Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 4f833bc..e79106d 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -30,7 +30,6 @@ import jalview.ext.jmol.JmolCommands;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 
@@ -70,8 +69,8 @@ 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;
@@ -126,7 +125,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return modelSet;
   }
@@ -152,13 +151,13 @@ 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
-                + " for atomSpec: " + atom);
+        jalview.bin.Console.errPrintln("Couldn't execute callback with "
+                + _listenerfn + " for atomSpec: " + atom);
         ex.printStackTrace();
       }
     }
@@ -173,8 +172,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
 
     if (JalviewLite.debug)
     {
-      System.err.println(this.getClass().getName() + " modelSet[0]: "
-              + modelSet[0]);
+      jalview.bin.Console.errPrintln(
+              this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
       ssm.reportMapping();
     }
 
@@ -198,7 +197,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         }
         // if (jvlite.debug)
         // {
-        // System.err.println("Mapped '" + modelSet[m] + "' to "
+        // jalview.bin.Console.errPrintln("Mapped '" + modelSet[m] + "' to "
         // + sequence[m].length + " sequences.");
         // }
       }
@@ -206,33 +205,35 @@ 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;
+              .isShowSequenceFeatures()
+                      ? new jalview.appletgui.FeatureRenderer(
+                              ((jalview.appletgui.AlignmentPanel) source).av)
+                      : null;
       if (fr != null)
       {
-        ((jalview.appletgui.FeatureRenderer) fr)
-                .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+        ((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<String[]>();
-      ArrayList<String> pdbfn = new ArrayList<String>();
-      StructureMappingcommandSet[] colcommands = JmolCommands
-              .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
-                      ((AlignmentViewPanel) source).getAlignment());
+      ArrayList<String[]> ccomands = new ArrayList<>();
+      ArrayList<String> pdbfn = new ArrayList<>();
+      String[] colcommands = new JmolCommands().colourBySequence(ssm,
+              modelSet, sequence, sr, (AlignmentViewPanel) source);
       if (colcommands == null)
       {
         return;
       }
       int sz = 0;
-      for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      // for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      for (String command : colcommands)
       {
-        sz += ccset.commands.length;
-        ccomands.add(ccset.commands);
-        pdbfn.add(ccset.mapping);
+        // sz += ccset.commands.length;
+        // ccomands.add(command); // ccset.commands);
+        // pdbfn.add(ccset.mapping);
       }
 
       String mclass, mhandle;
@@ -243,25 +244,23 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
         sz += ccset.length;
       }
-      if (jvlite.isJsMessageSetChanged(
-              mclass = "colourstruct",
+      if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
               mhandle = ((jalview.appletgui.AlignmentPanel) source).av
-                      .getViewId(), ccomandset))
+                      .getViewId(),
+              ccomandset))
       {
         jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
         // and notify javascript handler
-        String st[] = new String[] {
-            "colourstruct",
+        String st[] = new String[] { "colourstruct",
             "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
-            "" + ccomandset.length,
-            jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
-                    .size()])) };
+            "" + 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 "
+          jalview.bin.Console.errPrintln("Couldn't execute callback with "
                   + _listenerfn + " using args { " + st[0] + ", " + st[1]
                   + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
           ex.printStackTrace();
@@ -275,7 +274,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
        * executeJavascriptFunction( false, _listenerfn, st = new String[] {
        * "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
        * .getViewId(), handle, "" }); } catch (Exception ex) {
-       * System.err.println("Couldn't execute callback with " + _listenerfn +
+       * jalview.bin.Console.errPrintln("Couldn't execute callback with " + _listenerfn +
        * " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
        * "\n"); ex.printStackTrace();
        * 
@@ -298,12 +297,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalize() throws Throwable
-  {
-    jvlite = null;
-    super.finalize();
-  }
-
   @Override
   public void releaseReferences(Object svl)
   {