package jalview.api;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.NewickFile;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
+import java.applet.AppletContext;
import java.io.IOException;
import java.net.URL;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import netscape.javascript.JSObject;
public interface JalviewApp
{
public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
String[][] chains, String[] protocols);
- public void updateForLoader();
+ public void updateForAnnotations();
public AlignViewportI getViewport();
public void loadTree(NewickFile fin, String treeFile) throws IOException;
+ public Vector<Runnable> getJsExecQueue(JSFunctionExec jsFunctionExec);
+
+ public AppletContext getAppletContext();
+
+ public boolean isJsfallbackEnabled();
+
+ public JSObject getJSObject();
+
+ public StructureSelectionManagerProvider getStructureSelectionManagerProvider();
+
+ public void updateColoursFromMouseOver(Object source,
+ MouseOverStructureListener mouseOverStructureListener);
+
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame);
+
+ public String arrayToSeparatorList(String[] array);
+
+ public Hashtable<String, int[]> getJSHashes();
+
+ Hashtable<String, Hashtable<String, String[]>> getJSMessages();
+
+ public Object getFrameForSource(VamsasSource source);
+
+ public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
+ AlignViewportI vp);
+
}