X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FJalviewApp.java;fp=src%2Fjalview%2Fapi%2FJalviewApp.java;h=0548c85fb1ca4de1eb4cc5d2f68da67b17cb28ef;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=0000000000000000000000000000000000000000;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git

diff --git a/src/jalview/api/JalviewApp.java b/src/jalview/api/JalviewApp.java
new file mode 100644
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--- /dev/null
+++ b/src/jalview/api/JalviewApp.java
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+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);
+
+}