List<String> getFeatureGroups();
/**
- * get groups that are visible/invisible
+ * get groups that are visible/invisible -- JalviewLite only?
*
* @param visible
* @return
List<String> getGroups(boolean visible);
/**
- * Set visibility for a list of groups
+ * Set visibility for a list of groups -- JalviewLite only?
*
* @param toset
* @param visible
public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
String[][] chains, String[] protocols);
- public void updateForLoader();
+ public void updateForAnnotations();
public AlignViewportI getViewport();
return id + (frameType == null ? "" : "-" + frameType);
}
+ /**
+ * Handle all JalviewLite applet parameters
+ *
+ * @param aparser
+ * @param af
+ */
private void loadAppletParams(ArgsParser aparser, AlignFrame af)
{
Jalview me = this;
JalviewApp app = new JalviewApp()
{
-
@Override
public String getParameter(String name)
{
: "true".equalsIgnoreCase(stn));
}
+ /**
+ * Get the applet-like document base even though this is an application.
+ */
@Override
public URL getDocumentBase()
{
return Platform.getDocumentBase();
}
+ /**
+ * Get the applet-like code base even though this is an application.
+ */
@Override
public URL getCodeBase()
{
return Jalview.getCurrentAlignFrame().getViewport();
}
+ /**
+ * features
+ *
+ */
+ @Override
+ public boolean parseFeaturesFile(String filename,
+ DataSourceType protocol)
+ {
+ return af.parseFeaturesFile(filename, protocol);
+ }
+
+ /**
+ * scorefile
+ *
+ */
@Override
public boolean loadScoreFile(String sScoreFile) throws IOException
{
return true;
}
+ /**
+ * annotations, jpredfile, jnetfile
+ *
+ */
@Override
- public boolean parseFeaturesFile(String filename,
- DataSourceType protocol)
+ public void updateForAnnotations()
{
- return af.parseFeaturesFile(filename, protocol);
+ Jalview.getCurrentAlignFrame().updateForAnnotations();
}
@Override
public void loadTree(NewickFile fin, String treeFile)
throws IOException
{
- // n/a -- already done
+ // n/a -- already done by standard Jalview command line processing
}
@Override
}
@Override
- public void updateForLoader()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
public void setFeatureGroupState(String[] groups, boolean state)
{
// TODO Auto-generated method stub
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
}
@Override
- public void updateForLoader()
+ public void updateForAnnotations()
{
loaderFrame.alignPanel.fontChanged();
loaderFrame.alignPanel.setScrollValues(0, 0);
}
if (isAnnotation)
{
-
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
+ updateForAnnotations();
}
} catch (Exception ex)
{
}
/**
+ * Do all updates necessary after an annotation file such as jnet. Also called
+ * from Jalview.loadAppletParams for "annotations", "jnetFile"
+ */
+ public void updateForAnnotations()
+ {
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true, true);
+ }
+
+ /**
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/