selected region output also supports generation of annotations

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1795c1a..53b721d 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -696,10 +696,8 @@ public class AlignFrame
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty( "LAST_DIRECTORY"),
-        new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" },
-        new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" },
+        jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
+        jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
         currentFileFormat,
         false);
 
@@ -781,7 +779,7 @@ public class AlignFrame
       String output = f.formatSequences(
           format,
           (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
-          omitHidden, f.getCacheSuffixDefault(format));
+          omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 
       if (output == null)
       {
@@ -853,7 +851,7 @@ public class AlignFrame
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment,
-        omitHidden));
+        omitHidden, viewport.colSel));
   }
 
   /**