JAL-1486 JAL-1543 pushed alignment viewport->view->flat file logic into jalview.io...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 26fa854..3f9a425 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -22,7 +22,9 @@ package jalview.io;
 
 import java.io.File;
 import java.io.InputStream;
+import java.util.List;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.*;
 
 /**
@@ -405,6 +407,35 @@ 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