test/jalview/io/BSMLFileTest.java

   1 package jalview.io;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertTrue;
   5
   6 import jalview.datamodel.SequenceFeature;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.datamodel.features.SequenceFeaturesI;
   9
  10 import java.io.IOException;
  11 import java.util.List;
  12
  13 import org.testng.annotations.Test;
  14
  15 public class BSMLFileTest
  16 {
  17   @Test(groups="Functional")
  18   public void testParse_BSML() throws IOException
  19   {
  20     //@formatter:off
  21     String data = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n" +
  22             "<Bsml>\r\n" +
  23             "  <Definitions>\r\n" +
  24             "    <Sequences>\r\n" +
  25             "      <Sequence\r\n" +
  26             "        comment=\"Sequence Data Contained in 'Multiple-alignment' section\"\r\n" +
  27             "        id=\"SEQ-ID:181170\" length=\"30\" molecule=\"dna\" title=\"EP1\">\r\n" +
  28             "        <Feature-tables>\r\n" +
  29             "          <Feature-table title=\"GENE\">\r\n" +
  30             "            <Feature class=\"GENE\" title=\"TEST-001\">\r\n" +
  31             "              <Interval-loc complement=\"0\" endpos=\"20\" startpos=\"10\"/>\r\n" +
  32             "              <Resource id=\"GENE-ID:181171\"/>\r\n" +
  33             "            </Feature>\r\n" +
  34             "          </Feature-table>\r\n" +
  35             "        </Feature-tables>\r\n" +
  36             "      </Sequence>\r\n" +
  37             "    </Sequences>\r\n" +
  38             "    <Tables>\r\n" +
  39             "      <Multiple-alignment-table molecule-type=\"nucleotide\">\r\n" +
  40             "        <Sequence-alignment sequences=\"1\">\r\n" +
  41             "          <Sequence-data seq-name=\"EP1\">--AATTTT-ATTTAGTGTCT-----------</Sequence-data>\r\n" +
  42             "          <Alignment-consensus/>\r\n" +
  43             "        </Sequence-alignment>\r\n" +
  44             "      </Multiple-alignment-table>\r\n" +
  45             "    </Tables>\r\n" +
  46             "    <Notebook notebook=\"\"/>\r\n" +
  47             "  </Definitions>\r\n" +
  48             "</Bsml>\r\n" +
  49             "";
  50     BSMLFile cf = new BSMLFile(data, DataSourceType.PASTE);
  51 // why twice?    cf.parse();
  52     SequenceI[] seqs = cf.getSeqsAsArray();
  53     assertEquals(seqs.length, 1);
  54     SequenceI seq = seqs[0];
  55     assertEquals(seq.getName(), "EP1");
  56     assertEquals(seq.getStart(), 1);
  57     assertEquals(seq.getEnd(), 31);
  58     assertTrue(seq.getSequenceAsString().equals("--AATTTT-ATTTAGTGTCT-----------"));
  59     SequenceFeaturesI features = seq.getFeatures();
  60     List<SequenceFeature> genes = features.getAllFeatures("GENE");
  61     assertEquals(genes.size(), 1);
  62     SequenceFeature sf = genes.get(0);
  63     assertEquals(sf.getDescription(), "TEST-001");
  64     assertEquals(sf.begin + "," + sf.end, "10,20");
  65
  66   }
  67
  68 }