fileFormat enum wip changes

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

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 59ffbaa..c6c10bd 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -144,7 +144,8 @@ public class PfamFile extends AlignFile
     }
   }
 
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("");
 
@@ -155,7 +156,7 @@ public class PfamFile extends AlignFile
 
     while ((i < s.length) && (s[i] != null))
     {
-      String tmp = printId(s[i]);
+      String tmp = printId(s[i], jvsuffix);
 
       if (s[i].getSequence().length > max)
       {
@@ -179,7 +180,8 @@ public class PfamFile extends AlignFile
 
     while ((j < s.length) && (s[j] != null))
     {
-      out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+      out.append(new Format("%-" + maxid + "s")
+              .form(printId(s[j], jvsuffix) + " "));
 
       out.append(s[j].getSequenceAsString());
       out.append(newline);
@@ -190,10 +192,4 @@ public class PfamFile extends AlignFile
 
     return out.toString();
   }
-
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }