X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=84be72ceb4416c3d5815abfef60de041f0cb0cad;hb=refs%2Fheads%2Fbug%2FJAL-2576;hp=2a902b44992e8f1a53bb4a777c75f95138d40edd;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 2a902b4..84be72c 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -35,10 +35,10 @@ package jalview.io;
  * found in Emboss (thanks David Martin!)
  * 
  */
-import java.io.*;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
 
 public class PileUpfile extends MSFfile
 {
@@ -55,15 +55,16 @@ public class PileUpfile extends MSFfile
    * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param sourceType
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public PileUpfile(String inFile, String type) throws IOException
+  public PileUpfile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public PileUpfile(FileParse source) throws IOException
@@ -71,17 +72,8 @@ public class PileUpfile extends MSFfile
     super(source);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
-
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("PileUp");
     out.append(newline);
@@ -110,7 +102,8 @@ 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()
+      out.append(" Name: " + printId(s[i], jvsuffix) + " oo  Len:  "
+              + seq.length()
               + "  Check:  " + checksums[i] + "  Weight:  1.00");
       out.append(newline);
 
@@ -141,12 +134,7 @@ public class PileUpfile extends MSFfile
 
     int len = 50;
 
-    int nochunks = (max / len) + 1;
-
-    if ((max % len) == 0)
-    {
-      nochunks--;
-    }
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
@@ -154,7 +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 + " "));