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59 lines (52 loc) · 2.16 KB
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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.core.sequence;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.SequenceView;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
public class SequenceViewTest {
@Test
public void testGetCompoundAt() throws CompoundNotFoundException {
SequenceView<NucleotideCompound> s = new DNASequence("ATGC").getSubSequence(1, 4);
assertEquals("Compound @ 1", s.getCompoundAt(1).toString(), "A");
assertEquals("Compound @ 3", s.getCompoundAt(3).toString(), "G");
assertEquals("Compound @ 3", s.getSubSequence(2,3).getCompoundAt(1).toString(), "T");
}
@Test
public void testLastIndexOf() throws CompoundNotFoundException {
SequenceView<NucleotideCompound> s = new DNASequence("ATGC").getSubSequence(1, 4);
CompoundSet<NucleotideCompound> cs = s.getCompoundSet();
assertEquals("Last index of ", 4, s.getLastIndexOf(cs.getCompoundForString("C")));
s = new DNASequence("GAAAAAAAAG").getSubSequence(1, 10);
assertEquals("Last index of G is 10", 10,
s.getLastIndexOf(cs.getCompoundForString("G")));
assertEquals("Last index of G is 5", 6,
s.getSubSequence(5, 10).getLastIndexOf(cs.getCompoundForString("G")));
}
@Test
public void testInverse() throws CompoundNotFoundException {
SequenceView<NucleotideCompound> s = new DNASequence("ATGC").getSubSequence(2, 3).getInverse();
assertEquals("Reversed complementing view", s.getSequenceAsString(), "CA");
}
}