X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=4b1220b1ab98bb4d23e31c3106c0c5b473ec5ef2;hb=48a66195bf4aee8b2c479d3bbbf4c1fb8b824f5a;hp=9c73873397be19ac39176b0e52bf34c8c7e67c09;hpb=06476b6d02ef690bf684905cba39eb7b5db7525b;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 9c73873..4b1220b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -20,7 +20,6 @@
  */
 package jalview.datamodel;
 
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -48,15 +47,29 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 
-   * Calculates the maximum width of the alignment, including gaps.
+   * Answers the width of the alignment, including gaps, that is, the length of
+   * the longest sequence, or -1 if there are no sequences. Avoid calling this
+   * method repeatedly where possible, as it has to perform a calculation. Note
+   * that this width includes any hidden columns.
    * 
-   * @return Greatest sequence length within alignment, or -1 if no sequences
-   *         present
+   * @return
+   * @see AlignmentI#getVisibleWidth()
    */
   @Override
   int getWidth();
 
   /**
+   * 
+   * Answers the visible width of the alignment, including gaps, that is, the
+   * length of the longest sequence, excluding any hidden columns. Answers -1 if
+   * there are no sequences. Avoid calling this method repeatedly where
+   * possible, as it has to perform a calculation.
+   * 
+   * @return
+   */
+  int getVisibleWidth();
+
+  /**
    * Calculates if this set of sequences (visible and invisible) are all the
    * same length
    * 
@@ -389,7 +402,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * @return hashtable of alignment properties (or null if none are defined)
    */
-  Hashtable getProperties();
+  Map<Object, Object> getProperties();
 
   /**
    * add a reference to a frame of aligned codons for this alignment