X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=4ec077f9f2b0aa5a187434fd1a83f62d3cd73dc9;hb=c1589fc13c75e8c71455ff07a0041d37426a60f7;hp=8a563faa80df880eeaed89d9f078a258a3df7be3;hpb=a8aec438cd92c74061c89487b2431a52bb0c2799;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..4ec077f 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -63,9 +63,9 @@ public class FormatAdapter extends AppletFormatAdapter
       annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
               true);
       localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
-            true);
-    serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
-            true);
+              true);
+      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+              true);
     }
     else
     {
@@ -107,12 +107,10 @@ public class FormatAdapter extends AppletFormatAdapter
       {
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
-
-        startIndex = startEnd[0];
-        endIndex = startEnd[1];
-
         if (startEnd != null)
         {
+          startIndex = startEnd[0];
+          endIndex = startEnd[1];
           // get first non-gaped residue start position
           while (jalview.util.Comparison.isGap(seqs[i]
                   .getCharAt(startIndex)) && startIndex < endIndex)
@@ -128,9 +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],
@@ -271,14 +267,12 @@ public class FormatAdapter extends AppletFormatAdapter
           ColumnSelection colSel)
   {
     return formatSequences(format, alignment, omitHidden, exportRange,
-            suffix, colSel,
-            null);
+            suffix, colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
           String[] omitHidden, int[] exportRange, boolean suffix,
-          ColumnSelection colSel,
-          jalview.datamodel.SequenceGroup selgp)
+          ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
   {
     if (omitHidden != null)
     {
@@ -363,5 +357,4 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
-
 }