X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=f1dfffece42b9ac20a24bc866aafe963d1a9e1ed;hb=fae5909561b434d5fa0043584ace268c545dad9b;hp=55d771b205d5576be58c50ba69783af7f0cb5bb8;hpb=b3f66e3a4fd8d3f24a5a44f8716a41c84c4d1cb3;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 55d771b..f1dfffe 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,80 +1,170 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
+ * 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
+ */
 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)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param file DOCUMENT ME!
+   * @param protocol DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String Identify(String file, String protocol)
   {
     String reply = "PFAM";
-    try{
-
+    String error = "FILE NOT FOUND";
+    try
+    {
       BufferedReader reader = null;
 
-      if(protocol.equals("File"))
+      if (protocol.equals(AppletFormatAdapter.FILE))
+      {
         reader = new BufferedReader(new FileReader(file));
-
-      else if (protocol.equals("URL"))
+      }
+      else if (protocol.equals(AppletFormatAdapter.URL))
       {
-        reply = "URL NOT FOUND";
+        error = "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) );
+        reader = new BufferedReader(new InputStreamReader(
+            url.openStream()));
 
+      }
+      else if (protocol.equals(AppletFormatAdapter.PASTE))
+      {
+        reader = new BufferedReader(new StringReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      {
+        java.io.InputStream is = getClass().getResourceAsStream("/" +
+            file);
+        reader = new BufferedReader(new java.io.InputStreamReader(is));
+      }
 
       String data;
-      while( (data=reader.readLine())!=null)
+
+      while ( (data = reader.readLine()) != null)
       {
         data = data.toUpperCase();
-        if(data.indexOf("#")==0 || data.length()<1)
+
+        if ( (data.indexOf("# STOCKHOLM") > -1))
+        {
+          reply = "STH";
+
+          break;
+        }
+
+        if ( (data.indexOf("#") == 0) || (data.length() < 1))
+        {
           continue;
+        }
+
+        if (data.indexOf("PILEUP") > -1)
+        {
+          reply = "PileUp";
+
+          break;
+        }
 
-        if(data.indexOf("PILEUP")>-1)
+        if ( (data.indexOf("//") == 0) ||
+            ( (data.indexOf("!!") > -1) &&
+             (data.indexOf("!!") < data.indexOf(
+                 "_MULTIPLE_ALIGNMENT "))))
         {
           reply = "MSF";
+
           break;
         }
-        else if(data.indexOf("CLUSTAL")>-1)
+        else if (data.indexOf("CLUSTAL") > -1)
         {
           reply = "CLUSTAL";
+
           break;
         }
-        else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)
+        else if ( (data.indexOf(">P1;") > -1) ||
+                 (data.indexOf(">DL;") > -1))
         {
           reply = "PIR";
+
           break;
         }
-        else if(data.indexOf(">")>-1)
+        else if (data.indexOf(">") > -1)
         {
           // could be BLC file, read next line to confirm
           data = reader.readLine();
-          if(data.indexOf(">")>-1)
+
+          if (data.indexOf(">") > -1)
+          {
             reply = "BLC";
+          }
           else
-            reply = "FASTA";
+          {
+            //Is this a single line BLC file?
+            reader.readLine();
+            String data2 = reader.readLine();
+            if (data2 != null
+                && data.indexOf("*") > -1
+                && data.indexOf("*") == data2.indexOf("*"))
+            {
+              reply = "BLC";
+            }
+            else
+            {
+              reply = "FASTA";
+            }
+          }
 
-            break;
+          break;
+        }
+        else if (data.indexOf("HEADER") == 0 ||
+                 data.indexOf("ATOM") == 0)
+        {
+          reply = "PDB";
+          break;
+        }
+        else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+        {
+          // file looks like a concise JNet file
+          reply = "JnetFile";
+          break;
         }
       }
+
       reader.close();
     }
-    catch(Exception ex){
-      System.err.println("File Identification failed!"); ex.printStackTrace();}
+    catch (Exception ex)
+    {
+      System.err.println("File Identification failed!\n" + ex);
+      return error;
+    }
 
     return reply;
   }
-
-
 }