X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=290707dc7c3091017a96bd906b12d0a6ba395c9a;hb=90add82a33c05e218a92eb1cdb2c345da05465f8;hp=bd7882730794699965bb12d96069b1b98bb230f9;hpb=52402128d98c6744eb6348dd788fe6e8cd34575c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index bd78827..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
@@ -1837,7 +1808,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**