3 import jalview.datamodel.ColumnSelection;
4 import jalview.datamodel.HiddenColumns;
5 import jalview.datamodel.PDBEntry;
6 import jalview.datamodel.SequenceGroup;
7 import jalview.datamodel.SequenceI;
8 import jalview.io.DataSourceType;
9 import jalview.io.NewickFile;
10 import jalview.javascript.JSFunctionExec;
11 import jalview.javascript.MouseOverStructureListener;
12 import jalview.structure.SelectionSource;
13 import jalview.structure.VamsasSource;
15 import java.applet.AppletContext;
16 import java.io.IOException;
18 import java.util.Hashtable;
19 import java.util.Vector;
21 import netscape.javascript.JSObject;
23 public interface JalviewApp
25 public String getParameter(String name);
27 public boolean getDefaultParameter(String name, boolean def);
29 public URL getDocumentBase();
31 public URL getCodeBase();
33 public void setAlignPdbStructures(boolean defaultParameter);
35 public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
36 String[] chains, DataSourceType protocol);
38 public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
39 String[][] chains, String[] protocols);
41 public void updateForAnnotations();
43 public AlignViewportI getViewport();
45 public void setFeatureGroupState(String[] groups, boolean state);
47 public boolean parseFeaturesFile(String param, DataSourceType protocol);
49 public void newFeatureSettings();
51 public boolean loadScoreFile(String sScoreFile) throws IOException;
53 public void loadTree(NewickFile fin, String treeFile) throws IOException;
55 public Vector<Runnable> getJsExecQueue(JSFunctionExec jsFunctionExec);
57 public AppletContext getAppletContext();
59 public boolean isJsfallbackEnabled();
61 public JSObject getJSObject();
63 public StructureSelectionManagerProvider getStructureSelectionManagerProvider();
65 public void updateColoursFromMouseOver(Object source,
66 MouseOverStructureListener mouseOverStructureListener);
68 public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
69 HiddenColumns hidden, SelectionSource source, Object alignFrame);
71 public String arrayToSeparatorList(String[] array);
73 public Hashtable<String, int[]> getJSHashes();
75 Hashtable<String, Hashtable<String, String[]>> getJSMessages();
77 public Object getFrameForSource(VamsasSource source);
79 public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(