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 String getParameter(String name);

  public boolean getDefaultParameter(String name, boolean def);

  public URL getDocumentBase();

  public URL getCodeBase();

  public void setAlignPdbStructures(boolean defaultParameter);

  public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
          String[] chains, DataSourceType protocol);

  public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
          String[][] chains, String[] protocols);

  public void updateForAnnotations();

  public AlignViewportI getViewport();

  public void setFeatureGroupState(String[] groups, boolean state);

  public boolean parseFeaturesFile(String param, DataSourceType protocol);

  public void newFeatureSettings();

  public boolean loadScoreFile(String sScoreFile) throws IOException;

  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);

}