From 90add82a33c05e218a92eb1cdb2c345da05465f8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 12 Dec 2016 22:01:47 +0000
Subject: [PATCH] JAL-2360 simplify nucleotide flag, remove setter

---
 src/jalview/datamodel/Alignment.java  |   41 +++++----------------------------
 src/jalview/datamodel/AlignmentI.java |    6 -----
 2 files changed, 6 insertions(+), 41 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d651c1d..290707d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -54,11 +54,7 @@ public class Alignment implements AlignmentI
 
   protected char gapCharacter = '-';
 
-  protected int type = NUCLEOTIDE;
-
-  public static final int PROTEIN = 0;
-
-  public static final int NUCLEOTIDE = 1;
+  private boolean nucleotide = true;
 
   public boolean hasRNAStructure = false;
 
@@ -76,14 +72,7 @@ public class Alignment implements AlignmentI
     hiddenSequences = new HiddenSequences(this);
     codonFrameList = new ArrayList<AlignedCodonFrame>();
 
-    if (Comparison.isNucleotide(seqs))
-    {
-      type = NUCLEOTIDE;
-    }
-    else
-    {
-      type = PROTEIN;
-    }
+    nucleotide = Comparison.isNucleotide(seqs);
 
     sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
 
@@ -218,7 +207,9 @@ public class Alignment implements AlignmentI
   }
 
   /**
-   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+   * this currently does not recalculate whether or not the alignment is
+   * nucleotide, so mixed alignments may have undefined behaviour.
    * 
    * @param snew
    */
@@ -977,29 +968,9 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setNucleotide(boolean b)
-  {
-    if (b)
-    {
-      type = NUCLEOTIDE;
-    }
-    else
-    {
-      type = PROTEIN;
-    }
-  }
-
-  @Override
   public boolean isNucleotide()
   {
-    if (type == NUCLEOTIDE)
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
+    return nucleotide;
   }
 
   @Override
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7274e5f..1b5cc0b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -298,12 +298,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   boolean hasRNAStructure();
 
   /**
-   * Set alignment to be a nucleotide sequence
-   * 
-   */
-  void setNucleotide(boolean b);
-
-  /**
    * Get the associated dataset for the alignment.
    * 
    * @return Alignment containing dataset sequences or null of this is a
-- 
1.7.10.2