From 2a64503d035e47cf9a40e5de979fd22980e50106 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Feb 2005 13:20:33 +0000
Subject: [PATCH] isAligned method added

---
 src/jalview/datamodel/Alignment.java  |   11 +++++++++++
 src/jalview/datamodel/AlignmentI.java |    2 ++
 2 files changed, 13 insertions(+)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 0875450..62b9ea9 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -500,6 +500,17 @@ public class Alignment implements AlignmentI
   {
     return AAFrequency.calculate(sequences, 0, getWidth());
   }
+
+  public boolean isAligned()
+  {
+    int width = getWidth();
+    for (int i = 0; i < sequences.size(); i++)
+      if (getSequenceAt(i).getLength() != width)
+        return false;
+
+    return true;
+
+  }
 }
 
 
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 80b22ae..182b687 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -11,6 +11,8 @@ public interface AlignmentI {
   public int         getWidth() ;
   public int         getMaxIdLength() ;
 
+  public boolean isAligned();
+
   public Vector      getSequences();
   public SequenceI   getSequenceAt(int i);
 
-- 
1.7.10.2