import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
import java.awt.Color;
import java.awt.Container;
import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
-import java.security.AccessControlException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Hashtable;
*/
private int _modelFileNameMap[];
- // ////////////////////////////////
- // /StructureListener
- // @Override
- public synchronized String[] getPdbFilex()
- {
- if (viewer == null)
- {
- return new String[0];
- }
- if (modelFileNames == null)
- {
- List<String> mset = new ArrayList<>();
- _modelFileNameMap = new int[viewer.ms.mc];
- String m = viewer.ms.getModelFileName(0);
- if (m != null)
- {
- String filePath = m;
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet
- System.err.println(
- "jmolBinding: Using local file string from Jmol: " + m);
- }
- if (filePath.indexOf("/file:") != -1)
- {
- // applet path with docroot - discard as format won't match pdbfile
- filePath = m;
- }
- mset.add(filePath);
- _modelFileNameMap[0] = 0; // filename index for first model is always 0.
- }
- int j = 1;
- for (int i = 1; i < viewer.ms.mc; i++)
- {
- m = viewer.ms.getModelFileName(i);
- String filePath = m;
- if (m != null)
- {
- try
- {
- filePath = new File(m).getAbsolutePath();
- } catch (AccessControlException x)
- {
- // usually not allowed to do this in applet, so keep raw handle
- // System.err.println("jmolBinding: Using local file string from
- // Jmol: "+m);
- }
- }
-
- /*
- * add this model unless it is read from a structure file we have
- * already seen (example: 2MJW is an NMR structure with 10 models)
- */
- if (!mset.contains(filePath))
- {
- mset.add(filePath);
- _modelFileNameMap[j] = i; // record the model index for the filename
- j++;
- }
- }
- modelFileNames = mset.toArray(new String[mset.size()]);
- }
- return modelFileNames;
- }
-
@Override
public synchronized String[] getStructureFiles()
{
pdbfilename);
if (label != null)
{
+ // change comma to pipe separator (newline token for Jmol)
+ label = label.replace(',', '|');
StringTokenizer toks = new StringTokenizer(strInfo, " ");
StringBuilder sb = new StringBuilder();
sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
- fr.featuresAdded();
+ FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+ ((AppJmol) getViewer()).getAlignmentPanel().av
+ .applyFeaturesStyle(colours);
}
refreshGUI();
loadNotifiesHandled++;