-
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
- public String getAlignment(AlignFrame alf, String format, boolean includeStartEnd);
- public String[] getAlignmentOrder(AlignFrame alf);
- public String getAnnotation(AlignFrame alf);
- public Object getAppletParameter(String name, boolean asString);
- public URL getCodeBase();
- public URL getDocumentBase();
- public String[] getFeatureGroups();
- public String[] getFeatureGroupsOfState(boolean visible);
- public String getFeatures(AlignFrame alf, String format);
- public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
- public String getParameter(String name);
- public String[] getSelectedSequences(AlignFrame alf);
- public String[] getSelectedSequencesAsAlignment(AlignFrame alf, String format, boolean includeStartEnd);
- public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
- public AlignViewportI getViewport();
- public void highlight(AlignFrame alf, String sequenceId, String position, String alignedPosition);
- public AlignFrame loadAlignment(String text, String title);
- public void loadAnnotation(AlignFrame alf, String annotation);
- public boolean loadFeatures(AlignFrame alf, String features, boolean autoenabledisplay);
- public boolean loadScoreFile(String sScoreFile) throws IOException;
- public void newFeatureSettings();
- public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
- public Object openPcaPanel(AlignFrame af, String modelName);
- public Object openTreePanel(AlignFrame af, String treeType, String modelName);
- public String[] orderBy(AlignFrame alf, String order, String undoName);
- public Object parseArguments(String[] args);
- public boolean parseFeaturesFile(String param, DataSourceType protocol);
- public void removeSelectionListener(AlignFrame af, String listener);
- public void scrollViewTo(AlignFrame alf, String topRow, String leftHandColumn);
- public void select(AlignFrame alf, String[] sequenceIds, String[] columns);
- public void setFeatureGroupState(AlignFrame alf, String groups, boolean state);
- public void setSelectionListener(AlignFrame af, String listener);
- public void showOverview();
- public void updateForAnnotations();