X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=9a248e5abe40694c229844e40d6ec84c9e00889a;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=2442b4bb142254b668fd1e6fd908b52ed8834ade;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 2442b4b..9a248e5 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* 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
@@ -23,37 +23,73 @@ import java.io.*;
 import java.net.*;
 
 
-public class IdentifyFile {
-    public static String Identify(String file, String protocol) {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifyFile
+{
+    /**
+     * 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")) {
-                reader = new BufferedReader(new FileReader(file));
+            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("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));
+            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) {
+                if (data.indexOf("PILEUP") > -1)
+                {
                     reply = "PileUp";
 
                     break;
@@ -62,36 +98,61 @@ public class IdentifyFile {
                 if ((data.indexOf("//") == 0) ||
                         ((data.indexOf("!!") > -1) &&
                         (data.indexOf("!!") < data.indexOf(
-                            "_MULTIPLE_ALIGNMENT ")))) {
+                            "_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 || data.indexOf("*") >-1 )
+                    {
                         reply = "BLC";
-                    } else {
+                    }
+                    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();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
             System.err.println("File Identification failed!\n" + ex);
+            return error;
         }
 
         return reply;