X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=da514a21954dfe84495a0904fe447f00e82a7520;hb=ce89ec35928a6cb2f05a655c44c39a0249beb2d6;hp=8e1ede488cc885c3a5f43fa936498b6fb7e967b5;hpb=b4f141d24f090c73e5608214cef2e1dd2c3e21ad;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8e1ede4..da514a2 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -30,6 +30,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.SequenceStructureBinding;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.*;
 import jalview.structure.*;
 import jalview.io.*;
@@ -45,7 +46,7 @@ import jalview.schemes.*;
 
 public abstract class JalviewJmolBinding implements StructureListener,
         JmolStatusListener, SequenceStructureBinding,
-        JmolSelectionListener, ComponentListener
+        JmolSelectionListener, ComponentListener, StructureSelectionManagerProvider
 
 {
   /**
@@ -128,13 +129,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   public SequenceI[][] sequence;
 
-  StructureSelectionManager ssm;
+  public StructureSelectionManager ssm;
 
   public JmolViewer viewer;
 
-  public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+  public JalviewJmolBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           String[][] chains, String protocol)
   {
+    this.ssm = ssm;
     this.sequence = sequenceIs;
     this.chains = chains;
     this.pdbentry = pdbentry;
@@ -152,8 +154,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
      */
   }
 
-  public JalviewJmolBinding(JmolViewer viewer2)
+  public JalviewJmolBinding(StructureSelectionManager ssm, JmolViewer viewer2)
   {
+    this.ssm = ssm;
     viewer = viewer2;
     viewer.setJmolStatusListener(this);
     viewer.addSelectionListener(this);
@@ -227,8 +230,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
     // remove listeners for all structures in viewer
-    StructureSelectionManager.getStructureSelectionManager()
-            .removeStructureViewerListener(this, this.getPdbFile());
+    ssm.removeStructureViewerListener(this, this.getPdbFile());
     // and shut down jmol
     viewer.evalStringQuiet("zap");
     viewer.setJmolStatusListener(null);
@@ -568,7 +570,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     }
     AlignmentI alignment = alignmentv.getAlignment();
 
-    for (String cbyseq : JmolCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment)) {
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq: JmolCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment))
+      for (String cbyseq : cpdbbyseq.commands) {
       evalStateCommand(cbyseq);
     }
   }
@@ -1044,7 +1047,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
     chainFile = new Hashtable();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
-    ssm = StructureSelectionManager.getStructureSelectionManager();
     // first check if we've lost any structures
     if (oldmodels != null && oldmodels.length > 0)
     {
@@ -1532,4 +1534,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
       chains[pe] = null;
     }
   }
+  /**
+   * 
+   * @param pdbfile
+   * @return text report of alignment between pdbfile and any associated alignment sequences
+   */
+  public String printMapping(String pdbfile)
+  {
+    return ssm.printMapping(pdbfile);
+  }
+
 }