JAL-2145 documentation of getWidth()

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 4ae8ba2..f1db4c0 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -41,7 +41,8 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
-   * @return Greatest sequence length within alignment.
+   * @return Greatest sequence length within alignment, or -1 if no sequences
+   *         present
    */
   @Override
   int getWidth();
@@ -305,7 +306,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return Alignment containing dataset sequences or null of this is a
    *         dataset.
    */
-  Alignment getDataset();
+  AlignmentI getDataset();
 
   /**
    * Set the associated dataset for the alignment, or create one.
@@ -313,7 +314,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @param dataset
    *          The dataset alignment or null to construct one.
    */
-  void setDataset(Alignment dataset);
+  void setDataset(AlignmentI dataset);
 
   /**
    * pads sequences with gaps (to ensure the set looks like an alignment)
@@ -363,14 +364,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   void addCodonFrame(AlignedCodonFrame codons);
 
   /**
-   * add a set of aligned codons mappings for this alignment, apart from any
-   * duplicates which are ignored
-   * 
-   * @param codons
-   */
-  void addCodonFrames(Iterable<AlignedCodonFrame> codons);
-
-  /**
    * remove a particular codon frame reference from this alignment
    * 
    * @param codons