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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.bio.symbol;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.impl.SimpleGappedSequence;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.seq.io.SymbolTokenization;
/**
* Test for gapped symbol lists.
*
* @author Matthew Pocock
* @since 1.3
*/
public class GappedSymbolListTest extends TestCase {
private SymbolList symList;
private SymbolList symList1;
private SymbolList symList2;
private SymbolList symList3;
private SymbolList symList4;
public GappedSymbolListTest(String name) {
super(name);
}
protected void setUp()
throws Exception {
FiniteAlphabet dna = (FiniteAlphabet) AlphabetManager.alphabetForName("DNA");
SymbolTokenization tok = dna.getTokenization("token");
symList = new SimpleSymbolList(tok,"gtgtggga");
symList1 = new SimpleSymbolList(tok,"gtg-tggga");
symList2 = new SimpleSymbolList(tok,"gtg--tggga");
symList3 = new SimpleSymbolList(tok,"gtg---tggga");
symList4 = new SimpleSymbolList(tok,"gtg----tggga");
}
public void testIndividualInsertBlockRemove()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList));
gsl.addGapInSource(4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList1));
gsl.addGapInSource(4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList2));
gsl.addGapInSource(4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList3));
gsl.addGapInSource(4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList4));
gsl.removeGaps(4,4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList));
}
public void testBlockedInsertIndividualRemove()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
assertTrue("Gapped same as ungapped:\n" + gsl.seqString() + "\n" + symList.seqString(), SymbolUtils.compareSymbolLists(gsl, symList));
gsl.addGapsInSource(4,4);
assertTrue("Four gaps:\n" + gsl.seqString() + "\n" + symList4.seqString(), SymbolUtils.compareSymbolLists(gsl, symList4));
gsl.removeGap(4);
assertTrue("Three gaps:\n" + gsl.seqString() + "\n" + symList3.seqString(), SymbolUtils.compareSymbolLists(gsl, symList3));
gsl.removeGap(4);
assertTrue("Two gaps:\n" + gsl.seqString() + "\n" + symList2.seqString(), SymbolUtils.compareSymbolLists(gsl, symList2));
gsl.removeGap(4);
assertTrue("One gap:\n" + gsl.seqString() + "\n" + symList1.seqString(), SymbolUtils.compareSymbolLists(gsl, symList1));
gsl.removeGap(4);
assertTrue("All gaps removed:\n" + gsl.seqString() + "\n" + symList.seqString(), SymbolUtils.compareSymbolLists(gsl, symList));
}
public void testBlockedInsertBlockRemove()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList));
gsl.addGapsInSource(4,4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList4));
gsl.removeGaps(4,4);
assertTrue(SymbolUtils.compareSymbolLists(gsl, symList));
}
public void testBeginningGap()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
gsl.addGapInSource(1);
assertTrue(
"Begining gap is the empty gap: " +
Alphabet.EMPTY_ALPHABET.getGapSymbol() + " vs " +
gsl.symbolAt(1),
Alphabet.EMPTY_ALPHABET.getGapSymbol() == gsl.symbolAt(1)
);
}
public void testBeginningGaps()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
gsl.addGapsInSource(1, 4);
for(int i = 1; i <=4; i++) {
assertTrue(
"Begining gap " + i + " is the empty gap: " +
Alphabet.EMPTY_ALPHABET.getGapSymbol() + " vs " +
gsl.symbolAt(i),
Alphabet.EMPTY_ALPHABET.getGapSymbol() == gsl.symbolAt(i)
);
}
}
public void testTrailingGap()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
gsl.addGapInSource(symList.length() + 1);
assertTrue(
"Trailing gap is the empty gap: " +
Alphabet.EMPTY_ALPHABET.getGapSymbol() + " vs " +
gsl.symbolAt(gsl.length()),
Alphabet.EMPTY_ALPHABET.getGapSymbol() == gsl.symbolAt(gsl.length())
);
}
public void testTrailingGaps()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
gsl.addGapsInSource(symList.length() + 1, 4);
for(int i = 1; i <=4; i++) {
assertTrue(
"Trailing gap " + i + " is the empty gap: " +
Alphabet.EMPTY_ALPHABET.getGapSymbol() + " vs " +
gsl.symbolAt(gsl.length() + 1 - i),
Alphabet.EMPTY_ALPHABET.getGapSymbol() == gsl.symbolAt(gsl.length() + 1 - i)
);
}
}
public void testInternalGap()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
gsl.addGapInSource(4);
assertTrue(
"Internal gap is the apropreate gap: " +
gsl.getAlphabet().getGapSymbol() + " vs " +
gsl.symbolAt(4),
gsl.getAlphabet().getGapSymbol() == gsl.symbolAt(4)
);
}
public void testInternalGaps()
throws Exception {
GappedSymbolList gsl = new SimpleGappedSymbolList(symList);
gsl.addGapsInSource(4, 4);
for(int i = 4; i < 8; i++) {
assertTrue(
"Internal gap " + i + " is the apropreate gap: " +
gsl.getAlphabet().getGapSymbol() + " vs " +
gsl.symbolAt(i),
gsl.getAlphabet().getGapSymbol() == gsl.symbolAt(i)
);
}
}
public void testDavidBug()
throws Exception {
SymbolTokenization dnaToke1 = DNATools.getDNA().getTokenization("token");
SymbolList symbolList = new SimpleSymbolList(dnaToke1, "ACTGGACCTAAGG");
Sequence sequence = new SimpleSequence(symbolList, "test", "test", null);
SimpleGappedSequence gappedSequence = new SimpleGappedSequence(sequence);
gappedSequence.addGapsInView(4, 4);
gappedSequence.removeGap(7);
gappedSequence.removeGaps(4, 3);
gappedSequence.addGapsInView(7, 2);
gappedSequence.addGapsInView(9, 3);
gappedSequence.addGapsInView(12, 2);
gappedSequence.addGapsInView(14, 3);
gappedSequence.addGapsInView(17, 2);
gappedSequence.removeGap(18);
gappedSequence.removeGaps(11, 6);
String seqStr = gappedSequence.seqString();
seqStr=seqStr==null?null:seqStr;//trick
}
}
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