X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=1dbfdefeb8d2e92e58dd734fc16541522a9278fd;hb=0ed5b947087f831b8673f4c4e423bd4ef2238a89;hp=1408cd1f5c5d144df7401d10241722978c649891;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 1408cd1..1dbfdef 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -158,7 +158,7 @@ public class FormatAdapter extends AppletFormatAdapter
     //
     // try
     // {
-      boolean withSuffix = getCacheSuffixDefault(format);
+    boolean withSuffix = getCacheSuffixDefault(format);
     return format.getAlignmentFile().print(seqs, withSuffix);
       // null;
       //
@@ -242,14 +242,6 @@ public class FormatAdapter extends AppletFormatAdapter
             getCacheSuffixDefault(format), colSel, null);
   }
 
-  public String formatSequences(FileFormatI format, AlignmentI alignment,
-          String[] omitHidden, int[] exportRange, ColumnSelection colSel,
-          SequenceGroup sgp)
-  {
-    return formatSequences(format, alignment, omitHidden, exportRange,
-            getCacheSuffixDefault(format), colSel, sgp);
-  }
-
   /**
    * hack function to replace seuqences with visible sequence strings before
    * generating a string of the alignment in the given format.
@@ -337,4 +329,12 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
+  public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
+          throws IOException
+  {
+    FileParse fp = new FileParse(source.getInFile(),
+            source.getDataSourceType());
+    return readFromFile(fp, format);
+  }
+
 }