Jalview 2.6 source licence

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 2679b48..dc341b9 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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.
  * 
- * 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 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;
 
@@ -36,9 +35,9 @@ public class IdentifyFile
    *       instead.
    * 
    * @param file
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param protocol
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @return ID String
    */
   public String Identify(String file, String protocol)
@@ -66,7 +65,7 @@ public class IdentifyFile
   public String Identify(FileParse source)
   {
     return Identify(source, true); // preserves original behaviour prior to
-                                    // version 2.3
+    // version 2.3
   }
 
   /**
@@ -84,7 +83,7 @@ public class IdentifyFile
     int length = 0;
     boolean lineswereskipped = false;
     boolean isBinary = false; // true if length is non-zero and non-printable
-                              // characters are encountered
+    // characters are encountered
     try
     {
       if (!closeSource)
@@ -101,8 +100,8 @@ public class IdentifyFile
             char c = data.charAt(i);
             isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r'
                     && c != 5 && c != 27); // nominal binary character filter
-                                            // excluding CR, LF, tab,DEL and ^E
-                                            // for certain blast ids
+            // excluding CR, LF, tab,DEL and ^E
+            // for certain blast ids
           }
         }
         if (isBinary)
@@ -187,7 +186,7 @@ public class IdentifyFile
             {
               if (data.indexOf("*") == data2.indexOf("*"))
               {
-              reply = "BLC";
+                reply = "BLC";
               }
               // otherwise can still possibly be a PIR file
             }
@@ -200,8 +199,10 @@ public class IdentifyFile
               break;
             }
           }
-          // TODO final check for PIR content. require >P1;title\n<blah>\nterminated sequence to occur at least once. 
-          // the PIR/fasta ambiguity may be the use case that is needed to have a 'Parse as type XXX' parameter for the applet/application.
+          // TODO final check for PIR content. require
+          // >P1;title\n<blah>\nterminated sequence to occur at least once.
+          // the PIR/fasta ambiguity may be the use case that is needed to have
+          // a 'Parse as type XXX' parameter for the applet/application.
           break;
         }
         else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
@@ -209,21 +210,18 @@ public class IdentifyFile
           reply = "PDB";
           break;
         }
-        /*// TODO comment out SimpleBLAST identification for Jalview 2.4.1
-        else if (!lineswereskipped && data.indexOf("BLAST")<4)
-        {
-          reply = "SimpleBLAST";
-          break;
-            
-        }
-        // end comments for Jalview 2.4.1
+        /*
+         * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
+         * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
+         * "SimpleBLAST"; break;
          * 
+         * } // end comments for Jalview 2.4.1
          */
         else if (!lineswereskipped && data.charAt(0) != '*'
                 && data.charAt(0) != ' '
                 && data.indexOf(":") < data.indexOf(",")) // &&
-                                                          // data.indexOf(",")<data.indexOf(",",
-                                                          // data.indexOf(",")))
+        // data.indexOf(",")<data.indexOf(",",
+        // data.indexOf(",")))
         {
           // file looks like a concise JNet file
           reply = "JnetFile";
@@ -231,7 +229,7 @@ public class IdentifyFile
         }
 
         lineswereskipped = true; // this means there was some junk before any
-                                  // key file signature
+        // key file signature
       }
       if (closeSource)
       {