X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=f62ad81f999e5ba713fc471f2d88aaf4d7d379a0;hb=0e5be6925629dad5a92036d728f8856fde2d5488;hp=3e8f336fbb0f237b7ff65e29238300a0185d0ba2;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 3e8f336..f62ad81 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,27 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.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!
@@ -60,13 +66,10 @@ public class MSFfile extends AlignFile
     super(source);
   }
 
-  {
-    // TODO Auto-generated constructor stub
-  }
-
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     int i = 0;
@@ -216,9 +219,10 @@ 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;
@@ -227,7 +231,7 @@ 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());
@@ -284,7 +288,10 @@ 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];
@@ -297,7 +304,7 @@ 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)
       {
@@ -330,16 +337,14 @@ 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;
-
-    if ((max % len) == 0)
-    {
-      nochunks--;
-    }
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
@@ -367,7 +372,7 @@ public class MSFfile extends AlignFile
             }
             else
             {
-              out.append("\n");
+              out.append(newline);
             }
           }
           else
@@ -375,13 +380,13 @@ 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);
               }
             }
           }
@@ -390,7 +395,7 @@ public class MSFfile extends AlignFile
         j++;
       }
 
-      out.append("\n");
+      out.append(newline);
     }
 
     return out.toString();
@@ -401,6 +406,7 @@ public class MSFfile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());