Merge branch 'develop' into features/JAL-653_gffalignments

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index e2cd43a..de9e6bd 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -82,7 +82,7 @@ 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,
+      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
       "HTML" };
 
   /**
@@ -92,6 +92,7 @@ public class AppletFormatAdapter
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
       "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+      ".gff2,gff3",
       "jar,jvp", HtmlFile.FILE_EXT };
 
   /**
@@ -100,7 +101,7 @@ 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, "Jalview",
+      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
       HtmlFile.FILE_DESC };
 
   /**
@@ -310,6 +311,10 @@ public class AppletFormatAdapter
       {
         alignFile = new RnamlFile(inFile, type);
       }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
 
       al = new Alignment(alignFile.getSeqsAsArray());
 
@@ -433,10 +438,13 @@ public class AppletFormatAdapter
       {
         alignFile = new PhylipFile(source);
       }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
       else if (format.equals(JSONFile.FILE_DESC))
       {
         alignFile = new JSONFile(source);
-        // ((JSONFile) afile).setViewport(viewport);
         al = new Alignment(alignFile.getSeqsAsArray());
         alignFile.addAnnotations(al);
         alignFile.addSeqGroups(al);