JAL-3690 Introduce AlignCalcManager2 tests.

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

diff --git a/doc/JalviewJS-API.md b/doc/JalviewJS-API.md
index 1302021..64cae62 100644 (file)
--- a/doc/JalviewJS-API.md
+++ b/doc/JalviewJS-API.md
@@ -22,7 +22,6 @@
   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);
@@ -30,7 +29,6 @@
   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);
@@ -81,43 +79,43 @@
 - 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 Object getFrameForSource(VamsasSource source);