X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=3f5a436e27418d60274296b0e74cb8fc0c8dc904;hp=c1035bd4255f95ca0d6dd9984623c86e5c0fdece;hb=refs%2Fheads%2Fj2s%2Fdevelop-bh;hpb=c07eb2c5794833bd0241000d6844d783fe10cb82

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index c1035bd..3f5a436 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -25,7 +25,10 @@ import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.ext.jmol.JalviewJmolBinding;
+//import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
 
 import java.awt.Container;
 import java.util.ArrayList;
@@ -33,8 +36,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
+//import org.jmol.api.JmolAppConsoleInterface;
+//import org.jmol.java.BS;
 import org.jmol.viewer.Viewer;
 
 /**
@@ -43,165 +46,195 @@ import org.jmol.viewer.Viewer;
  * @author JimP
  * 
  */
-public class ExtJmol extends JalviewJmolBinding
+public class ExtJmol  extends AAStructureBindingModel //extends JalviewJmolBinding
 {
 
-  private AlignmentPanel ap;
-
-  protected ExtJmol(jalview.appletgui.AlignFrame alframe,
-          PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
-          String protocol)
-  {
-    super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
-            chains, protocol);
-  }
-
-  public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
-          SequenceI[][] seqs)
-  {
-    super(alignPanel.getStructureSelectionManager(), seqs, viewer);
-    ap = alignPanel;
-    notifyFileLoaded(null, null, null, null, 0);
-  }
-
-  public void updateColours(Object source)
-  {
-
-    // TODO Auto-generated method stub
-
-  }
-
-  public void showUrl(String arg0)
-  {
-    showUrl(arg0, "jmol");
-  }
-
-  @Override
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      return ap.getFeatureRenderer();
-    }
-    else
-    {
-      return null;
-    }
-  }
-
-  @Override
-  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
-  {
-    return ((AlignmentPanel) alignment).getSequenceRenderer();
-  }
-
-  @Override
-  public void notifyScriptTermination(String strStatus, int msWalltime)
-  {
-    // ignore
-  }
-
-  @Override
-  public void sendConsoleEcho(String strEcho)
-  {
-    // ignore
-  }
-
-  @Override
-  public void sendConsoleMessage(String strStatus)
-  {
-    // ignore
-  }
-
-  @Override
-  public void showUrl(String url, String target)
-  {
-    ap.alignFrame.showURL(url, target);
-  }
-
-  @Override
-  public void refreshGUI()
-  {
-    // ignore
-  }
-
-  public void selectionChanged(BS arg0)
-  {
-    System.out.println(arg0);
-  }
-
-  @Override
-  public void refreshPdbEntries()
-  {
-    List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
-    List<String> fileids = new ArrayList<String>();
-    SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
-    for (int s = 0; s < sq.length; s++)
-    {
-      Vector<PDBEntry> pdbids = sq[s].getPDBId();
-      if (pdbids != null)
-      {
-        for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
-        {
-          PDBEntry pentry = pdbids.elementAt(pe);
-          if (!fileids.contains(pentry.getId()))
-          {
-            pdbe.add(pentry);
-          }
-          else
-          {
-            fileids.add(pentry.getId());
-          }
-        }
-      }
-    }
-    PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
-    for (int pe = 0; pe < pdbe.size(); pe++)
-    {
-      newEntries[pe] = pdbe.get(pe);
-    }
-    setPdbentry(newEntries);
-  }
-
-  @Override
-  public void showConsole(boolean show)
-  {
-    // This never gets called because we haven't overriden the associated Jmol's
-    // console
-    System.err
-            .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
-                    + show);
-  }
-
-  @Override
-  protected JmolAppConsoleInterface createJmolConsole(
-          Container consolePanel, String buttonsToShow)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  protected void releaseUIResources()
-  {
-    ap = null;
-    closeConsole();
-
-  }
-
-  @Override
-  public void releaseReferences(Object svl)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public Map<String, Object> getJSpecViewProperty(String arg0)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
+	public ExtJmol(StructureSelectionManager ssm, PDBEntry[] pdbentry,
