Merge branch 'Jalview-JS/develop' into merge_js_develop

[jalview.git] / doc / JalviewJS-API.md

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+# public interface JalviewJSApi
+
+## full list of available methods (from JalviewLiteJsApi):
+
+  public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
+  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 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 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 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();
+
+## 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
+- 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 Object getFrameForSource(VamsasSource source);
+  public void setSeparator(String separator);
+  
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