From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 4 May 2017 10:37:19 +0000 (+0100)
Subject: fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label... 
X-Git-Tag: Release_2_10_2~3^2~105^2^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6684899d56d5bfb61faf814560010d7cb7b8bd95;p=jalview.git

fix for JAL-2507 - resolve stockholm per residue annotation type by annotation label or 'isRNA' RNA secondary structure annotation flag
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 2061f29..3b0dab4 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -978,15 +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;
             }
 
@@ -994,7 +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++)
             {