+			SequenceI[][] sequenceIs, String[][] chains, String protocol) {
+		super(ssm, pdbentry, sequenceIs, chains, protocol);
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public String[] getPdbFile() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public void updateColours(Object source) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void releaseReferences(Object svl) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void highlightAtoms(List<AtomSpec> atoms) {
+		// TODO Auto-generated method stub
+		
+	}
+
+//  private AlignmentPanel ap;
+//
+//  protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+//          PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+//          String protocol)
+//  {
+//    super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+//            chains, protocol);
+//  }
+//
+//  public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
+//          SequenceI[][] seqs)
+//  {
+//    super(alignPanel.getStructureSelectionManager(), seqs, viewer);
+//    ap = alignPanel;
+//    notifyFileLoaded(null, null, null, null, 0);
+//  }
+//
+//  public void updateColours(Object source)
+//  {
+//
+//    // TODO Auto-generated method stub
+//
+//  }
+//
+//  public void showUrl(String arg0)
+//  {
+//    showUrl(arg0, "jmol");
+//  }
+//
+//  @Override
+//  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+//  {
+//    AlignmentPanel ap = (AlignmentPanel) alignment;
+//    if (ap.av.isShowSequenceFeatures())
+//    {
+//      return ap.getFeatureRenderer();
+//    }
+//    else
+//    {
+//      return null;
+//    }
+//  }
+//
+//  @Override
+//  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+//  {
+//    return ((AlignmentPanel) alignment).getSequenceRenderer();
+//  }
+//
+//  @Override
+//  public void notifyScriptTermination(String strStatus, int msWalltime)
+//  {
+//    // ignore
+//  }
+//
+//  @Override
+//  public void sendConsoleEcho(String strEcho)
+//  {
+//    // ignore
+//  }
+//
+//  @Override
+//  public void sendConsoleMessage(String strStatus)
+//  {
+//    // ignore
+//  }
+//
+//  @Override
+//  public void showUrl(String url, String target)
+//  {
+//    ap.alignFrame.showURL(url, target);
+//  }
+//
+//  @Override
+//  public void refreshGUI()
+//  {
+//    // ignore
+//  }
+//
+//  public void selectionChanged(BS arg0)
+//  {
+//    System.out.println(arg0);
+//  }
+//
+//  @Override
+//  public void refreshPdbEntries()
+//  {
+//    List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
+//    List<String> fileids = new ArrayList<String>();
+//    SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
+//    for (int s = 0; s < sq.length; s++)
+//    {
+//      Vector<PDBEntry> pdbids = sq[s].getPDBId();
+//      if (pdbids != null)
+//      {
+//        for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
+//        {
+//          PDBEntry pentry = pdbids.elementAt(pe);
+//          if (!fileids.contains(pentry.getId()))
+//          {
+//            pdbe.add(pentry);
+//          }
+//          else
+//          {
+//            fileids.add(pentry.getId());
+//          }
+//        }
+//      }
+//    }
+//    PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
+//    for (int pe = 0; pe < pdbe.size(); pe++)
+//    {
+//      newEntries[pe] = pdbe.get(pe);
+//    }
+//    setPdbentry(newEntries);
+//  }
+//
+//  @Override
+//  public void showConsole(boolean show)
+//  {
+//    // This never gets called because we haven't overriden the associated Jmol's
+//    // console
+//    System.err
+//            .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+//                    + show);
+//  }
+//
+//  @Override
+//  protected JmolAppConsoleInterface createJmolConsole(
+//          Container consolePanel, String buttonsToShow)
+//  {
+//    // TODO Auto-generated method stub
+//    return null;
+//  }
+//
+//  @Override
+//  protected void releaseUIResources()
+//  {
+//    ap = null;
+//    closeConsole();
+//
+//  }
+//
+//  @Override
+//  public void releaseReferences(Object svl)
+//  {
+//    // TODO Auto-generated method stub
+//
+//  }
+//
+//  @Override
+//  public Map<String, Object> getJSpecViewProperty(String arg0)
+//  {
+//    // TODO Auto-generated method stub
+//    return null;
+//  }
+//
 }