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//
// testphylotree.cpp
// Mothur
//
// Created by Sarah Westcott on 8/29/16.
// Copyright © 2016 Schloss Lab. All rights reserved.
//
#include "testphylotree.hpp"
/**************************************************************************************************/
TestPhyloTree::TestPhyloTree() { //setup
m = MothurOut::getInstance();
string tax1WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
string tax2WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
string tax3WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
string tax4WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
string tax5WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
string tax1WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
string tax2WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
string tax3WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
string tax4WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
string tax5WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
phylo.addSeqToTree("seq1", tax1WithSpaces);
phylo.addSeqToTree("seq2", tax2WithSpaces);
phylo.addSeqToTree("seq3", tax3WithSpaces);
phylo.addSeqToTree("seq4", tax4WithSpaces);
phylo.addSeqToTree("seq5", tax5WithSpaces);
phylo.addSeqToTree("seq6", tax1WithOutSpaces);
phylo.addSeqToTree("seq7", tax2WithOutSpaces);
phylo.addSeqToTree("seq8", tax3WithOutSpaces);
phylo.addSeqToTree("seq9", tax4WithOutSpaces);
phylo.addSeqToTree("seq10", tax5WithOutSpaces);
}
/**************************************************************************************************/
TestPhyloTree::~TestPhyloTree() {}
/**************************************************************************************************
TEST_CASE("Testing PhyloTree Class") {
TestPhyloTree testPTree;
string tax1WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
string tax2WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
string tax3WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
string tax4WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
string tax5WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
string tax1WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
string tax2WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
string tax3WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
string tax4WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
string tax5WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
SECTION("Add Sequences to Tree") {
INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
CAPTURE(testPTree.addSeqToTree("seq1", tax1WithSpaces));
CHECK(testPTree.addSeqToTree("seq1", tax1WithSpaces) == 5);
CAPTURE(testPTree.addSeqToTree("seq2", tax2WithSpaces));
CHECK(testPTree.addSeqToTree("seq2", tax2WithSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq3", tax3WithSpaces));
CHECK(testPTree.addSeqToTree("seq3", tax3WithSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq4", tax4WithSpaces));
CHECK(testPTree.addSeqToTree("seq4", tax4WithSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq5", tax5WithSpaces));
CHECK(testPTree.addSeqToTree("seq5", tax5WithSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq6", tax1WithOutSpaces));
CHECK(testPTree.addSeqToTree("seq6", tax1WithOutSpaces) == 5);
CAPTURE(testPTree.addSeqToTree("seq7", tax2WithOutSpaces));
CHECK(testPTree.addSeqToTree("seq7", tax2WithOutSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq8", tax3WithOutSpaces));
CHECK(testPTree.addSeqToTree("seq8", tax3WithOutSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq9", tax4WithOutSpaces));
CHECK(testPTree.addSeqToTree("seq9", tax4WithOutSpaces) == 6);
CAPTURE(testPTree.addSeqToTree("seq10", tax5WithOutSpaces));
CHECK(testPTree.addSeqToTree("seq10", tax5WithOutSpaces) == 6);
}
SECTION("Get Seqs") {
INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
CAPTURE(testPTree.phylo.getSeqs("Bacteroidetes 7").size());
CHECK((testPTree.phylo.getSeqs("Bacteroidetes 7").size()) == 2);
vector<string> Bacteroidetes_7 = testPTree.phylo.getSeqs("Bacteroidetes 7");
CHECK(Bacteroidetes_7[0] == "seq1");
CHECK(Bacteroidetes_7[1] == "seq2");
CAPTURE(testPTree.phylo.getSeqs("Clostridia").size());
CHECK((testPTree.phylo.getSeqs("Clostridia").size()) == 3);
vector<string> Clostridia = testPTree.phylo.getSeqs("Clostridia");
CHECK(Clostridia[0] == "seq8");
CHECK(Clostridia[1] == "seq9");
CHECK(Clostridia[2] == "seq10");
}
SECTION("Get Genus Totals") {
INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
CAPTURE(testPTree.phylo.getGenusTotals().size());
CHECK(testPTree.phylo.getGenusTotals().size() == 10);
}
SECTION("Get Full Taxonomy") {
INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
CAPTURE(testPTree.phylo.getFullTaxonomy("seq1"));
CHECK(testPTree.phylo.getFullTaxonomy("seq1") == "Bacteria;Bacteroidetes 7;Bacteroidia;Bacteroidales;S24-7;");
CAPTURE(testPTree.phylo.getFullTaxonomy("seq10"));
CHECK(testPTree.phylo.getFullTaxonomy("seq1") == "Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Incertae_Sedis;");
}
}
**************************************************************************************************/
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