From 552a05df8deb46017d3e1931cfc9a196553f2a45 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 10 Sep 2018 13:45:57 +0100
Subject: [PATCH] JAL-3099 new method AlignmentI.getVisibleWidth()

---
 src/jalview/datamodel/Alignment.java  |   28 +++++++---------------------
 src/jalview/datamodel/AlignmentI.java |   20 +++++++++++++++++---
 2 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3ba35b6..11d28a0 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -720,31 +720,17 @@ public class Alignment implements AlignmentI
   
     return maxLength;
   }
-  /*
+
   @Override
-  public int getWidth()
+  public int getVisibleWidth()
   {
-    final Wrapper temp = new Wrapper();
-  
-    forEachSequence(new Consumer<SequenceI>()
+    int w = getWidth();
+    if (hiddenCols != null)
     {
-      @Override
-      public void accept(SequenceI s)
-      {
-        if (s.getLength() > temp.inner)
-        {
-          temp.inner = s.getLength();
-        }
-      }
-    }, 0, sequences.size() - 1);
-  
-    return temp.inner;
+      w -= hiddenCols.getSize();
+    }
+    return w;
   }
-  
-  public static class Wrapper
-  {
-    public int inner;
-  }*/
 
   /**
    * DOCUMENT ME!
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5fb16d6..f129a4c 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -48,15 +48,29 @@ 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
    * 
-- 
1.7.10.2