X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=bb822a06cabf7b70ab54d9d7540e4281d35e2dcf;hb=c87a31d2275d86ec5d64cc20844c6cd626037737;hp=74825cf8fb575ae26b7f2b95f77059151dbe0d60;hpb=6a33e605b75ae727af5420d9b90d86768ca3dc63;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 74825cf..bb822a0 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -26,17 +26,6 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.util.DBRefUtils;
-
 import java.io.File;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -50,6 +39,17 @@ import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
+
 public class StockholmFileTest
 {
 
@@ -107,9 +107,9 @@ public class StockholmFileTest
     // sequences retrieved in a Pfam domain alignment also have a PFAM database
     // reference
     SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
-    sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
     sq.addDBRef(new DBRefEntry("UNIPROT", "1", "P00224"));
     sq.addDBRef(new DBRefEntry("PFAM", "1", "P00224.1"));
+    sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
     AppletFormatAdapter af = new AppletFormatAdapter();
     String toStockholm = af.formatSequences(FileFormat.Stockholm,
             new Alignment(new SequenceI[]
@@ -125,10 +125,12 @@ public class StockholmFileTest
     AlignmentI fromStockholm = af.readFile(toStockholm,
             DataSourceType.PASTE, FileFormat.Stockholm);
     SequenceI importedSeq = fromStockholm.getSequenceAt(0);
-    assertTrue(importedSeq.getDBRefs().length == 1,
+    assertTrue(importedSeq.getDBRefs()
+            .size() == 1,
             "Expected just one database reference to be added to sequence.");
     assertTrue(
-            importedSeq.getDBRefs()[0].getAccessionId().indexOf(" ") == -1,
+            importedSeq.getDBRefs().get(0).getAccessionId().indexOf(
+                    " ") == -1,
             "Spaces were found in accession ID.");
     List<DBRefEntry> dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
             "P00224");
@@ -369,10 +371,11 @@ public class StockholmFileTest
                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                   .getSequenceFeatures() != null));
           // compare sequence features
-          if (seq_original[i].getSequenceFeatures() != null
+          if (!ignoreFeatures
+                  && seq_original[i].getSequenceFeatures() != null
                   && seq_new[in].getSequenceFeatures() != null)
           {
-            System.out.println("There are feature!!!");
+            System.out.println("Checking feature equivalence.");
             sequenceFeatures_original = seq_original[i]
                     .getSequenceFeatures();
             sequenceFeatures_new = seq_new[in].getSequenceFeatures();