X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=d6188091491f83d54bfe6e4f4460883c91b44d40;hb=c55e1fa5d2782cc46e515c11a91cf502f37386ab;hp=049606d87b3683dbb53e5fb30a043274af65e3fc;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 049606d..d618809 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.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.
  * 
@@ -37,9 +37,10 @@ public class ClustalFile extends AlignFile
   {
   }
 
-  public ClustalFile(String inFile, String type) throws IOException
+  public ClustalFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public ClustalFile(FileParse source) throws IOException
@@ -196,13 +197,7 @@ public class ClustalFile extends AlignFile
   }
 
   @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-    // TODO: locaRNA style aln output
-  }
-
-  public String print(SequenceI[] s)
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
 
@@ -213,12 +208,9 @@ public class ClustalFile extends AlignFile
 
     while ((i < s.length) && (s[i] != null))
     {
-      String tmp = printId(s[i]);
+      String tmp = printId(s[i], jvsuffix);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       if (tmp.length() > maxid)
       {
@@ -244,19 +236,20 @@ public class ClustalFile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+        out.append(new Format("%-" + maxid + "s").form(printId(s[j],
+                jvsuffix) + " "));
 
         int start = i * len;
         int end = start + len;
 
-        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].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length)
+          if (start < length)
           {
             out.append(s[j].getSequenceAsString().substring(start));
           }