X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=9fdd7b90a82befc998c7841766bf972f3472f498;hb=af259f508805faf2da90585ee9a67cd7853bf5aa;hp=e86c8ad79f8852be2aa0ecb0a2a4208eaf546928;hpb=483abbfd34bb2e47698f4cb04e21531c2b11924a;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e86c8ad..9fdd7b9 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -20,17 +20,22 @@
  */
 package jalview.io;
 
+import static org.testng.Assert.assertTrue;
 import static org.testng.AssertJUnit.assertEquals;
 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;
@@ -93,14 +98,55 @@ public class StockholmFileTest
   }
 
   /**
+   * JAL-3529 - verify uniprot refs for sequences are output for sequences
+   * retrieved via Pfam
+   */
+  @Test(groups = { "Functional" })
+  public void dbrefOutput() throws Exception
+  {
+    // sequences retrieved in a Pfam domain alignment also have a PFAM database
+    // reference
+    SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+    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[]
+            { sq }), false);
+    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,
+            "Expected just one database reference to be added to sequence.");
+    assertTrue(
+            importedSeq.getDBRefs()[0].getAccessionId().indexOf(" ") == -1,
+            "Spaces were found in accession ID.");
+    List<DBRefEntry> dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
+            "P00224");
+    assertTrue(dbrefs.size() == 1,
+            "Couldn't find Uniprot DBRef on re-imported sequence.");
+
+  }
+
+  /**
    * test alignment data in given file can be imported, exported and reimported
    * with no dataloss
    * 
    * @param f
-   *          - source datafile (IdentifyFile.identify() should work with it)
+   *                               - source datafile (IdentifyFile.identify()
+   *                               should work with it)
    * @param ioformat
-   *          - label for IO class used to write and read back in the data from
-   *          f
+   *                               - label for IO class used to write and read
+   *                               back in the data from f
    * @param ignoreFeatures
    * @param ignoreRowVisibility
    * @param allowNullAnnotations
@@ -257,8 +303,8 @@ public class StockholmFileTest
           assertEquals("Threshold line not identical.",
                   aa_original[i].threshold, aa_new[i].threshold);
           // graphGroup may differ, but pattern should be the same
-          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
-          Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+          Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2);
+          Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2);
           BitSet orig_g = orig_groups.get(o_ggrp);
           BitSet new_g = new_groups.get(n_ggrp);
           if (orig_g == null)