X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=8a563faa80df880eeaed89d9f078a258a3df7be3;hb=fddf3084802b37e5cee17829e32692a4aac3e60d;hp=d241308b7142ec69fa7bf8d3c5ba12a10c66a305;hpb=d7989f319488cc56440f822261bc5014c27e03c6;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index d241308..8a563fa 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,7 +20,8 @@
  */
 package jalview.io;
 
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -37,9 +38,9 @@ import jalview.datamodel.SequenceI;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
-  public FormatAdapter(AlignViewportI viewport)
+  public FormatAdapter(AlignmentViewPanel viewpanel)
   {
-    super(viewport);
+    super(viewpanel);
     init();
   }
 
@@ -49,6 +50,12 @@ public class FormatAdapter extends AppletFormatAdapter
     init();
   }
 
+  public FormatAdapter(AlignmentViewPanel alignPanel,
+          AlignExportSettingI settings)
+  {
+    super(alignPanel, settings);
+  }
+
   private void init()
   {
     if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
@@ -304,17 +311,17 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
-  public Alignment readFile(String inFile, String type, String format)
+  public AlignmentI readFile(String inFile, String type, String format)
           throws java.io.IOException
   {
-    Alignment al = super.readFile(inFile, type, format);
+    AlignmentI al = super.readFile(inFile, type, format);
     return al;
   }
 
   public AlignmentI readFromFile(FileParse source, String format)
           throws java.io.IOException
   {
-    Alignment al = (Alignment) super.readFromFile(source, format);
+    AlignmentI al = super.readFromFile(source, format);
     return al;
   }
 
@@ -341,14 +348,19 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   /**
-   * Create a flat file representation of a given view or selected region of a view
+   * Create a flat file representation of a given view or selected region of a
+   * view
+   * 
    * @param format
-   * @param av
+   * @param ap
+   *          alignment panel originating the view
    * @return String containing flat file
    */
-  public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+  public String formatSequences(String format, AlignmentViewPanel ap,
+          boolean selectedOnly)
   {
-    return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+    return formatSequences(format, getCacheSuffixDefault(format), ap,
+            selectedOnly);
   }