X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=6d94616f12ccbcbd2a2ba5d0140ee5f47e1bf730;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=ebca31bb8c025ca36ce16e320b5bf212395c6bb2;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index ebca31b..6d94616 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -107,7 +107,6 @@ public class FormatAdapter extends AppletFormatAdapter
       {
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
-
         if (startEnd != null)
         {
           startIndex = startEnd[0];
@@ -127,9 +126,7 @@ public class FormatAdapter extends AppletFormatAdapter
           }
 
           startRes = seqs[i].findPosition(startIndex);
-          startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
-                  : startRes;
-          endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+          endRes = seqs[i].findPosition(endIndex);
         }
 
         tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
@@ -308,20 +305,6 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
-  public AlignmentI readFile(String inFile, String type, String format)
-          throws java.io.IOException
-  {
-    AlignmentI al = super.readFile(inFile, type, format);
-    return al;
-  }
-
-  public AlignmentI readFromFile(FileParse source, String format)
-          throws java.io.IOException
-  {
-    AlignmentI al = 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