import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
+ viewer.dispose();
lastCommand = null;
viewer = null;
releaseUIResources();
System.out.println("JMOL CREATE IMAGE");
}
+ @Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
return null;
}
+ @Override
public String eval(String strEval)
{
// System.out.println(strEval);
// End StructureListener
// //////////////////////////
+ @Override
public float[][] functionXY(String functionName, int x, int y)
{
return null;
}
+ @Override
public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
{
// TODO Auto-generated method stub
{
if (atoms != null)
{
+ if (resetLastRes.length() > 0)
+ {
+ viewer.evalStringQuiet(resetLastRes.toString());
+ resetLastRes.setLength(0);
+ }
for (AtomSpec atom : atoms)
{
highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
}
jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
StringBuilder cmd = new StringBuilder(64);
cmd.append("select " + pdbResNum); // +modelNum
- resetLastRes.setLength(0);
resetLastRes.append("select " + pdbResNum); // +modelNum
cmd.append(":");
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
- MCview.PDBfile pdb = null;
+ StructureFile pdb = null;
String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
pdbfile, AppletFormatAdapter.PASTE);
- getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
if (matches)
{
// add an entry for every chain in the model
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(pdb.id + ":"
- + pdb.chains.elementAt(i).id);
+ String chid = new String(pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
chainNames.addElement(chid);
}
*/
public abstract void sendConsoleMessage(String strStatus);
+ @Override
public void setCallbackFunction(String callbackType,
String callbackFunction)
{