X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=ebca31bb8c025ca36ce16e320b5bf212395c6bb2;hb=8872ca6bcf761214bb3b4f428adec48bba95d80e;hp=8a563faa80df880eeaed89d9f078a258a3df7be3;hpb=a8aec438cd92c74061c89487b2431a52bb0c2799;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..ebca31b 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
     {
@@ -108,11 +108,10 @@ 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)
@@ -271,14 +270,12 @@ 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 +360,4 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
-
 }