X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=f7f718b0d34b73c8d3d65a4ddb84d1f934fce25b;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=50ed8051583ed6f0f790b958c7fd39415c1d7cc3;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 50ed805..f7f718b 100755
--- 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);
@@ -103,7 +92,7 @@ public class PileUpfile extends MSFfile
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length
+    out.append("   MSF: " + s[0].getLength()
             + "   Type: P    Check:  " + bigChecksum % 10000 + "   ..");
     out.append(newline);
     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 + " "));
 
@@ -161,8 +151,8 @@ public class PileUpfile extends MSFfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ((end < s[j].getSequence().length)
-                  && (start < s[j].getSequence().length))
+          int length = s[j].getLength();
+          if ((end < length) && (start < length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -177,7 +167,7 @@ public class PileUpfile extends MSFfile
           }
           else
           {
-            if (start < s[j].getSequence().length)
+            if (start < length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
               out.append(newline);