JAL-653 GFF recognition for identifyFile and format adapters

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index beb1385..27f08ae 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  *
  * This file is part of Jalview.
  *
@@ -30,6 +30,8 @@ import java.io.IOException;
  */
 public class IdentifyFile
 {
+  public static final String GFF3File = "GFF v2 or v3";
+
   /**
    * Identify a datasource's file content.
    *
@@ -130,20 +132,34 @@ public class IdentifyFile
         }
         data = data.toUpperCase();
 
-        if ((data.indexOf("# STOCKHOLM") > -1))
+        if (data.startsWith("##GFF-VERSION"))
+        {
+          reply = GFF3File;
+          break;
+        }
+        if (data.indexOf("# STOCKHOLM") > -1)
         {
           reply = "STH";
-
+          break;
+        }
+        // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+        if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+        {
+          reply = HtmlFile.FILE_DESC;
           break;
         }
 
-        if ((data.indexOf("<") > -1))
+        if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
         {
           reply = "RNAML";
-
           break;
         }
 
+         if (data.indexOf("{\"") > -1)
+         {
+         reply = JSONFile.FILE_DESC;
+         break;
+         }
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
           lineswereskipped = true;
@@ -275,6 +291,7 @@ public class IdentifyFile
           break;
         }
 
+
         /*
          * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
          * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
@@ -320,6 +337,7 @@ public class IdentifyFile
 
   public static void main(String[] args)
   {
+
     for (int i = 0; args != null && i < args.length; i++)
     {
       IdentifyFile ider = new IdentifyFile();