Examples with IsoformPEFFHeader org.nextprot.api.core.domain.IsoformPEFFHeader used on opensource projects

Example 1 with IsoformPEFFHeader

use of org.nextprot.api.core.domain.IsoformPEFFHeader in project nextprot-api by calipho-sib.

the class IsoformPEFFHeaderBuilderTest method testModResFormat.

@Test
public void testModResFormat() throws Exception {
    IsoformPEFFHeader peff = newIsoformPEFFHeaderBuilder("NX_Q15582-1").withModResFormats().build();
    Assert.assertEquals("\\ModRes=(28||O-linked (GalNAc...) serine)(49||Disulfide)(85||Disulfide)(74||Disulfide)(339||Disulfide)(84||Disulfide)(97||Disulfide)(214||Disulfide)(317||Disulfide)(473||Disulfide)(478||Disulfide)", peff.getModResFormat());
}

Example 2 with IsoformPEFFHeader

use of org.nextprot.api.core.domain.IsoformPEFFHeader in project nextprot-api by calipho-sib.

the class IsoformPEFFHeaderBuilderTest method testVariantComplexFormat.

@Test
public void testVariantComplexFormat() throws Exception {
    IsoformPEFFHeader peff = newIsoformPEFFHeaderBuilder("NX_P52701-1").withVariantComplexFormat().build();
    String expected = "\\VariantComplex=(53|53|AGP)(57|57|PGP)(259|259|)(272|272|)(282|282|VG)(374|374|)(385|385|)(492|492|)(510|510|)(538|539|*V)(543|544|)(546|546|)(638|638|)(641|641|)(754|754|)(768|768|)(809|809|)(854|854|)(881|881|KS)(882|885|*)(887|887|LI)(942|942|)(942|943|VH)(971|971|)(1014|1014|)(1014|1014|KL)(1088|1088|)(1129|1130|L)(1158|1158|)(1162|1162|)(1162|1162|AA)(1173|1176|)(1173|1176|SVY*)(1183|1183|)(1232|1232|)(1242|1242|)(1242|1243|P)(1244|1244|)(1244|1244|LL)(1254|1254|)(1254|1254|EE)(1254|1255|DY)(1282|1282|TI)(1310|1310|EE)(1317|1317|HRKAREFEKN)(1320|1321|EA)(1320|1321|GK)(1325|1325|)(1337|1337|CLAS)(1343|1343|ST)(1345|1347|)";
    String result = peff.getVariantComplexFormat();
    System.out.println("expect:" + expected);
    System.out.println("result:" + result);
    Assert.assertEquals(expected, result);
}

Example 3 with IsoformPEFFHeader

use of org.nextprot.api.core.domain.IsoformPEFFHeader in project nextprot-api by calipho-sib.

the class IsoformPEFFHeaderBuilderTest method testUndefinedPsiPTM.

@Test
public void testUndefinedPsiPTM() throws Exception {
    IsoformPEFFHeader peff = newIsoformPEFFHeaderBuilder("NX_Q02880-1").withModResFormats().build();
    String modResPSI = peff.getModResPsiFormat();
    Assert.assertTrue(!modResPSI.contains("(969|"));
    String modRes = peff.getModResFormat();
    Assert.assertEquals("\\ModRes=(969||PolyADP-ribosyl aspartic acid)", modRes);
}

Example 4 with IsoformPEFFHeader

use of org.nextprot.api.core.domain.IsoformPEFFHeader in project nextprot-api by calipho-sib.

the class IsoformPEFFHeaderBuilderTest method testUniqueIdFormat.

@Test
public void testUniqueIdFormat() throws Exception {
    IsoformPEFFHeader peff = newIsoformPEFFHeaderBuilder("NX_P52701-1").withEverything().build();
    Assert.assertEquals("\\DbUniqueId=NX_P52701-1", peff.getIsoformAccessionFormat());
}

Example 5 with IsoformPEFFHeader

use of org.nextprot.api.core.domain.IsoformPEFFHeader in project nextprot-api by calipho-sib.

the class IsoformPEFFHeaderBuilderTest method testProteinEvidenceFormat.

@Test
public void testProteinEvidenceFormat() throws Exception {
    IsoformPEFFHeader peff = newIsoformPEFFHeaderBuilder("NX_P52701-1").withProteinEvidenceFormat().build();
    Assert.assertEquals("\\PE=1", peff.getProteinEvidenceFormat());
}