X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=e34093dc836fcf6e2b7de7dbb14bb7f21b982411;hb=9b3219d225131af5a165553f206ebf8da304ee23;hp=239c53159f4dcffbd87d915d3684bf57965b8a5c;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 239c531..e34093d 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -86,7 +86,7 @@ public class AppletFormatAdapter
   public static final String[] READABLE_FORMATS = new String[] { "BLC",
       "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
       "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
-      IdentifyFile.GFF3File, "HTML" };
+      IdentifyFile.FeaturesFile, "HTML" };
 
   /**
    * List of readable format file extensions by application in order
@@ -103,7 +103,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[] { "Fasta",
       "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
-      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
       "Jalview", HtmlFile.FILE_DESC };
 
   /**
@@ -306,9 +306,9 @@ public class AppletFormatAdapter
       {
         alignFile = new RnamlFile(inFile, type);
       }
-      else if (format.equals(IdentifyFile.GFF3File))
+      else if (format.equals(IdentifyFile.FeaturesFile))
       {
-        alignFile = new Gff3File(inFile, type);
+        alignFile = new FeaturesFile(true, inFile, type);
       }
       return buildAlignmentFrom(alignFile);
     } catch (Exception e)
@@ -426,9 +426,10 @@ public class AppletFormatAdapter
       {
         alignFile = new PhylipFile(source);
       }
-      else if (format.equals(IdentifyFile.GFF3File))
+      else if (format.equals(IdentifyFile.FeaturesFile))
       {
-        alignFile = new Gff3File(inFile, type);
+        // enforce 'parseImmediately' here:
+        alignFile = new FeaturesFile(true, inFile, type);
       }
       else if (format.equals(JSONFile.FILE_DESC))
       {
@@ -669,7 +670,7 @@ public class AppletFormatAdapter
           long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
           AlignmentI al = afa.readFile(args[i], FILE,
-                  new IdentifyFile().Identify(args[i], FILE));
+                  new IdentifyFile().identify(args[i], FILE));
           t1 += System.currentTimeMillis();
           System.gc();
           memf += r.totalMemory() - r.freeMemory();
@@ -835,7 +836,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        String idformat = new jalview.io.IdentifyFile().Identify(file,
+        String idformat = new jalview.io.IdentifyFile().identify(file,
                 protocol);
         if (idformat == null)
         {