formatting

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 61b2950..244cc74 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -17,7 +17,7 @@ import jalview.schemes.RNAHelicesColour;
 
 /**
  * @author jimp
- *
+ * 
  */
 public interface AlignViewportI
 {
@@ -31,7 +31,7 @@ public interface AlignViewportI
   /**
    * calculate the height for visible annotation, revalidating bounds where
    * necessary ABSTRACT GUI METHOD
-   *
+   * 
    * @return total height of annotation
    */
   public int calcPanelHeight();
@@ -65,23 +65,28 @@ public interface AlignViewportI
   AlignmentAnnotation getAlignmentQualityAnnot();
 
   AlignmentAnnotation getAlignmentConservationAnnotation();
+
   /**
    * get the container for alignment consensus annotation
+   * 
    * @return
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
    * Test to see if viewport is still open and active
-   * @return true indicates that all references to viewport should be dropped 
+   * 
+   * @return true indicates that all references to viewport should be dropped
    */
   boolean isClosed();
+
   /**
    * get the associated calculation thread manager for the view
+   * 
    * @return
    */
   AlignCalcManagerI getCalcManager();
-  
+
   /**
    * get the percentage gaps allowed in a conservation calculation
    * 
@@ -90,24 +95,28 @@ public interface AlignViewportI
 
   /**
    * set the consensus result object for the viewport
+   * 
    * @param hconsensus
    */
   void setSequenceConsensusHash(Hashtable[] hconsensus);
 
   /**
    * 
-   * @return the alignment annotatino row for the structure consensus calculation
+   * @return the alignment annotatino row for the structure consensus
+   *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
 
   /**
    * set the Rna structure consensus result object for the viewport
-   * @param hStrucConsensus 
+   * 
+   * @param hStrucConsensus
    */
   void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
 
   /**
    * set global colourscheme
+   * 
    * @param rhc
    */
   void setGlobalColourScheme(ColourSchemeI rhc);
@@ -118,11 +127,18 @@ public interface AlignViewportI
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
 
   /**
-   * hides or shows dynamic annotation rows based on groups and group and alignment associated auto-annotation state flags
-   * apply the current group/autoannotation settings to the alignment view. 
-   * Usually you should call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to ensure the annotation panel bounds are set correctly.
-   * @param applyGlobalSettings - apply to all autoannotation rows or just the ones associated with the current visible region
-   * @param preserveNewGroupSettings - don't apply global settings to groups which don't already have group associated annotation
+   * hides or shows dynamic annotation rows based on groups and group and
+   * alignment associated auto-annotation state flags apply the current
+   * group/autoannotation settings to the alignment view. Usually you should
+   * call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to
+   * ensure the annotation panel bounds are set correctly.
+   * 
+   * @param applyGlobalSettings
+   *          - apply to all autoannotation rows or just the ones associated
+   *          with the current visible region
+   * @param preserveNewGroupSettings
+   *          - don't apply global settings to groups which don't already have
+   *          group associated annotation
    */
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);