X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=fdf00c0fa867e603d542489166509c336dff9b3c;hb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;hp=62f4d1317c5b822250f0016e04f62deeec435530;hpb=57dc00f8b62b404e14bd7e689ecc510ab24aeecf;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 62f4d13..fdf00c0 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -116,7 +116,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
     // / TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
-    jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+    jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
 
     jmb.setLoadingFromArchive(true);
     addAlignmentPanel(ap);
@@ -233,8 +233,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     progressBar = ap.alignFrame;
     // ////////////////////////////////
     // Is the pdb file already loaded?
-    String alreadyMapped = StructureSelectionManager
-            .getStructureSelectionManager().alreadyMappedToFile(
+    String alreadyMapped = jmb.ssm.alreadyMappedToFile(
                     pdbentry.getId());
 
     if (alreadyMapped != null)
@@ -247,8 +246,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
       if (option == JOptionPane.YES_OPTION)
       {
-        StructureSelectionManager.getStructureSelectionManager()
-                .setMapping(seq, chains, alreadyMapped,
+        jmb.ssm.setMapping(seq, chains, alreadyMapped,
                         AppletFormatAdapter.FILE);
         if (ap.seqPanel.seqCanvas.fr != null)
         {
@@ -309,7 +307,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     }
     // /////////////////////////////////
 
-    jmb = new AppJmolBinding(this, new PDBEntry[]
+    jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
     { pdbentry }, new SequenceI[][]
     { seq }, null, null);
     addAlignmentPanel(ap);
@@ -868,8 +866,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
       for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
       {
-        cap.appendText(StructureSelectionManager
-                .getStructureSelectionManager().printMapping(
+        cap.appendText(jmb.printMapping(
                         jmb.pdbentry[pdbe].getFile()));
         cap.appendText("\n");
       }