import java.util.List;
import java.util.Vector;
-import org.jmol.util.Logger;
-
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener
jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+ "_jmol_", ap.av.applet.getDocumentBase(),
ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
- Logger.setLogLevel(Logger.LEVEL_WARN);
} catch (Exception e)
{
System.err
* 'matched' array will hold 'true' for visible alignment columns where
* all sequences have a residue with a mapping to the PDB structure
*/
+ // TODO could use a BitSet for matched
boolean matched[] = new boolean[alignment.getWidth()];
for (int m = 0; m < matched.length; m++)
{
* generate select statements to select regions to superimpose structures
*/
{
+ // TODO extract method to construct selection statements
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
String chainCd = ":" + structures[pdbfnum].chain;
}
if (selectioncom.length() > 0)
{
+ // TODO is performing selectioncom redundant here? is done later on
// System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
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)
scriptWindow.setVisible(false);
}
- /*
- * -i for no info logging (less verbose)
- */
- jmb.allocateViewer(renderPanel, true, "", null, null, "-i",
+ jmb.allocateViewer(renderPanel, true, "", null, null, "",
scriptWindow, null);
// jmb.newJmolPopup("Jmol");
if (command == null)
public void drop(DropTargetDropEvent evt)
{
boolean success = true;
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
java.util.List<String> files = new ArrayList<String>();
java.util.List<String> protocols = new ArrayList<String>();
entry.setType(PDBEntry.Type.FILE);
}
}
- if (ids[p].getFile() != null)
+ // jprovider is null when executing 'New View'
+ if (ids[p].getFile() != null && jprovider != null)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
String pdbFile, String chain) throws SiftsException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- System.out.println("Getting mapping for: " + pdbId + "|" + chain
- + " : seq- " + seq.getName());
+ System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ + seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
int pdbStart = UNASSIGNED;
int pdbEnd = UNASSIGNED;
- Integer[] keys = mapping.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
- if (keys.length < 1)
+ if (mapping.isEmpty())
{
- throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+ throw new SiftsException(
+ "SIFTS mapping failed - falling back on Needleman-Wunsch");
}
+
+ Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+ Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];