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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/
*
*/
package org.biojava.nbio.structure.align;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.junit.Ignore;
import org.junit.Test;
import static org.junit.Assert.*;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
public class TestAlignmentConsistency {
// Check that indices of the aligned residues are unique
@Ignore("The test requires the network")
@Test
public void testDuplicateIndices() throws IOException, StructureException {
String[] algorithmIDs = {CeMain.algorithmName, FatCatRigid.algorithmName};
AtomCache cache = new AtomCache();
// 3j47 is a bunch of a-helices, so there are many valid ways to align chains
// structurally between each other.
List<Chain> chains = cache.getStructure("3j47").getChains();
for(String algorithmID:algorithmIDs) {
StructureAlignment algorithm = StructureAlignmentFactory.getAlgorithm(algorithmID);
System.out.println("Testing "+algorithmID);
for (int c1 = 0; c1<chains.size()-1;c1++) {
for (int c2=chains.size()-1;c2>c1;c2--) {
Atom[] ca1 = StructureTools.getAtomCAArray(chains.get(c1));
Atom[] ca2 = StructureTools.getAtomCAArray(chains.get(c2));
AFPChain afpChain_fc = algorithm.align(ca1, ca2);
assertEquals(1,afpChain_fc.getOptAln().length);
int[][] optAln = afpChain_fc.getOptAln()[0];
// two chains aligned
assertEquals(2,optAln.length);
//same number of aligned residues between the chains
assertEquals(optAln[0].length,optAln[1].length);
// no indices duplicated in the alignments
for (int[] optAlnSeq : optAln) {
long count_unique = Arrays.stream(optAlnSeq).distinct().count();
long count_all = optAlnSeq.length;
assertEquals(count_unique, count_all);
}
}
}
}
}
}
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