Jalview-JS/JAL-3253-applet adds shell JalviewJSApi methods to Jalview

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index c27d7af..ac6fcd6 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -44,6 +44,7 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
+import jalview.javascript.JalviewLiteJsApi;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
@@ -94,7 +95,7 @@ import groovy.util.GroovyScriptEngine;
  * @author $author$
  * @version $Revision$
  */
-public class Jalview implements ApplicationSingletonI
+public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 {
 
   public static Jalview getInstance()
@@ -1381,4 +1382,416 @@ public class Jalview implements ApplicationSingletonI
     new JalviewAppLoader(true).load(app);
   }
 
+  @Override
+  public String getSelectedSequences()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequences(String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf,
+          String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void highlight(String sequenceId, String position,
+          String alignedPosition)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void highlightIn(jalview.appletgui.AlignFrame alf,
+          String sequenceId, String position, String alignedPosition)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void select(String sequenceIds, String columns)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void select(String sequenceIds, String columns, String sep)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
+          String columns)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
+          String columns, String sep)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignmentFrom(
+          jalview.appletgui.AlignFrame alf, String format, String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentOrder()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf,
+          String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String orderBy(String order, String undoName)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String orderBy(String order, String undoName, String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String orderAlignmentBy(jalview.appletgui.AlignFrame alf,
+          String order, String undoName, String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignment(String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
+          String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignment(String format, String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
+          String format, String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void loadAnnotation(String annotation)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void loadAnnotationFrom(jalview.appletgui.AlignFrame alf,
+          String annotation)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void loadFeatures(String features, boolean autoenabledisplay)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public boolean loadFeaturesFrom(jalview.appletgui.AlignFrame alf,
+          String features, boolean autoenabledisplay)
+  {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  @Override
+  public String getFeatures(String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeaturesFrom(jalview.appletgui.AlignFrame alf,
+          String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAnnotation()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAnnotationFrom(jalview.appletgui.AlignFrame alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public jalview.appletgui.AlignFrame newView()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public jalview.appletgui.AlignFrame newView(String name)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public jalview.appletgui.AlignFrame newViewFrom(
+          jalview.appletgui.AlignFrame alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public jalview.appletgui.AlignFrame newViewFrom(
+          jalview.appletgui.AlignFrame alf, String name)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public jalview.appletgui.AlignFrame loadAlignment(String text,
+          String title)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void setMouseoverListener(String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setMouseoverListener(jalview.appletgui.AlignFrame af,
+          String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setSelectionListener(String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setSelectionListener(jalview.appletgui.AlignFrame af,
+          String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setStructureListener(String listener, String modelSet)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void removeJavascriptListener(jalview.appletgui.AlignFrame af,
+          String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void mouseOverStructure(String pdbResNum, String chain,
+          String pdbfile)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public boolean addPdbFile(jalview.appletgui.AlignFrame alFrame,
+          String sequenceId, String pdbEntryString, String pdbFile)
+  {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  @Override
+  public void scrollViewToIn(jalview.appletgui.AlignFrame alf,
+          String topRow, String leftHandColumn)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void scrollViewToRowIn(jalview.appletgui.AlignFrame alf,
+          String topRow)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void scrollViewToColumnIn(jalview.appletgui.AlignFrame alf,
+          String leftHandColumn)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getFeatureGroups()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeatureGroupsOn(jalview.appletgui.AlignFrame alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeatureGroupsOfState(boolean visible)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeatureGroupsOfStateOn(jalview.appletgui.AlignFrame alf,
+          boolean visible)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void setFeatureGroupStateOn(jalview.appletgui.AlignFrame alf,
+          String groups, boolean state)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setFeatureGroupState(String groups, boolean state)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getSeparator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void setSeparator(String separator)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getJsMessage(String messageclass, String viewId)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }