javadoc

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d0c5674..ff21931 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -643,9 +643,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * 
+   * @return null or the currently selected sequence region
    */
   public SequenceGroup getSelectionGroup()
   {
@@ -653,10 +653,10 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * 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)
   {
@@ -664,9 +664,8 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * GUI state
+   * @return true if conservation based shading is enabled
    */
   public boolean getConservationSelected()
   {
@@ -674,10 +673,9 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
+   * GUI state
    * @param b
-   *          DOCUMENT ME!
+   *          enable conservation based shading
    */
   public void setConservationSelected(boolean b)
   {
@@ -685,9 +683,8 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * GUI state
+   * @return true if percent identity threshold is applied to shading
    */
   public boolean getAbovePIDThreshold()
   {
@@ -695,10 +692,10 @@ public class AlignViewport implements SelectionSource, VamsasSource
   }
 
   /**
-   * DOCUMENT ME!
+   * GUI state
    * 
-   * @param b
-   *          DOCUMENT ME!
+   * 
+   * @param b indicate if percent identity threshold is applied to shading
    */
   public void setAbovePIDThreshold(boolean b)
   {

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 74f6911..e60424e 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -366,10 +366,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @param b
-   *          DOCUMENT ME!
+   * @param b Hide or show annotation panel
+   *          
    */
   public void setAnnotationVisible(boolean b)
   {
@@ -381,6 +380,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
+  /**
+   * automatically adjust annotation panel height for new annotation
+   * whilst ensuring the alignment is still visible.
+   */
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary