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//
// testsharedrabundvectors.cpp
// Mothur
//
// Created by Sarah Westcott on 8/10/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#include "testsharedrabundvectors.hpp"
#include "dataset.h"
/**************************************************************************************************/
TestSharedRabundVectors::TestSharedRabundVectors() : SharedRAbundVectors() { //setup
m = MothurOut::getInstance();
TestDataSet data; sharedFile = data.getSharedFile();
}
/**************************************************************************************************/
TestSharedRabundVectors::~TestSharedRabundVectors() {}//teardown
/**************************************************************************************************/
TEST(Test_Container_SharedRabundVectors, Constructors) {
TestSharedRabundVectors test;
SharedRAbundVectors temp;
EXPECT_EQ(temp.getNumBins(), 0);
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
EXPECT_EQ(nextLabel, "");
EXPECT_EQ(labelTag, "Otu");
EXPECT_EQ(userGroups[0], "F003D000");
SharedRAbundVectors copy(fileRead);
EXPECT_EQ(copy.getLabel(), "0.03");
EXPECT_EQ(labelTag, "Otu");
EXPECT_EQ(userGroups[0], "F003D000");
}
TEST(Test_Container_SharedRabundVectors, GetsSets) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
EXPECT_EQ(nextLabel, "");
EXPECT_EQ(labelTag, "Otu");
EXPECT_EQ(userGroups[0], "F003D000");
//setLabels
fileRead.setLabels("0.99");
EXPECT_EQ(fileRead.getLabel(), "0.99");
//getOTUTotal
EXPECT_EQ(fileRead.getOTUTotal(4), 12);
//getOTU
vector<int> otu5 = fileRead.getOTU(4);
EXPECT_EQ(otu5[0], 0);
EXPECT_EQ(otu5[1], 2);
//get
EXPECT_EQ(fileRead.get(4, "F003D000"), 0);
EXPECT_EQ(fileRead.get(4, "F003D002"), 2);
EXPECT_EQ(fileRead.get(0, "F003D142"), 6);
//set
fileRead.set(4, 10, "F003D000");
EXPECT_EQ(fileRead.get(4, "F003D000"), 10);
fileRead.set(4, 15, "F003D002");
EXPECT_EQ(fileRead.get(4, "F003D002"), 15);
fileRead.set(0, 3, "F003D142");
EXPECT_EQ(fileRead.get(0, "F003D142"), 3);
//getOTUNames
vector<string> otuNames = fileRead.getOTUNames();
EXPECT_EQ(otuNames[10], "Otu11");
//setOTUNames
otuNames[5] = "Otu99";
fileRead.setOTUNames(otuNames);
EXPECT_EQ(fileRead.getOTUNames()[5], "Otu99");
EXPECT_EQ(fileRead.getOTUName(5), "Otu99");
fileRead.setOTUName(5, "Otu6");
EXPECT_EQ(fileRead.getOTUName(5), "Otu6");
//getNumBins
EXPECT_EQ(fileRead.getNumBins(), 58);
//getNumSeqsSmallestGroup
EXPECT_EQ(fileRead.getNumSeqsSmallestGroup(), 15);
//getNamesGroups
EXPECT_EQ(fileRead.getNamesGroups()[1], "F003D002");
//getNumGroups
EXPECT_EQ(fileRead.getNumGroups(), 10);
//getNumSeqs
EXPECT_EQ(fileRead.getNumSeqs("F003D002"), 31);
}
TEST(Test_Container_SharedRabundVectors, PushBack) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
//getNumGroups
EXPECT_EQ(fileRead.getNumGroups(), 10);
vector<int> abunds(58, 5);
SharedRAbundVector* temp = new SharedRAbundVector(abunds);
temp->setGroup("myabunds");
fileRead.push_back(temp);
//getNumGroups
EXPECT_EQ(fileRead.getNumGroups(), 11);
vector<int> otuAbunds(11, 2); string otuLabel = "Otu59";
fileRead.push_back(otuAbunds, otuLabel);
EXPECT_EQ(fileRead.getNumBins(), 59);
}
TEST(Test_Container_SharedRabundVectors, eliminateZeroOTUS) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
EXPECT_EQ(fileRead.getNumBins(), 58);
fileRead.set(16, 0, "F003D142");
EXPECT_EQ(fileRead.get(16, "F003D142"), 0); //zero out bin
fileRead.eliminateZeroOTUS(); //remove zeroed out bin
EXPECT_EQ(fileRead.getNumBins(), 57);
}
TEST(Test_Container_SharedRabundVectors, Removes) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
EXPECT_EQ(fileRead.getNumBins(), 58);
EXPECT_EQ(fileRead.removeOTU(16), 2);
EXPECT_EQ(fileRead.getNumBins(), 57);
vector<string> groups;
groups.push_back("F003D142");
groups.push_back("F003D002");
groups.push_back("F003D004");
groups.push_back("F003D006");
fileRead.removeGroups(groups);
EXPECT_EQ(fileRead.getNumBins(), 41);
EXPECT_EQ(fileRead.getNumSeqsSmallestGroup(), 15);
fileRead.removeGroups(20); //remove groups with abundance less than 20
EXPECT_EQ(fileRead.getNumGroups(), 4);
}
TEST(Test_Container_SharedRabundVectors, SizeClear) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
EXPECT_EQ(fileRead.size(), 10);
fileRead.clear();
EXPECT_EQ(fileRead.getNumBins(), 0);
}
TEST(Test_Container_SharedRabundVectors, GetRabundVector) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
RAbundVector temp = fileRead.getRAbundVector();
EXPECT_EQ(temp.get(0), 24);
RAbundVector temp2 = fileRead.getRAbundVector("F003D142");
EXPECT_EQ(temp2.get(0), 6);
}
TEST(Test_Container_SharedRabundVectors, GetSabundVector) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
SAbundVector temp = fileRead.getSAbundVector();
EXPECT_EQ(temp.get(5), 1); //number of OTUs with abundance of 5
EXPECT_EQ(temp.get(1), 35); //number of OTUs with abundance of 1
EXPECT_EQ(temp.getMaxRank(), 24);
}
TEST(Test_Container_SharedRabundVectors, GetSharedRAbundVectors) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
vector<SharedRAbundVector*> temp = fileRead.getSharedRAbundVectors();
EXPECT_EQ(temp[0]->get(5), 0); //first groups abundance of OTU5
EXPECT_EQ(temp[1]->get(5), 2); //first groups abundance of OTU5
EXPECT_EQ(temp[0]->get(0), 1); //first groups abundance of OTU1
}
TEST(Test_Container_SharedRabundVectors, GetSharedRAbundFloatVectors) {
TestSharedRabundVectors test;
ifstream in;
Utils util; util.openInputFile(test.sharedFile, in);
vector<string> userGroups; string nextLabel, labelTag;
SharedRAbundVectors fileRead(in, userGroups, nextLabel, labelTag);
vector<SharedRAbundFloatVector*> temp = fileRead.getSharedRAbundFloatVectors();
EXPECT_EQ(temp[0]->get(5), 0.0); //first groups abundance of OTU5 as a float. This is not the same as if we ran get.relabund() command
EXPECT_EQ(temp[1]->get(5), 2.0); //first groups abundance of OTU5 as a float. This is not the same as if we ran get.relabund() command
EXPECT_EQ(temp[0]->get(0), 1.0); //first groups abundance of OTU1 as a float. This is not the same as if we ran get.relabund() command
}
/**************************************************************************************************/
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