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;
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;
/**
* @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;
+// }
+//
}
git://source.jalview.org / jalview.git / blobdiff