remove conflict on javascript api

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index c9977fd..c61c516 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -48,9 +48,9 @@ public class JalviewLite
    */
   public String getSelectedSequences()
   {
-    return getSelectedSequences(currentAlignFrame);
+    return getSelectedSequencesFrom(currentAlignFrame);
   }
-  public String getSelectedSequences(AlignFrame alf)
+  public String getSelectedSequencesFrom(AlignFrame alf)
   {
     StringBuffer result = new StringBuffer("");
 
@@ -71,17 +71,17 @@ public class JalviewLite
   
   public String getAlignment(String format)
   {
-    return getAlignment(currentAlignFrame, format, "true");
+    return getAlignmentFrom(currentAlignFrame, format, "true");
   }
-  public String getAlignment(AlignFrame alf, String format)
+  public String getAlignmentFrom(AlignFrame alf, String format)
   {
-    return getAlignment(alf, format, "true");
+    return getAlignmentFrom(alf, format, "true");
   }
   public String getAlignment(String format, String suffix)
   {
-    return getAlignment(currentAlignFrame, format, suffix);
+    return getAlignmentFrom(currentAlignFrame, format, suffix);
   }
-  public String getAlignment(AlignFrame alf, String format, String suffix)
+  public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
   {
     try
     {
@@ -100,9 +100,9 @@ public class JalviewLite
 
   public void loadAnnotation(String annotation)
   {
-    loadAnnotation(currentAlignFrame, annotation);
+    loadAnnotationFrom(currentAlignFrame, annotation);
   }
-  public void loadAnnotation(AlignFrame alf, String annotation)
+  public void loadAnnotationFrom(AlignFrame alf, String annotation)
   {
     if (new AnnotationFile().readAnnotationFile(
         alf.getAlignViewport().getAlignment(), annotation,
@@ -119,34 +119,34 @@ public class JalviewLite
 
   public String getFeatures(String format)
   {
-    return getFeatures(currentAlignFrame, format);
+    return getFeaturesFrom(currentAlignFrame, format);
   }
-  public String getFeatures(AlignFrame alf, String format)
+  public String getFeaturesFrom(AlignFrame alf, String format)
   {
     return alf.outputFeatures(false, format);
   }
   public String getAnnotation()
   {
-    return getAnnotation(currentAlignFrame);
+    return getAnnotationFrom(currentAlignFrame);
   }
-  public String getAnnotation(AlignFrame alf)
+  public String getAnnotationFrom(AlignFrame alf)
   {
     return alf.outputAnnotations(false);
   }
   public AlignFrame newView()
   {
-    return newView(currentAlignFrame);
+    return newViewFrom(currentAlignFrame);
   }
   public AlignFrame newView(String name)
   {
-    return newView(currentAlignFrame, name);
+    return newViewFrom(currentAlignFrame, name);
   }
 
-  public AlignFrame newView(AlignFrame alf)
+  public AlignFrame newViewFrom(AlignFrame alf)
   {
     return alf.newView(null);
   }
-  public AlignFrame newView(AlignFrame alf, String name)
+  public AlignFrame newViewFrom(AlignFrame alf, String name)
   {
     return alf.newView(name);
   }
@@ -797,7 +797,16 @@ public class JalviewLite
     String lst = ArraytotabbedList(currentAlignFrame.getFeatureGroups());
     return lst;
   }
-
+  /**
+   * @param alf alignframe to get feature groups on
+   * @return
+   * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+   */
+  public String getFeatureGroupsOn(AlignFrame alf)
+  {
+    String lst = ArraytotabbedList(alf.getFeatureGroups());
+    return lst;
+  }
   /**
    * @param visible
    * @return
@@ -808,17 +817,26 @@ public class JalviewLite
     return ArraytotabbedList(currentAlignFrame.getFeatureGroupsOfState(visible));
   }
   /**
+   * @param alf align frame to get groups of state visible
+   * @param visible
+   * @return
+   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+   */
+  public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+  {
+    return ArraytotabbedList(alf.getFeatureGroupsOfState(visible));
+  }  /**
    * @param groups tab separated list of group names 
    * @param state true or false
    * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
    */
-  public void setFeatureGroupState(AlignFrame alf, String groups, boolean state)
+  public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
   {
     boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
     alf.setFeatureGroupState(tabbedListToArray(groups), st);
   }
   public void setFeatureGroupState(String groups, boolean state)
   {
-    setFeatureGroupState(currentAlignFrame, groups, state);
+    setFeatureGroupStateOn(currentAlignFrame, groups, state);
   }
 }