X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=a47e1ea3c19a77e4c7f2cc873e863ec9e4271fdd;hb=db1b28364c2034ea432c0668100c1ec9e0d17523;hp=3fd0505738e23bbdd0da3dde1e7f9bd8868c491b;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 3fd0505..a47e1ea 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -800,9 +800,9 @@ public class StockholmFile extends AlignFile
   {
     String convert1, convert2 = null;
 
-    convert1 = OPEN_PAREN.replaceAll(annots);
-    convert2 = CLOSE_PAREN.replaceAll(convert1);
-    annots = convert2;
+    // convert1 = OPEN_PAREN.replaceAll(annots);
+    // convert2 = CLOSE_PAREN.replaceAll(convert1);
+    // annots = convert2;
 
     String type = label;
     if (label.contains("_cons"))
@@ -830,8 +830,7 @@ public class StockholmFile extends AlignFile
         {
           if (DETECT_BRACKETS.search(pos))
           {
-            ann.secondaryStructure = Rna.getRNASecStrucState(
-                    pos).charAt(0);
+            ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
           }
           else
           {
@@ -979,15 +978,19 @@ public class StockholmFile extends AlignFile
         {
           for (int j = 0; j < alAnot.length; j++)
           {
-            if (ds.getSequenceFeatures() != null)
+
+            String key = type2id(alAnot[j].label);
+            boolean isrna = alAnot[j].isValidStruc();
+
+            if (isrna)
             {
-              feature = ds.getSequenceFeatures()[0].type;
+              // hardwire to secondary structure if there is RNA secondary
+              // structure on the annotation
+              key = "SS";
             }
-            // ?bug - feature may still have previous loop value
-            String key = type2id(feature);
-
             if (key == null)
             {
+
               continue;
             }
 
@@ -995,7 +998,6 @@ public class StockholmFile extends AlignFile
             out.append(new Format("%-" + maxid + "s").form("#=GR "
                     + printId(s[i], jvSuffix) + " " + key + " "));
             ann = alAnot[j].annotations;
-            boolean isrna = alAnot[j].isValidStruc();
             String seq = "";
             for (int k = 0; k < ann.length; k++)
             {