Fasta files with * read not identified as BLC

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 2442b4b..024da61 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -23,37 +23,73 @@ import java.io.*;
 import java.net.*;\r
 \r
 \r
-public class IdentifyFile {\r
-    public static String Identify(String file, String protocol) {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class IdentifyFile\r
+{\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param file DOCUMENT ME!\r
+     * @param protocol DOCUMENT ME!\r
+     *\r
+     * @return DOCUMENT ME!\r
+     */\r
+    public String Identify(String file, String protocol)\r
+    {\r
         String reply = "PFAM";\r
-\r
-        try {\r
+        String error =  "FILE NOT FOUND";\r
+        try\r
+        {\r
             BufferedReader reader = null;\r
 \r
-            if (protocol.equals("File")) {\r
-                reader = new BufferedReader(new FileReader(file));\r
+            if (protocol.equals(AppletFormatAdapter.FILE))\r
+            {\r
+              reader = new BufferedReader(new FileReader(file));\r
+            }\r
+            else if (protocol.equals(AppletFormatAdapter.URL))\r
+            {\r
+              error = "URL NOT FOUND";\r
+              URL url = new URL(file);\r
+              reader = new BufferedReader(new InputStreamReader(\r
+                  url.openStream()));\r
+\r
             }\r
-            else if (protocol.equals("URL")) {\r
-                reply = "URL NOT FOUND";\r
-\r
-                URL url = new URL(file);\r
-                reader = new BufferedReader(new InputStreamReader(\r
-                            url.openStream()));\r
-                reply = "error";\r
-            } else if (protocol.equals("Paste")) {\r
-                reader = new BufferedReader(new StringReader(file));\r
+            else if (protocol.equals(AppletFormatAdapter.PASTE))\r
+            {\r
+              reader = new BufferedReader(new StringReader(file));\r
+            }\r
+            else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
+            {\r
+              java.io.InputStream is = getClass().getResourceAsStream("/" +\r
+                  file);\r
+              reader = new BufferedReader(new java.io.InputStreamReader(is));\r
             }\r
 \r
             String data;\r
 \r
-            while ((data = reader.readLine()) != null) {\r
+            while ((data = reader.readLine()) != null)\r
+            {\r
                 data = data.toUpperCase();\r
 \r
-                if ((data.indexOf("#") == 0) || (data.length() < 1)) {\r
+                if ( (data.indexOf("# STOCKHOLM") > -1))\r
+                {\r
+                  reply = "STH";\r
+\r
+                  break;\r
+                }\r
+\r
+                if ((data.indexOf("#") == 0) || (data.length() < 1))\r
+                {\r
                     continue;\r
                 }\r
 \r
-                if (data.indexOf("PILEUP") > -1) {\r
+                if (data.indexOf("PILEUP") > -1)\r
+                {\r
                     reply = "PileUp";\r
 \r
                     break;\r
@@ -62,36 +98,67 @@ public class IdentifyFile {
                 if ((data.indexOf("//") == 0) ||\r
                         ((data.indexOf("!!") > -1) &&\r
                         (data.indexOf("!!") < data.indexOf(\r
-                            "_MULTIPLE_ALIGNMENT ")))) {\r
+                            "_MULTIPLE_ALIGNMENT "))))\r
+                {\r
                     reply = "MSF";\r
 \r
                     break;\r
-                } else if (data.indexOf("CLUSTAL") > -1) {\r
+                }\r
+                else if (data.indexOf("CLUSTAL") > -1)\r
+                {\r
                     reply = "CLUSTAL";\r
 \r
                     break;\r
-                } else if ((data.indexOf(">P1;") > -1) ||\r
-                        (data.indexOf(">DL;") > -1)) {\r
+                }\r
+                else if ((data.indexOf(">P1;") > -1) ||\r
+                        (data.indexOf(">DL;") > -1))\r
+                {\r
                     reply = "PIR";\r
 \r
                     break;\r
-                } else if (data.indexOf(">") > -1) {\r
+                }\r
+                else if (data.indexOf(">") > -1)\r
+                {\r
                     // could be BLC file, read next line to confirm\r
                     data = reader.readLine();\r
 \r
-                    if (data.indexOf(">") > -1) {\r
+                    if (data.indexOf(">") > -1)\r
+                    {\r
                         reply = "BLC";\r
-                    } else {\r
+                    }\r
+                    //Is this a single line BLC file?\r
+                    data = reader.readLine();\r
+                    if(data!=null && data.length()==1)\r
+                    {\r
+                      reply = "BLC";\r
+                    }\r
+                    else\r
+                    {\r
                         reply = "FASTA";\r
                     }\r
 \r
                     break;\r
-                }\r
+                  }\r
+                  else if (data.indexOf("HEADER") > -1 ||\r
+                           data.indexOf("ATOM") > -1)\r
+                  {\r
+                    reply = "PDB";\r
+                    break;\r
+                  }\r
+                  else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
+                  {\r
+                    // file looks like a concise JNet file\r
+                    reply = "JnetFile";\r
+                    break;\r
+                  }\r
             }\r
 \r
             reader.close();\r
-        } catch (Exception ex) {\r
+        }\r
+        catch (Exception ex)\r
+        {\r
             System.err.println("File Identification failed!\n" + ex);\r
+            return error;\r
         }\r
 \r
         return reply;\r