X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=dd281767486ffde30bda227ff3ab6ed71c46531c;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=cd465419ba703a83e6f072b5fbb6cfda9c3be900;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index cd46541..dd28176 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -1,41 +1,43 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
  */
 package jalview.io;
 
 /**
- * <p>Title: </p>
- *  PileUpfile
- * <p>Description: </p>
- *
- *  Read and write PileUp style MSF Files.
- *  This used to be the MSFFile class, and was written according to the EBI's idea
- *  of a subset of the MSF alignment format. But, that was updated to reflect current
- *  GCG style IO fashion, as found in Emboss (thanks David Martin!)
- *
- **/
+ * <p>
+ * Title:
+ * </p>
+ * PileUpfile
+ * <p>
+ * Description:
+ * </p>
+ * 
+ * Read and write PileUp style MSF Files. This used to be the MSFFile class, and
+ * was written according to the EBI's idea of a subset of the MSF alignment
+ * format. But, that was updated to reflect current GCG style IO fashion, as
+ * found in Emboss (thanks David Martin!)
+ * 
+ */
 import java.io.*;
 
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class PileUpfile
-    extends MSFfile
+public class PileUpfile extends MSFfile
 {
 
   /**
@@ -47,24 +49,28 @@ public class PileUpfile
 
   /**
    * Creates a new MSFfile object.
-   *
-   * @param inFile DOCUMENT ME!
-   * @param type DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @param inFile
+   *          DOCUMENT ME!
+   * @param type
+   *          DOCUMENT ME!
+   * 
+   * @throws IOException
+   *           DOCUMENT ME!
    */
-  public PileUpfile(String inFile, String type)
-      throws IOException
+  public PileUpfile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
+
   public PileUpfile(FileParse source) throws IOException
   {
     super(source);
   }
+
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String print()
@@ -89,17 +95,16 @@ public class PileUpfile
       i++;
     }
 
-    out.append("   MSF: " + s[0].getSequence().length +
-               "   Type: P    Check:  " + bigChecksum % 10000 + "   ..\n\n\n");
+    out.append("   MSF: " + s[0].getSequence().length
+            + "   Type: P    Check:  " + bigChecksum % 10000
+            + "   ..\n\n\n");
 
     i = 0;
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequenceAsString();
-      out.append(" Name: " + printId(s[i]) +
-                 " oo  Len:  " +
-                 seq.length() + "  Check:  " + checksums[i] +
-                 "  Weight:  1.00\n");
+      out.append(" Name: " + printId(s[i]) + " oo  Len:  " + seq.length()
+              + "  Check:  " + checksums[i] + "  Weight:  1.00\n");
 
       if (seq.length() > max)
       {
@@ -126,7 +131,7 @@ public class PileUpfile
 
     int nochunks = (max / len) + 1;
 
-    if ( (max % len) == 0)
+    if ((max % len) == 0)
     {
       nochunks--;
     }
@@ -135,7 +140,7 @@ public class PileUpfile
     {
       int j = 0;
 
-      while ( (j < s.length) && (s[j] != null))
+      while ((j < s.length) && (s[j] != null))
       {
         String name = printId(s[j]);
 
@@ -146,8 +151,8 @@ public class PileUpfile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ( (end < s[j].getSequence().length) &&
-              (start < s[j].getSequence().length))
+          if ((end < s[j].getSequence().length)
+                  && (start < s[j].getSequence().length))
           {
             out.append(s[j].getSequence(start, end));