Ye olde SequenceFeatureFetcher

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index dbee007..6b32fe1 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -39,30 +39,35 @@ public class IdentifyFile
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public static String Identify(String file, String protocol)\r
+    public String Identify(String file, String protocol)\r
     {\r
         String reply = "PFAM";\r
-\r
+        String error =  "FILE NOT FOUND";\r
         try\r
         {\r
             BufferedReader reader = null;\r
 \r
-            if (protocol.equals("File"))\r
+            if (protocol.equals(AppletFormatAdapter.FILE))\r
             {\r
-                reader = new BufferedReader(new FileReader(file));\r
+              reader = new BufferedReader(new FileReader(file));\r
             }\r
-            else if (protocol.equals("URL"))\r
+            else if (protocol.equals(AppletFormatAdapter.URL))\r
             {\r
-                reply = "URL NOT FOUND";\r
+              error = "URL NOT FOUND";\r
+              URL url = new URL(file);\r
+              reader = new BufferedReader(new InputStreamReader(\r
+                  url.openStream()));\r
 \r
-                URL url = new URL(file);\r
-                reader = new BufferedReader(new InputStreamReader(\r
-                            url.openStream()));\r
-                reply = "error";\r
             }\r
-            else if (protocol.equals("Paste"))\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
-                reader = new BufferedReader(new StringReader(file));\r
+              java.io.InputStream is = getClass().getResourceAsStream("/" +\r
+                  file);\r
+              reader = new BufferedReader(new java.io.InputStreamReader(is));\r
             }\r
 \r
             String data;\r
@@ -110,7 +115,7 @@ public class IdentifyFile
                     // could be BLC file, read next line to confirm\r
                     data = reader.readLine();\r
 \r
-                    if (data.indexOf(">") > -1)\r
+                    if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )\r
                     {\r
                         reply = "BLC";\r
                     }\r
@@ -121,6 +126,12 @@ public class IdentifyFile
 \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
@@ -128,8 +139,8 @@ public class IdentifyFile
         catch (Exception ex)\r
         {\r
             System.err.println("File Identification failed!\n" + ex);\r
+            return error;\r
         }\r
-\r
         return reply;\r
     }\r
 }\r