-## public interface JalviewJSApi
+# public interface JalviewJSApi
-# full list of available methods:
+## full list of available methods (from JalviewLiteJsApi):
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 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 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 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 showOverview();
public void updateForAnnotations();
-# proposed alias list:
+## addition available methods (from JalviewLite):
+
+ public static String getBuildDate()
+ public static String getInstallation()
+ public static String getVersion()
+
+
+
+## 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();
+- moves AlignFrame to last parameter, as it is likely to be unnecessary
+public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile, AlignFrame alFrame);
+public String getAlignment(String format, boolean addSuffix, AlignFrame alf);
+public String[] getAlignmentOrder(AlignFrame alf);
+public String getAnnotation(AlignFrame alf);
+public URL getCodeBase();
+public URL getDocumentBase();
+public String[] getFeatureGroups(AlignFrame alf);
+public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf);
+public String getFeatures(String format, AlignFrame alf);
+public String getParameter(String name);
+public Object getParameterAsObject(String name);
+public SequenceI[] getSelectedSequences(AlignFrame alf);
+public AlignFrame newView();
+public AlignFrame newView(String name);
+public AlignFrame newViewFrom(AlignFrame alf);
+public AlignFrame newViewFrom(AlignFrame alf, String name);
+public String getSelectedSequencesAsAlignment(String format, boolean addSuffix, AlignFrame alf);
+public void highlight(String sequenceId, String position, String alignedPosition, AlignFrame alf);
+public AlignFrame loadAlignment(String data, String title, int width, int height);
+public void loadAnnotation(String annotation, AlignFrame alf);
+public boolean loadFeatures(String features, boolean autoenabledisplay, AlignFrame alf);
+public boolean loadScoreFile(String sScoreFile, AlignFrame alf);
+public Object openPcaPanel(String modelName, AlignFrame alf);
+public Object openTreePanel(String treeType, String modelName, AlignFrame alf);
+public boolean orderAlignment(String[] ids, String undoName, AlignFrame alf);
+public Object parseArguments(String[] args);
+public void removeSelectionListener(String listener, AlignFrame af);
+public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf);
+public void select(String[] sequenceIds, String[] columns, AlignFrame alf);
+public void setFeatureGroupState(String[] groups, boolean state, AlignFrame alf);
+public void setSelectionListener(String listener, AlignFrame alf);
+public void showOverview();
+public void showStructure(String pdbID, String fileType, AlignFrame alf);
+
+
# 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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