayList<>();
-      ArrayList<String> pdbfn = new ArrayList<>();
+      ArrayList<String[]> ccomands = new ArrayList<String[]>();
+      ArrayList<String> pdbfn = new ArrayList<String>();
       StructureMappingcommandSet[] colcommands = JmolCommands
               .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
                       (AlignmentViewPanel) source);
@@ -233,6 +237,7 @@ public class MouseOverStructureListener extends JSFunctionExec
         pdbfn.add(ccset.mapping);
       }
 
+      String mclass, mhandle;
       String ccomandset[] = new String[sz];
       sz = 0;
       for (String[] ccset : ccomands)
@@ -240,16 +245,28 @@ public class MouseOverStructureListener extends JSFunctionExec
         System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
         sz += ccset.length;
       }
-      String mclass = "colourstruct";
-      String mhandle = vp.getViewId();
-      if (isJsMessageSetChanged(mclass, mhandle, ccomandset, jvlite))
+      if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
+              mhandle = ((jalview.appletgui.AlignmentPanel) source).av
+                      .getViewId(),
+              ccomandset))
       {
-        setJsMessageSet(mclass, mhandle, ccomandset, jvlite);
+        jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
         // and notify javascript handler
-        String st[] = new String[] { mclass, mhandle,
+        String st[] = new String[] { "colourstruct",
+            "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
             "" + ccomandset.length, jvlite.arrayToSeparatorList(
                     pdbfn.toArray(new String[pdbfn.size()])) };
-        executeJavascriptFunction(true, 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();
+
+        }
       }
       /*
        * new Thread(new Runnable() { public void run() { // and send to
@@ -266,7 +283,6 @@ public class MouseOverStructureListener extends JSFunctionExec
        */
     }
 
-    jvlite.updateColoursFromMouseOver(source, this);
   }
 
   @Override
@@ -296,19 +312,4 @@ 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();
-
-    }
-  }
-
 }