From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 21 Feb 2018 15:41:27 +0000 (+0000)
Subject: JAL-2914 process #gff-version as a valid GFF3 pragma and suppress unknown pragma... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3900c35baa85360e632d91fa9a845d8eb9d727e3;p=jalview.git

JAL-2914 process #gff-version as a valid GFF3 pragma and suppress unknown pragma warning for lines with only one #
---

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d2282b1..d307a51 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -197,7 +197,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         // skip comments/process pragmas
         if (line.length() == 0 || line.startsWith("#"))
         {
-          if (line.toLowerCase().startsWith("##"))
+          if (line.toLowerCase().startsWith("##")
+                  || line.indexOf("gff-version") > -1)
           {
             processGffPragma(line, gffProps, align, newseqs);
           }
@@ -1093,8 +1094,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       // close off any open 'forward references'
       return;
     }
-
-    String[] tokens = line.substring(2).split(" ");
+    int startpragma = (line.charAt(1) == '#') ? 2 : 1; // lax
+    String[] tokens = line.substring(startpragma).split(" ");
     String pragma = tokens[0];
     String value = tokens.length == 1 ? null : tokens[1];
 
@@ -1141,7 +1142,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     }
     else
     {
-      System.err.println("Ignoring unknown pragma: " + line);
+      if (startpragma == 2)
+      {
+        // only complain if it was a genuine pragma line starting with ##
+        System.err.println("Ignoring unknown pragma: " + line);
+      }
     }
   }
 }