JAL-1780 JAL-653 organise imports

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5601f27..1633212 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -25,7 +25,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -82,7 +81,7 @@ 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 +91,7 @@ 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 +100,7 @@ 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 };
 
   /**
@@ -292,6 +292,7 @@ public class AppletFormatAdapter
         {
           al.addGroup(sg);
         }
+
         return al;
       }
       else if (format.equals(HtmlFile.FILE_DESC))
@@ -309,6 +310,10 @@ public class AppletFormatAdapter
       {
         alignFile = new RnamlFile(inFile, type);
       }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
 
       al = new Alignment(alignFile.getSeqsAsArray());
 
@@ -432,10 +437,13 @@ 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);