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 396ef2d..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)
@@ -543,4 +544,13 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+
+  /**
+   * Calculate the visible start and end index of an alignment. The result is
+   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+   * 
+   * @param hiddenCols
+   * @return
+   */
+  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
 }