Jalview 2.6 source licence

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

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 1cb016c..5a15862 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -1,20 +1,19 @@
 /*
- * 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;
 
@@ -24,12 +23,11 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class FastaFile
-    extends AlignFile
+public class FastaFile extends AlignFile
 {
   /**
    * Length of a sequence line
@@ -47,14 +45,16 @@ public class FastaFile
 
   /**
    * Creates a new FastaFile 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 FastaFile(String inFile, String type)
-      throws IOException
+  public FastaFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
@@ -66,11 +66,11 @@ public class FastaFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @throws IOException DOCUMENT ME!
+   * 
+   * @throws IOException
+   *           DOCUMENT ME!
    */
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
     StringBuffer sb = new StringBuffer();
     boolean firstLine = true;
@@ -80,7 +80,7 @@ public class FastaFile
 
     boolean annotation = false;
 
-    while ( (line = nextLine()) != null)
+    while ((line = nextLine()) != null)
     {
       line = line.trim();
       if (line.length() > 0)
@@ -96,12 +96,10 @@ public class FastaFile
               for (int i = 0; i < sb.length(); i++)
               {
                 anots[i] = new Annotation(anotString.substring(i, i + 1),
-                                          null,
-                                          ' ', 0);
+                        null, ' ', 0);
               }
-              AlignmentAnnotation aa = new AlignmentAnnotation(
-                  seq.getName().substring(2), seq.getDescription(),
-                  anots);
+              AlignmentAnnotation aa = new AlignmentAnnotation(seq
+                      .getName().substring(2), seq.getDescription(), anots);
 
               annotations.addElement(aa);
             }
@@ -144,13 +142,11 @@ public class FastaFile
       String anotString = sb.toString();
       for (int i = 0; i < sb.length(); i++)
       {
-        anots[i] = new Annotation(anotString.substring(i, i + 1),
-                                  null,
-                                  ' ', 0);
+        anots[i] = new Annotation(anotString.substring(i, i + 1), null,
+                ' ', 0);
       }
-      AlignmentAnnotation aa = new AlignmentAnnotation(
-          seq.getName().substring(2), seq.getDescription(),
-          anots);
+      AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
+              .substring(2), seq.getDescription(), anots);
 
       annotations.addElement(aa);
     }
@@ -163,9 +159,9 @@ public class FastaFile
   }
 
   /**
-   * called by AppletFormatAdapter to generate
-   * an annotated alignment, rather than bare
-   * sequences.
+   * called by AppletFormatAdapter to generate an annotated alignment, rather
+   * than bare sequences.
+   * 
    * @param al
    */
   public void addAnnotations(Alignment al)
@@ -173,21 +169,25 @@ public class FastaFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = (AlignmentAnnotation) annotations.elementAt(i);
+      AlignmentAnnotation aa = (AlignmentAnnotation) annotations
+              .elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
-      al.addAnnotation( aa );
+      al.addAnnotation(aa);
     }
   }
 
-
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param len DOCUMENT ME!
-   * @param gaps DOCUMENT ME!
-   * @param displayId DOCUMENT ME!
-   *
+   * 
+   * @param s
+   *          DOCUMENT ME!
+   * @param len
+   *          DOCUMENT ME!
+   * @param gaps
+   *          DOCUMENT ME!
+   * @param displayId
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public String print(SequenceI[] s)
@@ -195,7 +195,7 @@ public class FastaFile
     out = new StringBuffer();
     int i = 0;
 
-    while ( (i < s.length) && (s[i] != null))
+    while ((i < s.length) && (s[i] != null))
     {
       out.append(">" + printId(s[i]));
       if (s[i].getDescription() != null)
@@ -218,7 +218,8 @@ public class FastaFile
         }
         else if (start < s[i].getLength())
         {
-          out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");
+          out.append(s[i].getSequenceAsString(start, s[i].getLength())
+                  + "\n");
         }
       }
 
@@ -230,7 +231,7 @@ public class FastaFile
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String print()