JAL-2374 javadoc - qualify that sequence argument to findGroup must be in the Alignme...

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2df099a..5d185cd 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -157,10 +157,11 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Returns the first group (in the order in which groups were added) that
-   * includes the given sequence and aligned position (base 0), or null if none
-   * found
+   * includes the given sequence instance and aligned position (base 0), or null
+   * if none found
    * 
    * @param seq
+   *          - must be contained in the alignment (not a dataset sequence)
    * @param position
    * 
    * @return
@@ -285,13 +286,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   char getGapCharacter();
 
   /**
-   * Test for all nucleotide alignment
-   * 
-   * @return true if alignment is nucleotide sequence
-   */
-  boolean isNucleotide();
-
-  /**
    * Test if alignment contains RNA structure
    * 
    * @return true if RNA structure AligmnentAnnotation was added to alignment
@@ -299,12 +293,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   boolean hasRNAStructure();
 
   /**
-   * Set alignment to be a nucleotide sequence
-   * 
-   */
-  void setNucleotide(boolean b);
-
-  /**
    * Get the associated dataset for the alignment.
    * 
    * @return Alignment containing dataset sequences or null of this is a