develop merge

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 285a953..65fd72f 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -87,7 +87,7 @@ 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", "mmCIF" };
+      IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
 
   /**
    * List of readable format file extensions by application in order
@@ -104,7 +104,7 @@ 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, "mmCIF" };
 
   /**
@@ -328,9 +328,9 @@ 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(inFile, type);
       }
       return buildAlignmentFrom(alignFile);
     } catch (Exception e)
@@ -468,9 +468,9 @@ public class AppletFormatAdapter
       {
         alignFile = new PhylipFile(source);
       }
-      else if (format.equals(IdentifyFile.GFF3File))
+      else if (format.equals(IdentifyFile.FeaturesFile))
       {
-        alignFile = new Gff3File(inFile, type);
+        alignFile = new FeaturesFile(inFile, type);
       }
       else if (format.equals(JSONFile.FILE_DESC))
       {
@@ -711,7 +711,7 @@ 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();
@@ -877,7 +877,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        String idformat = new jalview.io.IdentifyFile().Identify(file,
+        String idformat = new jalview.io.IdentifyFile().identify(file,
                 protocol);
         if (idformat == null)
         {