import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.io.IOException;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, String type)
+ public JmolParser(String inFile, String type)
throws IOException
{
super(inFile, type);
}
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
{
super(fp);
}
*/
if (jmolModel.ms.mc > 0)
{
+ // ideally we do this
+ // try
+ // {
+ // setStructureFileType(jmolModel.evalString("show _fileType"));
+ // } catch (Exception q)
+ // {
+ // }
+ // ;
+ // instead, we distinguish .cif from non-.cif by filename
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
+ .toString() : "PDB");
+
transformJmolModelToJalview(jmolModel.ms);
}
}
{
try
{
+ /*
+ * params -o (output to sysout) -i (no info logging, less verbose)
+ * -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", this);
+ null, "-x -o -n -i", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
// significantAtoms.add(curAtom);
// diff < 5 then mark as valid and update termination Atom
if (chainTerMap.containsKey(curAtomChId))
{
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
// atom with previously terminated chain encountered
else if (chainTerMap.containsKey(curAtomChId))
{
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);