X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=df5353c318c9f003d26519b058c2da21adc73998;hb=e07fc11d5aaf4d1237d83e5f7ea0909dea09902e;hp=8ca0c35c9da212afcd5ba2188d710d0d1d853754;hpb=13317fa1bc7bf640dc1967ce4438676e89390ad3;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8ca0c35..df5353c 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -255,6 +255,41 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
+  public Alignment readFile(String inFile, String type, String format)
+          throws java.io.IOException
+  {
+    Alignment al;
+    if (format.equals("HTML"))
+    {
+      afile = new HtmlFile(inFile, type);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(al);
+    }
+    else
+    {
+      al = super.readFile(inFile, type, format);
+    }
+
+    return al;
+  }
+
+  public AlignmentI readFromFile(FileParse source, String format)
+          throws java.io.IOException
+  {
+    Alignment al;
+    if (format.equals("HTML"))
+    {
+      afile = new HtmlFile(source);
+      al = new Alignment(afile.getSeqsAsArray());
+      afile.addAnnotations(al);
+    }
+    else
+    {
+      al = (Alignment) super.readFromFile(source, format);
+    }
+    return al;
+  }
+
   /**
    * validate format is valid for IO in Application. This is basically the
    * AppletFormatAdapter.isValidFormat call with additional checks for