+## public interface JalviewJSApi
+
+# full list of available methods:
+
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
+ public String arrayToSeparatorList(String[] array);
+ public String getAlignment(String format);
+ public String getAlignment(String format, String suffix);
+ public String getAlignmentFrom(AlignFrame alf, String format);
+ public String getAlignmentFrom(AlignFrame alf, String format, String suffix);
+ public String getAlignmentOrder();
+ public String getAlignmentOrderFrom(AlignFrame alf);
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep);
+ public String getAnnotation();
+ public String getAnnotationFrom(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 getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible);
+ public String getFeatureGroupsOn(AlignFrame alf);
+ public String getFeatures(String format);
+ public String getFeaturesFrom(AlignFrame alf, String format);
+ public Object getFrameForSource(VamsasSource source);
+ public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
+ public String getParameter(String name);
+ public String getSelectedSequences();
+ public String getSelectedSequences(String sep);
+ public String getSelectedSequencesAsAlignment(String format, String suffix);
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix);
+ public String getSelectedSequencesFrom(AlignFrame alf);
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep);
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
+ public String getSeparator();
+ public AlignViewportI getViewport();
+ public void highlight(String sequenceId, String position, String alignedPosition);
+ public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition);
+ public AlignFrame loadAlignment(String text, String title);
+ public void loadAnnotation(String annotation);
+ public void loadAnnotationFrom(AlignFrame alf, String annotation);
+ public void loadFeatures(String features, boolean autoenabledisplay);
+ public boolean loadFeaturesFrom(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 orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep);
+ public String orderBy(String order, String undoName);
+ public String orderBy(String order, String undoName, String sep);
+ public Object parseArguments(String[] args);
+ public boolean parseFeaturesFile(String param, DataSourceType protocol);
+ public void removeSelectionListener(AlignFrame af, String listener);
+ public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
+ public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn);
+ public void scrollViewToRowIn(AlignFrame alf, String topRow);
+ public void select(String sequenceIds, String columns);
+ public void select(String sequenceIds, String columns, String sep);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep);
+ public String[] separatorListToArray(String list);
+ public void setFeatureGroupState(String groups, boolean state);
+ public void setFeatureGroupState(String[] groups, boolean state);
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state);
+ public void setSelectionListener(AlignFrame af, String listener);
+ public void setSelectionListener(String listener);
+ public void setSeparator(String separator);
+ public void showOverview();
+ public void updateForAnnotations();
+
+# proposed alias list:
+
+- remove overloaded methods
+- indicate null options
+- use standard arrays; no need for special separators
+- possibly return more actual objects, not just strings
+
+ 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();
+
+# unknown methods/shouldn't be in interface?
+
+ public String arrayToSeparatorList(String[] array);
+ public Object getFrameForSource(VamsasSource source);
+ public String getSeparator();
+ public String[] separatorListToArray(String list);
+ public void setSeparator(String separator);
+
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