3 import jalview.datamodel.PDBEntry;
4 import jalview.datamodel.SequenceI;
5 import jalview.io.DataSourceType;
6 import jalview.io.NewickFile;
8 import java.io.IOException;
11 public interface JalviewApp
13 public String getParameter(String name);
15 public boolean getDefaultParameter(String name, boolean def);
17 public URL getDocumentBase();
19 public URL getCodeBase();
21 public void setAlignPdbStructures(boolean defaultParameter);
23 public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
24 String[] chains, DataSourceType protocol);
26 public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
27 String[][] chains, String[] protocols);
29 public void updateForAnnotations();
31 public AlignViewportI getViewport();
33 public void setFeatureGroupState(String[] groups, boolean state);
35 public boolean parseFeaturesFile(String param, DataSourceType protocol);
37 public void newFeatureSettings();
39 public boolean loadScoreFile(String sScoreFile) throws IOException;
41 public void loadTree(NewickFile fin, String treeFile) throws IOException;