JAL-1925 update source version in license

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 73d0f0f..b3cdfe8 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,28 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.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!
@@ -44,12 +49,12 @@ public class MSFfile extends AlignFile
    * Creates a new MSFfile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public MSFfile(String inFile, String type) throws IOException
   {
@@ -61,10 +66,6 @@ public class MSFfile extends AlignFile
     super(source);
   }
 
-  {
-    // TODO Auto-generated constructor stub
-  }
-
   /**
    * DOCUMENT ME!
    */
@@ -170,7 +171,7 @@ public class MSFfile extends AlignFile
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -203,9 +204,9 @@ public class MSFfile extends AlignFile
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param is_NA
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -217,9 +218,10 @@ public class MSFfile extends AlignFile
     SequenceI[] s = new SequenceI[seqs.length];
 
     StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
-            + "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't
-                                              // remember NA or AA yet.
-
+            + "_MULTIPLE_ALIGNMENT 1.0");
+    // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+    out.append(newline);
+    out.append(newline);
     int max = 0;
     int maxid = 0;
     int i = 0;
@@ -228,7 +230,7 @@ public class MSFfile extends AlignFile
     {
       // Replace all internal gaps with . and external spaces with ~
       s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
-              .replace('-', '.'));
+              .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
 
       StringBuffer sb = new StringBuffer();
       sb.append(s[i].getSequence());
@@ -285,7 +287,10 @@ public class MSFfile extends AlignFile
     long maxNB = 0;
     out.append("   MSF: " + s[0].getSequence().length + "   Type: "
             + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000)
-            + "   ..\n\n\n");
+            + "   ..");
+    out.append(newline);
+    out.append(newline);
+    out.append(newline);
 
     String[] nameBlock = new String[s.length];
     String[] idBlock = new String[s.length];
@@ -298,7 +303,7 @@ public class MSFfile extends AlignFile
 
       idBlock[i] = new String("Len: "
               + maxLenpad.form(s[i].getSequence().length) + "  Check: "
-              + maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
+              + maxChkpad.form(checksums[i]) + "  Weight: 1.00" + newline);
 
       if (s[i].getName().length() > maxid)
       {
@@ -331,8 +336,11 @@ public class MSFfile extends AlignFile
     }
 
     maxid++;
-    out.append("\n\n//\n\n");
-
+    out.append(newline);
+    out.append(newline);
+    out.append("//");
+    out.append(newline);
+    out.append(newline);
     int len = 50;
 
     int nochunks = (max / len) + 1;
@@ -368,7 +376,7 @@ public class MSFfile extends AlignFile
             }
             else
             {
-              out.append("\n");
+              out.append(newline);
             }
           }
           else
@@ -376,13 +384,13 @@ public class MSFfile extends AlignFile
             if (start < s[j].getSequence().length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
-              out.append("\n");
+              out.append(newline);
             }
             else
             {
               if (k == 0)
               {
-                out.append("\n");
+                out.append(newline);
               }
             }
           }
@@ -391,7 +399,7 @@ public class MSFfile extends AlignFile
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();