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;
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
{
// 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[]
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");
|| (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();