Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 79c6531..84be72c 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -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
@@ -71,19 +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);
@@ -112,7 +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);
 
@@ -151,7 +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 + " "));