From: bsoares <bsoares@134.36.162.41>
Date: Tue, 31 Jul 2018 08:58:21 +0000 (+0100)
Subject: Stockholm file for test
X-Git-Tag: Release_2_10_5~34^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=c4c5d134453fa4138d8857742ff05c09350d1283;hp=-c;p=jalview.git

Stockholm file for test
---

c4c5d134453fa4138d8857742ff05c09350d1283
diff --git a/examples/rna_ss_test.stk b/examples/rna_ss_test.stk
new file mode 100644
index 0000000..e716e0c
--- /dev/null
+++ b/examples/rna_ss_test.stk
@@ -0,0 +1,6 @@
+# STOCKHOLM 1.0
+#=GF ID RNA.SS.TEST
+#=GF TP RNA;
+Test.sequence         AAAAAA
+#=GC SS_cons          (EHhe)
+//
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 4273e6c..2427167 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -54,7 +54,8 @@ public class StockholmFileTest
   }
 
   static String PfamFile = "examples/PF00111_seed.stk",
-          RfamFile = "examples/RF00031_folded.stk";
+          RfamFile = "examples/RF00031_folded.stk",
+          RnaSSTestFile = "examples/rna_ss_test.stk";
 
   @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
@@ -230,8 +231,8 @@ public class StockholmFileTest
     // we might want to revise this in future
     int aa_new_size = (aa_new == null ? 0 : aa_new.length);
     int aa_original_size = (aa_original == null ? 0 : aa_original.length);
-    Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
-    Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
+    Map<Integer, BitSet> orig_groups = new HashMap<>();
+    Map<Integer, BitSet> new_groups = new HashMap<>();
 
     if (aa_new != null && aa_original != null)
     {