Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / appletgui / js / MouseOverStructureListener.java

diff --git a/src/jalview/appletgui/js/MouseOverStructureListener.java b/src/jalview/appletgui/js/MouseOverStructureListener.java
index 7a16009..feac3b1 100644 (file)
--- a/src/jalview/appletgui/js/MouseOverStructureListener.java
+++ b/src/jalview/appletgui/js/MouseOverStructureListener.java
@@ -31,7 +31,6 @@ 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;
 
@@ -221,21 +220,22 @@ public class MouseOverStructureListener extends JSFunctionExec
 
       // 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,
+      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;