Merge remote-tracking branch 'origin/releases/Release_2_10_2_Branch' into features...

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

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 50ed805..7b5ce0d 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -72,19 +72,8 @@ public class PileUpfile extends MSFfile
     super(source);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
-
   @Override
-  public String print(SequenceI[] s)
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("PileUp");
     out.append(newline);
@@ -113,8 +102,9 @@ public class PileUpfile extends MSFfile
     while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
-      out.append(" Name: " + printId(s[i]) + " oo  Len:  " + seq.length()
-              + "  Check:  " + checksums[i] + "  Weight:  1.00");
+      out.append(" Name: " + printId(s[i], jvsuffix) + " oo  Len:  "
+              + seq.length() + "  Check:  " + checksums[i]
+              + "  Weight:  1.00");
       out.append(newline);
 
       if (seq.length() > max)
@@ -152,7 +142,7 @@ public class PileUpfile extends MSFfile
 
       while ((j < s.length) && (s[j] != null))
       {
-        String name = printId(s[j]);
+        String name = printId(s[j], jvsuffix);
 
         out.append(new Format("%-" + maxid + "s").form(name + " "));