JAL-1759 merge from develop

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1089ec..4c83ac1 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -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.
    *
@@ -96,7 +98,7 @@ public class IdentifyFile
       }
       while ((data = source.nextLine()) != null)
       {
-        length += data.length();
+        length += data.trim().length();
         if (!lineswereskipped)
         {
           for (int i = 0; !isBinary && i < data.length(); i++)
@@ -130,7 +132,12 @@ 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;