src/jalview/api/JalviewApp.java

   1 package jalview.api;
   2
   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;
  14
  15 import java.applet.AppletContext;
  16 import java.io.IOException;
  17 import java.net.URL;
  18 import java.util.Hashtable;
  19 import java.util.Vector;
  20
  21 import netscape.javascript.JSObject;
  22
  23 public interface JalviewApp
  24 {
  25   public String getParameter(String name);
  26
  27   public boolean getDefaultParameter(String name, boolean def);
  28
  29   public URL getDocumentBase();
  30
  31   public URL getCodeBase();
  32
  33   public void setAlignPdbStructures(boolean defaultParameter);
  34
  35   public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
  36           String[] chains, DataSourceType protocol);
  37
  38   public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
  39           String[][] chains, String[] protocols);
  40
  41   public void updateForAnnotations();
  42
  43   public AlignViewportI getViewport();
  44
  45   public void setFeatureGroupState(String[] groups, boolean state);
  46
  47   public boolean parseFeaturesFile(String param, DataSourceType protocol);
  48
  49   public void newFeatureSettings();
  50
  51   public boolean loadScoreFile(String sScoreFile) throws IOException;
  52
  53   public void loadTree(NewickFile fin, String treeFile) throws IOException;
  54
  55   public Vector<Runnable> getJsExecQueue(JSFunctionExec jsFunctionExec);
  56
  57   public AppletContext getAppletContext();
  58
  59   public boolean isJsfallbackEnabled();
  60
  61   public JSObject getJSObject();
  62
  63   public StructureSelectionManagerProvider getStructureSelectionManagerProvider();
  64
  65   public void updateColoursFromMouseOver(Object source,
  66           MouseOverStructureListener mouseOverStructureListener);
  67
  68   public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
  69           HiddenColumns hidden, SelectionSource source, Object alignFrame);
  70
  71   public String arrayToSeparatorList(String[] array);
  72
  73   public Hashtable<String, int[]> getJSHashes();
  74
  75   Hashtable<String, Hashtable<String, String[]>> getJSMessages();
  76
  77   public Object getFrameForSource(VamsasSource source);
  78
  79   public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
  80           AlignViewportI vp);
  81
  82 }