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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Sep 5, 2013
* Author: andreas
*
*/
package org.biojava.nbio.structure.io;
import org.biojava.nbio.structure.io.sifts.*;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import java.io.InputStream;
import java.util.List;
import java.util.zip.GZIPInputStream;
public class TestSiftsParsing {
@Ignore("The test requires the network")
@Test
public void test4DIA() throws Exception {
List<SiftsEntity> entities = SiftsMappingProvider.getSiftsMapping("4DIA");
Assert.assertNotNull(entities);
Assert.assertEquals(1, entities.size());
for (SiftsEntity e : entities) {
//System.out.println(e.getEntityId() + " " +e.getType());
Assert.assertTrue(e.getSegments().size() > 0);
for (SiftsSegment seg : e.getSegments()) {
Assert.assertTrue(seg.getResidues().size() > 0);
for (SiftsResidue res : seg.getResidues()) {
if (res.getUniProtResName() != null) {
Assert.assertNotNull(res.getUniProtAccessionId());
Assert.assertNotNull(res.getUniProtResName());
// test for github ticket #280
if (res.getUniProtPos() == 129) {
Assert.assertTrue(res.getNotObserved());
}
}
}
}
}
}
@Ignore("The test requires the network")
@Test
public void test4jn3() throws Exception {
List<SiftsEntity> entities = SiftsMappingProvider.getSiftsMapping("4jn3");
Assert.assertNotNull(entities);
Assert.assertEquals(2, entities.size());
for (SiftsEntity e : entities) {
//System.out.println(e.getEntityId() + " " +e.getType());
Assert.assertTrue(e.getSegments().size() > 0);
for (SiftsSegment seg : e.getSegments()) {
Assert.assertTrue(seg.getResidues().size() > 0);
//System.out.println(seg.getResidues().size());
//System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd()) ;
//
for (SiftsResidue res : seg.getResidues()) {
//System.out.println(" " + res);
if (res.getUniProtResName() != null) {
Assert.assertNotNull(res.getUniProtAccessionId());
Assert.assertNotNull(res.getUniProtResName());
}
}
}
}
}
@Test
public void test4DOU() throws Exception {
// get file from test resource folder, since the file from EBI seems to have issues (on 20170405).
InputStream inStream = new GZIPInputStream(this.getClass().getResourceAsStream("/org/biojava/nbio/structure/io/4dou.sifts.xml.gz"));
SiftsXMLParser parser = new SiftsXMLParser();
parser.parseXmlFile(inStream);
List<SiftsEntity> entities = parser.getEntities();
Assert.assertNotNull(entities);
Assert.assertEquals(1, entities.size());
for (SiftsEntity e : entities) {
//System.out.println(e.getEntityId() + " " +e.getType());
// 4DOU has 3 segments
Assert.assertEquals("SiftsEntity does not have 3 segments, but " + e.getSegments().size(), 3, e.getSegments().size());
// test segment 1:
//SiftsSegment seg1 = e.getSegments().get(0);
//System.out.println(" Segment: " + seg1.getSegId() + " " + seg1.getStart() + " " + seg1.getEnd() + " res. size: " + seg1.getResidues().size());
//assertTrue(seg1.getResidues().size() == 17);
for (SiftsSegment seg : e.getSegments()) {
Assert.assertTrue(seg.getResidues().size() > 0);
//System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd() + " res. size: " + seg.getResidues().size()) ;
for (SiftsResidue res : seg.getResidues()) {
if (res.getUniProtResName() != null) {
//System.out.println(" " + res);
Assert.assertNotNull(res.getUniProtAccessionId());
Assert.assertNotNull(res.getUniProtResName());
}
}
//break;
}
}
}
@Ignore("The test requires the network")
@Test
public void test4O6W() throws Exception {
List<SiftsEntity> entities = SiftsMappingProvider.getSiftsMapping("4O6W");
Assert.assertNotNull(entities);
Assert.assertEquals(2, entities.size());
int ecount = 0;
for (SiftsEntity e : entities) {
ecount++;
// we only test the 2nd segment in entity #1
if (ecount != 1)
continue;
Assert.assertEquals("A", e.getEntityId());
Assert.assertEquals("protein", e.getType());
// 4O6W A has 2 segments
Assert.assertEquals(2, e.getSegments().size());
// test segment 2:
SiftsSegment seg = e.getSegments().get(1);
//SiftsSegment seg1 = e.getSegments().get(0);
//System.out.println(" Segment: " + seg1.getSegId() + " " + seg1.getStart() + " " + seg1.getEnd() + " res. size: " + seg1.getResidues().size());
//assertTrue(seg1.getResidues().size() == 17);
Assert.assertTrue(seg.getResidues().size() > 0);
for (SiftsResidue res : seg.getResidues()) {
if (res.getUniProtResName() != null) {
//System.out.println(" " + res);
Assert.assertNotNull(res.getUniProtAccessionId());
Assert.assertNotNull(res.getUniProtResName());
}
if (res.getPdbResNum().equals("502")) {
Assert.assertTrue(res.getNotObserved());
}
}
//break;
}
}
}
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