public class JalviewAppLoader
{
- private JalviewApp app;
+ private JalviewApp app; // Jalview or JalviewJS or JalviewLite
private boolean debug;
loadAnnotations();
loadJnetFile();
loadPdbFiles();
+ callInitCallback();
}
/**
* <param name="PDBfile3" value="1q0o Q45135_9MICO">
*/
- int pdbFileCount = 0;
// Accumulate pdbs here if they are heading for the same view (if
// alignPdbStructures is true)
Vector<Object[]> pdbs = new Vector<>();
.getSequencesArray())
: null;
+ int pdbFileCount = 0;
String param;
do
{
chains = tmp2.toArray(new String[tmp2.size()]);
}
}
+ pdb.setId(param);
ret[0] = param;
- DataSourceType protocol = resolveFileProtocol(app,
- ret);
+ DataSourceType protocol = resolveFileProtocol(app, ret);
// TODO check JAL-357 for files in a jar (CLASSLOADER)
pdb.setFile(ret[0]);
app.getViewport().getAlignment(), 0, false);
// false == do not add sequence profile from concise output
app.getViewport().getAlignment().setupJPredAlignment();
- app.updateForLoader();
+ app.updateForAnnotations();
result = true;
} catch (Exception ex)
{
if (new AnnotationFile().annotateAlignmentView(app.getViewport(),
param, protocol))
{
- app.updateForLoader();
+ app.updateForAnnotations();
result = true;
}
else
}
}
+ public void callInitCallback()
+ {
+ String initjscallback = app.getParameter("oninit");
+ if (initjscallback == null)
+ {
+ return;
+ }
+ initjscallback = initjscallback.trim();
+ if (initjscallback.length() > 0)
+ {
+ // TODO
+ }
+ }
+
}