JAL-4308 reduce number of refs to 5, always have canonical reference first.

[jalview.git] / src / jalview / io / PIRFile.java

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 8402d24..adfc1cb 100755 (executable)
--- 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;
@@ -58,7 +59,7 @@ public class PIRFile extends AlignFile
     {
       if (line.length() == 0)
       {
-        // System.out.println("blank line");
+        // jalview.bin.Console.outPrintln("blank line");
         continue;
       }
       if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
@@ -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)
           {