import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import java.util.Map;
import java.util.Vector;
-import javajs.awt.Dimension;
-
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
{
Viewer viewer = null;
- public JmolParser(String inFile, String type) throws IOException
+ public JmolParser(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public JmolParser(FileParse fp) throws IOException
try
{
/*
- * params -o (output to sysout) -i (no info logging, less verbose)
- * -n (nodisplay) -x (exit when finished)
+ * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
* see http://wiki.jmol.org/index.php/Jmol_Application
*/
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n -i", this);
+ null, "-x -o -n", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
if (pdbId == null)
{
setId(safeName(getDataName()));
+ setPDBIdAvailable(false);
}
else
{
setId(pdbId);
+ setPDBIdAvailable(true);
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
* Not implemented - returns null
*/
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
* Not implemented - returns null
*/
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
return null;
}