FileFormatI further tweaks, clean compile

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 1408cd1..724170e 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -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);
+  }
+
 }