package jalview.io;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;

import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeaturesI;

import java.io.IOException;
import java.util.List;

import org.testng.annotations.Test;

public class BSMLFileTest
{
  @Test(groups="Functional")
  public void testParse_BSML() throws IOException
  {
    //@formatter:off
    String data = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n" + 
            "<Bsml>\r\n" + 
            "  <Definitions>\r\n" + 
            "    <Sequences>\r\n" + 
            "      <Sequence\r\n" + 
            "        comment=\"Sequence Data Contained in 'Multiple-alignment' section\"\r\n" + 
            "        id=\"SEQ-ID:181170\" length=\"30\" molecule=\"dna\" title=\"EP1\">\r\n" + 
            "        <Feature-tables>\r\n" + 
            "          <Feature-table title=\"GENE\">\r\n" + 
            "            <Feature class=\"GENE\" title=\"TEST-001\">\r\n" + 
            "              <Interval-loc complement=\"0\" endpos=\"20\" startpos=\"10\"/>\r\n" + 
            "              <Resource id=\"GENE-ID:181171\"/>\r\n" + 
            "            </Feature>\r\n" + 
            "          </Feature-table>\r\n" + 
            "        </Feature-tables>\r\n" + 
            "      </Sequence>\r\n" + 
            "    </Sequences>\r\n" + 
            "    <Tables>\r\n" + 
            "      <Multiple-alignment-table molecule-type=\"nucleotide\">\r\n" + 
            "        <Sequence-alignment sequences=\"1\">\r\n" + 
            "          <Sequence-data seq-name=\"EP1\">--AATTTT-ATTTAGTGTCT-----------</Sequence-data>\r\n" + 
            "          <Alignment-consensus/>\r\n" + 
            "        </Sequence-alignment>\r\n" + 
            "      </Multiple-alignment-table>\r\n" + 
            "    </Tables>\r\n" + 
            "    <Notebook notebook=\"\"/>\r\n" + 
            "  </Definitions>\r\n" + 
            "</Bsml>\r\n" + 
            "";
    BSMLFile cf = new BSMLFile(data, DataSourceType.PASTE);
// why twice?    cf.parse();
    SequenceI[] seqs = cf.getSeqsAsArray();
    assertEquals(seqs.length, 1);
    SequenceI seq = seqs[0];
    assertEquals(seq.getName(), "EP1");
    assertEquals(seq.getStart(), 1);
    assertEquals(seq.getEnd(), 31);
    assertTrue(seq.getSequenceAsString().equals("--AATTTT-ATTTAGTGTCT-----------"));
    SequenceFeaturesI features = seq.getFeatures();
    List<SequenceFeature> genes = features.getAllFeatures("GENE");
    assertEquals(genes.size(), 1);
    SequenceFeature sf = genes.get(0);
    assertEquals(sf.getDescription(), "TEST-001");
    assertEquals(sf.begin + "," + sf.end, "10,20");
    
  }

}