Merge branch 'feature/JAL-2664' into feature/JAL-2527

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 9036eb4..4dbf950 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -58,7 +58,7 @@ public class MSFfile extends AlignFile
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public MSFfile(String inFile, String type) throws IOException
+  public MSFfile(String inFile, DataSourceType type) throws IOException
   {
     super(inFile, type);
   }
@@ -216,7 +216,8 @@ public class MSFfile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
-  public String print(SequenceI[] sqs)
+  @Override
+  public String print(SequenceI[] sqs, boolean jvSuffix)
   {
 
     boolean is_NA = Comparison.isNucleotide(sqs);
@@ -277,10 +278,10 @@ public class MSFfile extends AlignFile
       i++;
     }
 
-    Format maxLenpad = new Format("%" + (new String("" + max)).length()
-            + "d");
-    Format maxChkpad = new Format("%" + (new String("1" + max)).length()
-            + "d");
+    Format maxLenpad = new Format(
+            "%" + (new String("" + max)).length() + "d");
+    Format maxChkpad = new Format(
+            "%" + (new String("1" + max)).length() + "d");
     i = 0;
 
     int bigChecksum = 0;
@@ -307,7 +308,7 @@ public class MSFfile extends AlignFile
     while ((i < s.length) && (s[i] != null))
     {
 
-      nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
+      nameBlock[i] = new String("  Name: " + printId(s[i], jvSuffix) + " ");
 
       idBlock[i] = new String("Len: "
               + maxLenpad.form(s[i].getSequence().length) + "  Check: "
@@ -359,7 +360,7 @@ public class MSFfile extends AlignFile
 
       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 + " "));
 
@@ -407,15 +408,4 @@ public class MSFfile extends AlignFile
 
     return out.toString();
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }