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package org.biojava.bio.symbol;
import junit.framework.TestCase;
import junit.framework.TestSuite;
import org.biojava.bio.seq.DNATools;
/** List of tests for for UkkonenSuffixTree.
* @author Francois Pepin
* @version $Revision: 4171 $
*/
public class UkkonenSuffixTreeTest extends TestCase {
public UkkonenSuffixTreeTest(String name){
super(name);
}
UkkonenSuffixTree test;
String mississippi= "mississippi";
protected void setUp(){
test = new UkkonenSuffixTree();
}
public static void main(String args[]){
junit.textui.TestRunner.run(new TestSuite(UkkonenSuffixTreeTest.class));
}
public void testMultiple() {
// Bug #2260
try {
new UkkonenSuffixTree(mississippi+"$"+mississippi);
} catch (NullPointerException e) {
e.printStackTrace();
}
}
public void testNumberNodes(){
test.addSequence(mississippi, "name", false);
//System.out.println(test.getRoot().children.size());
assertEquals(19,test.getAllNodes(test.getRoot(), null, false).size());
assertEquals(12,test.getAllNodes(test.getRoot(), null, true).size());
}
public void testSymbolListAddition(){
SymbolList here=null;
try{
here = DNATools.createDNA("taccaccagga");
test = new UkkonenSuffixTree((FiniteAlphabet)here.getAlphabet());
test.addSymbolList(here, "name", false);
}catch(IllegalSymbolException e){e.printStackTrace();}
assertEquals(19,test.getAllNodes(test.getRoot(), null, false).size());
assertEquals(12,test.getAllNodes(test.getRoot(), null, true).size());
}
/*public void testSymbolListConversion(){
SymbolList here=null;
SymbolList here2=null;
try{
here = DNATools.createDNA("taccaccagga");
test = new UkkonenSuffixTree((FiniteAlphabet)here.getAlphabet());
//here2= test.stringToSymbolList(test.symbolListToString(here));
}catch(IllegalSymbolException e){e.printStackTrace();}
for (int i=1;i<=here.length();i++)
assertEquals(here.symbolAt(i),here2.symbolAt(i));
}*/
// adding twice the same string should be the same
public void testDuplicateAddition(){
test.addSequence(mississippi, "name", false);
test.addSequence(mississippi, "name", false);
assertEquals(19,test.getAllNodes(test.getRoot(), null, false).size());
assertEquals(12,test.getAllNodes(test.getRoot(), null, true).size());
}
public void testGetterMethods()
{
SymbolList here=null;
try{
here = DNATools.createDNA("taccaccagga");
test = new UkkonenSuffixTree((FiniteAlphabet)here.getAlphabet());
test.addSymbolList(here, "name", false);
}catch(IllegalSymbolException e){e.printStackTrace();}
assertTrue(test.getRoot().getParent()==null);
//bad test that mixes SymbolLists and CharSequence, but it still works.
assertTrue(test.getRoot().hasChild(new Character('g')));
assertTrue(test.getRoot().getChild(new Character(UkkonenSuffixTree.DEFAULT_TERM_CHAR)).isTerminal());
}
public void testlongAddition(){
test.addSequence(dna, "name", false);
int before = test.getAllNodes(test.getRoot(), null, false).size();
test.addSequence(dna, "name", false);
int after = test.getAllNodes(test.getRoot(), null, false).size();
assertEquals(before, after);
//test.printTree();
}
private String dna=
"GGCTCAGTCCCGACGTGGAACTCAGCAGCGGAGGCTGGACGCTTGCATGGCGCTTGAGGCAAGTTCGGGGCTCATTTTGGAAGTTTTCTTTCTAGCACAGACATCCAACTCTGCTCCTATGCCAGTCAGATAATTAAGGAATTAAGTAATAATTGTGCTCTGCAAATTATGATAGTGATCTGTATTTACTACGTGCATATATTTTGGGCCAGTGAATTTTTTTCTAAGCTAATATAGTTATTTGGACTTTTGACATGACTTTGTGTTTAATTAAAACAAAAAAAGAAATTGCAGAAGTGTTGTAAGCTTGTAAAAAAATTCAAACAATGCAGACAAATGTGTCTCGCAGTCTTCCACTCAGTATCATTTTTGTTTGTACCTTATCAGAAATGTTTCTATGTACAAGTCTTTAAAATCATTTCGAACTTGCTTTGTCCACTGAGTATATTATGGACATCTTTTCATGGCAGGACATATAGATGTGTTAATGGCATTAAAAATAAAACAAAAAACTGATTCGGCCGGGTACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGATCGAGGAGGGAGGATCACCTGAGGTCAGGAGTTACAGACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGCGGAGGTTGCGGTGAGCCGAGATCGCACCGTTGCACTCCAGCCTGGGCGACAGAGCGAAACTGTCTCAAACAAACAAACAAAAAAACCTGATACATGGTATGGGAAGTACATTGTTTAAACAATGCATGGAGATTTAGGTTGTTTCCAGTTTTTACTGGCACAGATACGGCAATGAATATAATTTTATGTATACATTCATACAAATATATCGGTGGAAAATTCCTAGAAGTGGAATGGCTGGGTCAGTGGGCATTCATATTGAGAAATTGGAAGGATGTTGTCAAACTCTGCAAATCAGAGTATTTTAGTCTTAACCTCTCTTCTTCACACCCTTTTCCTTGGAAGAAAGCTAAATTTAGACTTTTAAACACAAAACTCCATTTTGAGACCCCTGAAAATCTGGGTTCAAAGTGTTTGAAAATTAAAGCAGAGGCTTTAATTTGTACTTATTTAGGTATAATTTGTACTTTAAAGTTGTTCCAGAAAACAAGGCAAATACTGAAAAGCATTTCATCTGAAGTTTCTTTCTGGTATTGAACAGAGTTGGATGGAGAGTGAATGCAGGTTACCGATGTGTTCGCAGGAACAAAACGGGAGGGAGAGTAACACAGGTGCACGGCTTCATATTGATTTATCAAAGAACTTGCTTTTGGACTGTTAAAAAATGTGTTGCACAGTTCTGACACTTTTACACAATGATGAGCTTACAAAGGGGAAAATGCTTAACATAAACATAGTTTCAAAGAAGGTAAGTCCTAGTTTTTCCACGAGCTGTTTTTTTTTTTGAGAGAGAGTAGTCCCAAAATTTCCCTATTATGTGGTTTTTCATCCAAAGTGTTGTAATCCGTGTGTTCTAACCCGCATATTACGATTACTCAAGAAATGCAAAATAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCAATTTGGGAGGCCGAGGCAGGTGGATCACGAGGTCAGGAGATCAAGACCATCCTAGCTAACACGGTGCAAACCCATCTACTAAAAATAAAAAATATTAGCTGGGCGTGGCGGCAGGCGCCTGTAGTCCCAACTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCCAAGATCCGGCCACTGCACTCCAGCCTGGGCGACAGAGGGAGACTCCGTCTCAAAAATAAAAATAAAAATAAAAAAAGAAAAAAGAAATGCAAAATAATGTGAACACGTCATCGAGACTGCGGTCTACAATTGTGGTTGCCATGATGGGGTGGGTCGGAAGACACCGAGGCTGCTTGAATCATGTTCCTGGCAGGTTAATTTTGTTCCTTTTAGGGCATCTAAATGTTGGAGTTGGCTTTCCTGGCAGAGAGTCCAGTTGTGAGTGGAGTATTGGGTGGAGGCCCCACCCTCCCCAGGTTTTCTGCAGCTTGTTCCTGGCTCTTCTGGGGCTTCTCTGAGGACCCCGATTGGTCCTGGGGCTTCTTTAGTGGTGGGCCTGGGCCAGTTCCTTCCGTTGCTCACCTCTCCCCGAAGCTTAAGGATAACATTTCGGGAAGATCATGAGAGAACGTGAACCAAAAAAAAAAAAAAAAATTCAGGTAGGGTGGGAGCTAAGTTAGTTTAGTATTTGGGATTTTTGTTTTGTTTTGTTTGAGACAGAGTCTCAAACAAAGACCCCGCGCCTGGCCTGGGGGTCTTTTTTTGAGTCAGCAGTTGAGTTTGAAAATCCCCTTCCTTGGAATCCGCCCAGGCTGTTTTCTCTGGTGGATGCTTATTGCCCCTGCTAACTTCAGCTGCGGTCTCTCTGCTCGCCTTGCCCTCCCCATCCTCCTTAGACCTTTTAAGCTTCACTTTCCTTTCCTTGCTGCCCCGCCTCCCTGTCTCCCCAGTGTGATCTACCCTGAAAGGCTGCTGTATTTTGTTTCCCTTTGGGACCGAGCCTGCTCAAATGATCTGCTCCATGAGGTTTTACTGCTATATCCTACTGAAGTATCTGGGAGGTCTTGGCGGAGAAGAGGACAACATCTTGGAAAATGCAGCCTGGAACCTCTCTGCTCTCTTTCATCAGCTTTCCCTCAATGATGAGCTCAAAATCCTCTTTCTTGCTGATGGAATTGTCTGCTGTCATCATTTCAGTTGAGTCCTCCTAGGCTGGGCCTTGTAAGAAGAACAACTGTTTATAACTATTGAAAGTCAATATTTACTAAGAAAAAGAGGTTGTTGTTATCTGAGCCATCCAACATGAATTTAAGAATATATTCCAGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGATGGGTGGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCATGCGTGGTGGCACATGCCTGTAGTTCCAACTATTTGGGACACTAAGGCAGGGGAAGTGCTTGAACTCGGGAGGCAGAGGTTGCAGTGAGCTGAGATTGTACCACTGCACTCCAGCCTGGGTAAAAAGAGTGAAATTCCATCTCAAAAAAAAAAAAGGAGACAGGGTCTTGCCCTGTTGCCCAGGCTGGAGTGCCGTGGCACGATCATAACTCACTGTGGCCTCAAATTCCTGGGCTCAACTGATTCTCCTGCCTCAGTCTCCCAAGTAGCTGGGACCACAAGTACATGCCACCATGCTAGGCTAATTTTATTTTTATTTTTAGAAAATAAAATATTTTTTATTTTATTTAGGCAACATGCTATGTTGCCTAGACTGGTCTTGAACTCCTGGCTTCAAGCTATCCTCTTGCCTCAGCCAACCAAAGTGCTGGGATTGCAGGTGTGAACTGCCATGCCTGGCTTTCTATTCTCTATTTCTAGGAGATAAGCTTTTTGAGCTTTCACATATGAGTGTGAACATGTGGTATTTATCTTTCTGTGCCTAGGTTATTCCACTTAACGTAATGTACTCCAGGCTCATCCATGTTGATGGGAATTACAGGATTTCATTCTCTTGTAATGGCTGAATAACATCCCATTTTGTGTATATAGTCCACATGTTCTTTATCCATTCCTCTTTTGATAGACACTTAGGTTGATTCCGTATCTCGGGTATTATGAGCAGTGCTGCAGTAAACATGAGAGTGCAAATATCTCTTCAACATACTGATTCCCTTTCCTTTGGATATATATTCAGCAGT";
}
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