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josemduartejosemduarte
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New test to demonstrate issue with cloning
1 parent 2a6ff38 commit 0d07e69

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Lines changed: 40 additions & 6 deletions

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‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java‎

Lines changed: 40 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -22,27 +22,28 @@
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*/
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package org.biojava.nbio.structure.test;
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25-
import junit.framework.TestCase;
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import org.biojava.nbio.structure.*;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.io.FileParsingParameters;
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import org.biojava.nbio.structure.io.PDBFileParser;
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import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
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import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
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import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
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import org.junit.Before;
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import org.junit.Test;
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import java.io.IOException;
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import java.io.InputStream;
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import static org.junit.Assume.assumeNoException;
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import static org.junit.Assert.*;
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public class StructureToolsTest extends TestCase {
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public class StructureToolsTest {
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Structure structure, structure2, structure3, structure4;
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@Override
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protected void setUp() throws IOException
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@Before
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public void setUp() throws IOException
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{
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InputStream inStream = this.getClass().getResourceAsStream("/5pti.pdb");
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assertNotNull(inStream);
@@ -85,12 +86,13 @@ protected void setUp() throws IOException
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inStream.close();
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}
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@Test
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public void testGetCAAtoms(){
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Atom[] cas = StructureTools.getRepresentativeAtomArray(structure);
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assertEquals("did not find the expected number of Atoms (58), but got " + cas.length,58,cas.length);
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}
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@Test
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public void testGetAtomsConsistency() throws IOException, StructureException{
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//Save the existing ChemCompProvider
@@ -120,11 +122,13 @@ public void testGetAtomsConsistency() throws IOException, StructureException{
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ChemCompGroupFactory.setChemCompProvider(provider);
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}
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@Test
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public void testGetNrAtoms(){
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int length = StructureTools.getNrAtoms(structure);
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assertEquals("did not find the expected number of Atoms (1087), but got " + length,1087,length);
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}
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@Test
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@SuppressWarnings("deprecation")
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public void testGetSubRanges() throws StructureException {
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String range;
@@ -239,6 +243,7 @@ public void testGetSubRanges() throws StructureException {
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} catch(IllegalArgumentException ex) {} //expected
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}
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@Test
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public void testRevisedConvention() throws IOException, StructureException{
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AtomCache cache = new AtomCache();
@@ -319,6 +324,7 @@ public void testRevisedConvention() throws IOException, StructureException{
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* Test some subranges that we used to have problems with
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* @throws StructureException
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*/
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@Test
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@SuppressWarnings("deprecation")
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public void testGetSubRangesExtended() throws StructureException {
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String range;
@@ -380,6 +386,7 @@ public void testGetSubRangesExtended() throws StructureException {
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* Test insertion codes
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* @throws StructureException
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*/
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@Test
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@SuppressWarnings("deprecation")
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public void testGetSubRangesInsertionCodes() throws StructureException {
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String range;
@@ -437,6 +444,7 @@ public void testGroupsWithinShell() {
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//TODO
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}
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@Test
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public void testCAmmCIF() throws StructureException {
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//Save the existing ChemCompProvider
@@ -473,5 +481,31 @@ public void testCAmmCIF() throws StructureException {
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ChemCompGroupFactory.setChemCompProvider(provider);
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}
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@Test
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public void testGetRepresentativeAtomsProtein() throws StructureException, IOException {
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Structure s = StructureIO.getStructure("1smt");
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Chain c = s.getChain(0);
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Atom[] atoms = StructureTools.getRepresentativeAtomArray(c);
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assertEquals(98,atoms.length);
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Chain clonedChain = (Chain)c.clone();
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atoms = StructureTools.getRepresentativeAtomArray(clonedChain);
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assertEquals(98,atoms.length);
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}
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@Test
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public void testGetRepresentativeAtomsDna() throws StructureException, IOException {
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Structure s = StructureIO.getStructure("2pvi");
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Chain c = s.getChainByPDB("C");
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Atom[] atoms = StructureTools.getRepresentativeAtomArray(c); // chain C (1st nucleotide chain)
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// actually it should be 13, but at the moment one of the nucleotides is not caught correctly because it's non-standard
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assertEquals(12,atoms.length);
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Chain clonedChain = (Chain)c.clone();
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atoms = StructureTools.getRepresentativeAtomArray(clonedChain); // chain C (1st nucleotide chain)
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assertEquals(12,atoms.length);
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}
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}

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