X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=bd1400b5eba09f412f17dd415d3810bf79a56ec1;hb=5b3d1cf1e78adbeeedf14eec91b6a0be75ca21e4;hp=e7f1435ec4073ad65b3fd691532701181d0d6632;hpb=223ccb5ee354120aa99f3f8887a9d094267f6546;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e7f1435..bd1400b 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -37,6 +37,7 @@ import java.util.BitSet;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -436,4 +437,50 @@ public class StockholmFileTest
       }
     }
   }
+
+  String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG";
+  String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+          + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+          + "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t"
+          + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
+  String annFileFullWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+          + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+          + "(|(|(|(||{|{||[|[||)|)|)|)||}|}|]|]\t0.0\nROWPROPERTIES\t"
+          + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
+  @Test(groups = { "Functional" })
+  public void secondaryStructureForRNASequence() throws Exception
+  {
+    roundTripSSForRNA(aliFile, annFile);
+  }
+
+  @Test(groups = { "Functional" })
+  public void fullWUSSsecondaryStructureForRNASequence() throws Exception
+  {
+    roundTripSSForRNA(aliFile, annFileFullWuss);
+  }
+
+  private static void roundTripSSForRNA(String aliFile, String annFile)
+          throws Exception
+  {
+    AlignmentI al = new AppletFormatAdapter().readFile(aliFile,
+            DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+    AnnotationFile aaf = new AnnotationFile();
+    aaf.readAnnotationFile(al, annFile, DataSourceType.PASTE);
+    al.getAlignmentAnnotation()[0].visible = true;
+
+    // TODO: create a better 'save as <format>' pattern
+    StockholmFile sf = new StockholmFile(al);
+
+    String stockholmFile = sf.print(al.getSequencesArray(), true);
+
+    AlignmentI newAl = new AppletFormatAdapter().readFile(stockholmFile,
+            DataSourceType.PASTE, jalview.io.FileFormat.Stockholm);
+    // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport()
+    // .getAlignment(), Arrays.asList("Secondary Structure"), newAl
+    // .getViewport().getAlignment().getSequences(), true, true);
+    testAlignmentEquivalence(al, newAl, true, true);
+
+  }
 }