added comment to @gmungoc todo about referencing PDB entities in Javascript - also...

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

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 8a32c5b..cd70291 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -150,8 +150,13 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     {
       try
       {
+        // TODO is this right? StructureSelectionManager passes pdbFile as the
+        // field that is interpreted (in 2.8.2) as pdbId?
+        // 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.getPdbId(), "" + atom.getChain(),
+        { "mouseover", "" + atom.getPdbFile(),
+                    "" + atom.getChain(),
             "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
       } catch (Exception ex)
       {
@@ -200,7 +205,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
               .getSequenceRenderer();
       FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
-              .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
+              .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
               ((jalview.appletgui.AlignmentPanel) source).av) : null;
       if (fr != null)
       {