Examples with ChromosomeReportWriter org.nextprot.api.core.service.export.ChromosomeReportWriter used on opensource projects

Example 1 with ChromosomeReportWriter

use of org.nextprot.api.core.service.export.ChromosomeReportWriter in project nextprot-api by calipho-sib.

the class ChromosomeReportTXTWriterTest method writeChromosomeReport.

@Test
public void writeChromosomeReport() throws Exception {
    ChromosomeReport report = new ChromosomeReport();
    report.setDataRelease("2017-01-23");
    ChromosomeReport.Summary summary = new ChromosomeReport.Summary();
    summary.setChromosome("Y");
    summary.setEntryReportCount(58);
    summary.setEntryCount(48);
    report.setSummary(summary);
    EntryReport entryReport1 = newEntryReport("SRY", "NX_Q05066", "Yp11.2", "2786855", "2787699", ProteinExistence.PROTEIN_LEVEL, false, true, true, true, 1, 47, 1, "Sex-determining region Y protein");
    EntryReport entryReport2 = newEntryReport("RBMY1C", "NX_P0DJD4", "Yq11.23", "-", "-", ProteinExistence.PROTEIN_LEVEL, false, true, false, false, 1, 0, 0, "RNA-binding motif protein, Y chromosome, family 1 member C");
    EntryReport entryReport3 = newEntryReport("MFSD14A", "NX_Q96MC6", "1p21.2", "100038097", "100083377", ProteinExistence.PROTEIN_LEVEL, false, false, false, false, 1, 141, 3, "Hippocampus abundant transcript 1 protein");
    report.setEntryReports(Arrays.asList(entryReport1, entryReport2, entryReport3));
    StringOutputStream sos = new StringOutputStream();
    ChromosomeReportWriter writer = new ChromosomeReportTXTWriter(sos);
    writer.write(report);
    String[] observedLines = sos.toString().split("\\n");
    Assert.assertEquals(28, observedLines.length);
    Assert.assertEquals("Gene          neXtProt      Chromosomal  Start      Stop       Coding  Protein          Prote- Anti- 3D    Dise- Iso-  Vari-  PTMs Description", observedLines[16]);
    Assert.assertEquals("name          AC            location     position   position   strand  existence        omics  body        ase   forms ants        ", observedLines[17]);
    Assert.assertEquals("SRY           NX_Q05066     Yp11.2          2786855    2787699 reverse protein level    no     yes   yes   yes       1    47     1 Sex-determining region Y protein", observedLines[19]);
    Assert.assertEquals("RBMY1C        NX_P0DJD4     Yq11.23               -          - reverse protein level    no     yes   no    no        1     0     0 RNA-binding motif protein, Y chromosome, family 1 member C", observedLines[20]);
    Assert.assertEquals("MFSD14A       NX_Q96MC6     1p21.2        100038097  100083377 reverse protein level    no     no    no    no        1   141     3 Hippocampus abundant transcript 1 protein", observedLines[21]);
}