X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=d9ed5166d9f88d04d0818007dc6114cd8f297b7f;hb=91d83d4836ba3f8c6c395d46d607faf693946e66;hp=8402d2476aa4962c40ff3e8ad9af4f1648d882de;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 8402d24..d9ed516 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.io.IOException;
 import java.util.Vector;
@@ -103,14 +104,9 @@ public class PIRFile extends AlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
-    return print(getSeqsAsArray());
-  }
-
-  public String print(SequenceI[] s)
-  {
-    boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+    boolean is_NA = Comparison.isNucleotide(s);
     int len = 72;
     StringBuffer out = new StringBuffer();
     int i = 0;
@@ -162,7 +158,7 @@ public class PIRFile extends AlignFile
         }
         else
         {
-          out.append(">P1;" + printId(s[i]));
+          out.append(">P1;" + printId(s[i], jvsuffix));
           out.append(newline);
           if (s[i].getDescription() != null)
           {