JAL-1807 explicit imports (jalview.io.*)

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 64e098d..ab2c497 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,28 +1,34 @@
 /*
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.util.Format;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -61,10 +67,6 @@ public class MSFfile extends AlignFile
     super(source);
   }
 
-  {
-    // TODO Auto-generated constructor stub
-  }
-
   /**
    * DOCUMENT ME!
    */
@@ -212,7 +214,7 @@ public class MSFfile extends AlignFile
   public String print(SequenceI[] seqs)
   {
 
-    boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+    boolean is_NA = Comparison.isNucleotide(seqs);
 
     SequenceI[] s = new SequenceI[seqs.length];
 
@@ -301,8 +303,8 @@ public class MSFfile extends AlignFile
       nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
 
       idBlock[i] = new String("Len: "
-              + maxLenpad.form(s[i].getSequence().length) + "  Check: "
-              + maxChkpad.form(checksums[i]) + "  Weight: 1.00" + newline);
+              + maxLenpad.formLong(s[i].getSequence().length) + "  Check: "
+              + maxChkpad.formLong(checksums[i]) + "  Weight: 1.00" + newline);
 
       if (s[i].getName().length() > maxid)
       {