*/
package jalview.gui;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
private static final String SPACE = " ";
- private static final String BACKSLASH = "\"";
+ private static final String QUOTE = "\"";
AppJmolBinding jmb;
jmb.setFinishedInit(true);
}
- boolean allChainsSelected = false;
-
@Override
void showSelectedChains()
{
StringBuilder fileList = new StringBuilder();
for (String s : files)
{
- fileList.append(SPACE).append(BACKSLASH)
- .append(Platform.escapeString(s)).append(BACKSLASH);
+ fileList.append(SPACE).append(QUOTE)
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
String filesString = fileList.toString();
}
// refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentViewPanel avp : _colourwith)
{
- jmb.updateColours(ap);
+ jmb.updateColours(avp);
}
// do superposition if asked to
if (alignAddedStructures)
String file = jmb.getPdbEntry(pi).getFile();
if (file == null)
{
+ // todo: extract block as method and pull up (also ChimeraViewFrame)
// retrieve the pdb and store it locally
AlignmentI pdbseq = null;
pdbid = jmb.getPdbEntry(pi).getId();
addingStructures = true; // already files loaded.
for (int c = 0; c < filesInViewer.length; c++)
{
- if (filesInViewer[c].equals(file))
+ if (Platform.pathEquals(filesInViewer[c], file))
{
file = null;
break;