JAL-1355

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 26fa854..ce15f0e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -22,8 +22,11 @@ package jalview.io;
 
 import java.io.File;
 import java.io.InputStream;
+import java.util.List;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting
@@ -405,6 +408,35 @@ public class AppletFormatAdapter
     }
   }
 
+
+  /**
+   * create an alignment flatfile from a Jalview alignment view 
+   * @param format
+   * @param jvsuffix
+   * @param av
+   * @param selectedOnly
+   * @return flatfile in a string
+   */
+  public String formatSequences(String format, boolean jvsuffix,
+          AlignViewportI av, boolean selectedOnly)
+  {
+
+    AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
+    AlignmentI aselview = selvew.getVisibleAlignment(av
+            .getGapCharacter());
+    List<AlignmentAnnotation> ala = (av
+            .getVisibleAlignmentAnnotation(selectedOnly));
+    if (ala != null)
+    {
+      for (AlignmentAnnotation aa : ala)
+      {
+        aselview.addAnnotation(aa);
+      }
+    }
+    
+    return formatSequences(format, aselview, jvsuffix);
+  }
+  
   /**
    * Construct an output class for an alignment in a particular filetype TODO:
    * allow caller to detect errors and warnings encountered when generating
@@ -470,8 +502,7 @@ public class AppletFormatAdapter
 
       else
       {
-        throw new Exception(
-                "Implementation error: Unknown file format string");
+        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);