JalviewAppLoader for moving code from JalviewLite relating to applet

[jalview.git] / src / jalview / api / JalviewApp.java

diff --git a/src/jalview/api/JalviewApp.java b/src/jalview/api/JalviewApp.java
new file mode 100644 (file)
index 0000000..1d67bc2
--- /dev/null
+++ b/src/jalview/api/JalviewApp.java
@@ -0,0 +1,43 @@
+package jalview.api;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.NewickFile;
+
+import java.io.IOException;
+import java.net.URL;
+
+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 updateForLoader();
+
+  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;
+
+}