JAL-2344 handle null format, simplify JalviewFileChooser constructor

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index aec1a5d..5d58d42 100755 (executable)
--- 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
@@ -47,11 +48,13 @@ public class ClustalFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
   }
 
+  @Override
   public void parse() throws IOException
   {
     int i = 0;
@@ -193,13 +196,8 @@ public class ClustalFile extends AlignFile
     }
   }
 
-  public String print()
-  {
-    return print(getSeqsAsArray());
-    // TODO: locaRNA style aln output
-  }
-
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
 
@@ -210,7 +208,7 @@ 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)
       {
@@ -233,7 +231,7 @@ public class ClustalFile extends AlignFile
     maxid++;
 
     int len = 60;
-    int nochunks = (max / len) + 1;
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
@@ -241,7 +239,8 @@ 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;