X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FJalviewApp.java;h=0548c85fb1ca4de1eb4cc5d2f68da67b17cb28ef;hb=80634498762666e6acc92368716bf1a4d4f42f7b;hp=1d67bc2ee3b90ed32bd2a440cc0ad5b2cce66592;hpb=4b0220906ff60a04786c3f3eb95fa306407f27c7;p=jalview.git

diff --git a/src/jalview/api/JalviewApp.java b/src/jalview/api/JalviewApp.java
index 1d67bc2..0548c85 100644
--- a/src/jalview/api/JalviewApp.java
+++ b/src/jalview/api/JalviewApp.java
@@ -1,12 +1,24 @@
 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
 {
@@ -26,7 +38,7 @@ public interface JalviewApp
   public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
           String[][] chains, String[] protocols);
 
-  public void updateForLoader();
+  public void updateForAnnotations();
 
   public AlignViewportI getViewport();
 
@@ -40,4 +52,31 @@ public interface JalviewApp
 
   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);
+
 }