X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=024da61824bd52629872ae7e8e53c4ec78d63d0f;hb=beca055dbed389362bb692de3c15fa5487c1ebd3;hp=eebde9b745f2820c23f468742b1816da5f962b41;hpb=128c1c559ce7749ba5a39d30e6108f5ce8f4b99e;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index eebde9b..024da61 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,86 +1,166 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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
+*/
 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("!!")>-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 String Identify(String file, String protocol)
+    {
+        String reply = "PFAM";
+        String error =  "FILE NOT FOUND";
+        try
         {
-          reply = "PIR";
-          break;
+            BufferedReader reader = null;
+
+            if (protocol.equals(AppletFormatAdapter.FILE))
+            {
+              reader = new BufferedReader(new FileReader(file));
+            }
+            else if (protocol.equals(AppletFormatAdapter.URL))
+            {
+              error = "URL NOT FOUND";
+              URL url = new URL(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)
+            {
+                data = data.toUpperCase();
+
+                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("//") == 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)
+                    {
+                        reply = "BLC";
+                    }
+                    //Is this a single line BLC file?
+                    data = reader.readLine();
+                    if(data!=null && data.length()==1)
+                    {
+                      reply = "BLC";
+                    }
+                    else
+                    {
+                        reply = "FASTA";
+                    }
+
+                    break;
+                  }
+                  else if (data.indexOf("HEADER") > -1 ||
+                           data.indexOf("ATOM") > -1)
+                  {
+                    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();
         }
-        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();
-    }
-    catch(Exception ex){
-      System.err.println("File Identification failed!"); ex.printStackTrace();}
-
-    return reply;
-  }
-
 
+        return reply;
+    }
 }