X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=f4beccb42d77ccad84cbd77cd53c9c17d981fe59;hb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;hp=f1cf1e0bc94529e16b6ba2af4ef1c21b9e36fa3d;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1cf1e0..f4beccb 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -16,83 +16,120 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.io;
 
 import java.io.*;
+
 import java.net.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class IdentifyFile
 {
-  public static String Identify(String file, String protocol)
-  {
-    String reply = "PFAM";
-    try{
-
-      BufferedReader reader = null;
-
-      if(protocol.equals("File"))
-        reader = new BufferedReader(new FileReader(file));
-
-      else if (protocol.equals("URL"))
-      {
-        reply = "URL NOT FOUND";
-        URL url = new URL(file);
-        reader = new BufferedReader(new InputStreamReader( url.openStream() ) );
-        reply = "error";
-      }
-      else if( protocol.equals("Paste"))
-        reader = new BufferedReader( new StringReader(file) );
-
-
-      String data;
-      while( (data=reader.readLine())!=null)
-      {
-        data = data.toUpperCase();
-        if(data.indexOf("#")==0 || data.length()<1)
-          continue;
-
-        if(data.indexOf("PILEUP")>-1)
-        {
-          reply = "PileUp";
-          break;
-        }
-        if((data.indexOf("//")==0)
-           || ((data.indexOf("!!")>-1)
-           && (data.indexOf("!!")<data.indexOf("_MULTIPLE_ALIGNMENT "))))
-        {
-          reply = "MSF";
-          break;
-        }
-        else if(data.indexOf("CLUSTAL")>-1)
-        {
-          reply = "CLUSTAL";
-          break;
-        }
-        else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     * @param protocol DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String Identify(String file, String protocol)
+    {
+        String reply = "PFAM";
+        String error =  "FILE NOT FOUND";
+
+        try
         {
-          reply = "PIR";
-          break;
+            BufferedReader reader = null;
+
+            if (protocol.equalsIgnoreCase("File"))
+            {
+                reader = new BufferedReader(new FileReader(file));
+            }
+            else if (protocol.equalsIgnoreCase("URL"))
+            {
+                error = "URL NOT FOUND";
+                URL url = new URL(file);
+                reader = new BufferedReader(new InputStreamReader(
+                            url.openStream()));
+
+            }
+            else if (protocol.equalsIgnoreCase("Paste"))
+            {
+                reader = new BufferedReader(new StringReader(file));
+            }
+
+            String data;
+
+            while ((data = reader.readLine()) != null)
+            {
+                data = data.toUpperCase();
+
+                if ((data.indexOf("#") == 0) || (data.length() < 1))
+                {
+                    continue;
+                }
+
+                if (data.indexOf("PILEUP") > -1)
+                {
+                    reply = "PileUp";
+
+                    break;
+                }
+
+                if ((data.indexOf("//") == 0) ||
+                        ((data.indexOf("!!") > -1) &&
+                        (data.indexOf("!!") < data.indexOf(
+                            "_MULTIPLE_ALIGNMENT "))))
+                {
+                    reply = "MSF";
+
+                    break;
+                }
+                else if (data.indexOf("CLUSTAL") > -1)
+                {
+                    reply = "CLUSTAL";
+
+                    break;
+                }
+                else if ((data.indexOf(">P1;") > -1) ||
+                        (data.indexOf(">DL;") > -1))
+                {
+                    reply = "PIR";
+
+                    break;
+                }
+                else if (data.indexOf(">") > -1)
+                {
+                    // could be BLC file, read next line to confirm
+                    data = reader.readLine();
+
+                    if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )
+                    {
+                        reply = "BLC";
+                    }
+                    else
+                    {
+                        reply = "FASTA";
+                    }
+
+                    break;
+                }
+            }
+
+            reader.close();
         }
-        else if(data.indexOf(">")>-1)
+        catch (Exception ex)
         {
-          // could be BLC file, read next line to confirm
-          data = reader.readLine();
-          if(data.indexOf(">")>-1)
-            reply = "BLC";
-          else
-            reply = "FASTA";
-
-            break;
+            System.err.println("File Identification failed!\n" + ex);
+            return error;
         }
-      }
-      reader.close();
+        return reply;
     }
-    catch(Exception ex){
-      System.err.println("File Identification failed!\n"+ex);}
-
-    return reply;
-  }
-
-
 }