X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=adfc1cbdd8173d6e31c73a5f357b48c72c011040;hb=1ef93cb2817f75699773f049b8d25e5b509c2830;hp=5f5c23c4c834e4f79788f56bb3a93e454ba65996;hpb=8dbeca869699c196f4239fb1f8909d5a4c23ee86;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 5f5c23c..adfc1cb 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;
@@ -36,9 +37,10 @@ public class PIRFile extends AlignFile
   {
   }
 
-  public PIRFile(String inFile, String type) throws IOException
+  public PIRFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public PIRFile(FileParse source) throws IOException
@@ -57,7 +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)
@@ -102,14 +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;
@@ -161,7 +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)
           {