X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=5b74306015d349247413be8e3b206458eadeeafb;hb=7dc7404ce7a339c600130e9828e3efc05b1e3270;hp=a16aa075aa3e99f95d58236548ee577ade2b0615;hpb=79b76c7dbb5322cb7b188035fb2fdf676ee974fa;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index a16aa07..5b74306 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
 {
 
@@ -114,15 +114,23 @@ public class StockholmFileTest
     String toStockholm = af.formatSequences(FileFormat.Stockholm,
             new Alignment(new SequenceI[]
             { sq }), false);
-    assertTrue(toStockholm.matches("AC\\s+P00224"),
+    System.out.println(toStockholm);
+    // bleh - java.util.Regex sucks
+    assertTrue(
+            Pattern.compile(
+                    "^#=GS\\s+FER2_SPIOL(/\\d+-\\d+)?\\s+AC\\s+P00224$",
+                    Pattern.MULTILINE).matcher(toStockholm)
+                    .find(),
             "Couldn't locate UNIPROT Accession in generated Stockholm file.");
     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");