diff --git a/test/uk/ac/sanger/artemis/io/Utils.java b/test/uk/ac/sanger/artemis/io/Utils.java index 6395e94b028be31ecac37fab1d7ab89039db8c1a..ab840fef067fe8e6c0bb8ab546f473717cad7ba3 100644 --- a/test/uk/ac/sanger/artemis/io/Utils.java +++ b/test/uk/ac/sanger/artemis/io/Utils.java @@ -24,23 +24,31 @@ import java.io.IOException; import java.net.URL; import junit.framework.Assert; +import uk.ac.sanger.artemis.EntryGroup; +import uk.ac.sanger.artemis.Feature; +import uk.ac.sanger.artemis.FeatureSegmentVector; +import uk.ac.sanger.artemis.FeatureVector; import uk.ac.sanger.artemis.Options; +import uk.ac.sanger.artemis.Selection; +import uk.ac.sanger.artemis.SimpleEntryGroup; import uk.ac.sanger.artemis.io.DocumentEntryFactory; import uk.ac.sanger.artemis.io.Entry; import uk.ac.sanger.artemis.io.EntryInformationException; import uk.ac.sanger.artemis.sequence.AminoAcidSequence; import uk.ac.sanger.artemis.sequence.Bases; +import uk.ac.sanger.artemis.sequence.NoSequenceException; import uk.ac.sanger.artemis.util.Document; import uk.ac.sanger.artemis.util.DocumentFactory; +import uk.ac.sanger.artemis.util.OutOfRangeException; import uk.ac.sanger.artemis.util.StringVector; public class Utils { - protected static Entry getEntry(final String fileName) + public static Entry getEntry(final String fileName) { try { - URL entryFile = ValidateFeatureTest.class.getResource(fileName); + URL entryFile = Utils.class.getResource(fileName); final Document doc = DocumentFactory.makeDocument(entryFile.getFile()); return DocumentEntryFactory.makeDocumentEntry( Options.getArtemisEntryInformation(),doc,null); @@ -56,6 +64,27 @@ public class Utils return null; } + public static EntryGroup getEntryGroup(final String fileName) + { + try + { + final Entry new_embl_entry = getEntry(fileName); + final uk.ac.sanger.artemis.Entry entry = new uk.ac.sanger.artemis.Entry(new_embl_entry); + final EntryGroup egrp = new SimpleEntryGroup(entry.getBases()); + egrp.add(entry); + return egrp; + } + catch(OutOfRangeException e) + { + Assert.fail(e.getMessage()); + } + catch(NoSequenceException e) + { + Assert.fail(e.getMessage()); + } + return null; + } + /** * Method to change the translation table being used * @param n - genetic code table number