javadoc

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 033b3bc..ff21931 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -48,6 +48,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
 
 /**
  * DOCUMENT ME!
@@ -55,7 +56,7 @@ import jalview.structure.StructureSelectionManager;
  * @author $author$
  * @version $Revision$
  */
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
 {
   private static final int RIGHT_JUSTIFY = 1;
 
@@ -642,9 +643,9 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * 
+   * @return null or the currently selected sequence region
    */
   public SequenceGroup getSelectionGroup()
   {
@@ -652,10 +653,10 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
+   * Set the selection group for this window.
    * 
-   * @param sg
-   *          DOCUMENT ME!
+   * @param sg - group holding references to sequences in this alignment view
+   *          
    */
   public void setSelectionGroup(SequenceGroup sg)
   {
@@ -663,9 +664,8 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * GUI state
+   * @return true if conservation based shading is enabled
    */
   public boolean getConservationSelected()
   {
@@ -673,10 +673,9 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
+   * GUI state
    * @param b
-   *          DOCUMENT ME!
+   *          enable conservation based shading
    */
   public void setConservationSelected(boolean b)
   {
@@ -684,9 +683,8 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * GUI state
+   * @return true if percent identity threshold is applied to shading
    */
   public boolean getAbovePIDThreshold()
   {
@@ -694,10 +692,10 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   * DOCUMENT ME!
+   * GUI state
    * 
-   * @param b
-   *          DOCUMENT ME!
+   * 
+   * @param b indicate if percent identity threshold is applied to shading
    */
   public void setAbovePIDThreshold(boolean b)
   {