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//
// testcounttable.cpp
// Mothur
//
// Created by Sarah Westcott on 10/25/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#include "testcounttable.hpp"
/**************************************************************************************************/
TestCountTable::TestCountTable() { //setup
m = MothurOut::getInstance();
TestDataSet data;
vector<string> filenames = data.getSubsetFNGFiles();
fastafile = filenames[0];
namefile = filenames[1];
groupfile = filenames[2];
countfile = data.getCountTableFile();
}
/**************************************************************************************************/
TestCountTable::~TestCountTable() {}//teardown
/**************************************************************************************************/
//Testing createTable functions
TEST(Test_Container_CountTable, createTables) {
//int createTable(string, string, bool); //namefile, groupfile, createGroup
TestCountTable testData;
CountTable ct;
ct.createTable(testData.namefile, testData.groupfile, false);
EXPECT_EQ(ct.getNumGroups(), 10);
EXPECT_EQ(ct.getNumSeqs(), 200);
//int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames
set<string> seqNames;
seqNames.insert("seq1"); seqNames.insert("seq2"); seqNames.insert("seq3"); seqNames.insert("seq4"); seqNames.insert("seq5");
set<string> groupNames;
groupNames.insert("group1"); groupNames.insert("group2");
map<string, string> groupMap;
groupMap["seq1"] = "group1"; groupMap["seq2"] = "group1"; groupMap["seq3"] = "group1"; groupMap["seq4"] = "group2"; groupMap["seq5"] = "group2";
ct.clearTable();
ct.createTable(seqNames, groupMap, groupNames);
EXPECT_EQ(ct.getNumGroups(), 2);
EXPECT_EQ(ct.getNumSeqs(), 5);
//int readTable(string, bool, bool); //filename, readGroups, mothurRunning
ct.clearTable();
ct.readTable(testData.countfile, true, true);
EXPECT_EQ(ct.getNumGroups(), 10);
EXPECT_EQ(ct.getNumSeqs(), 200);
ct.clearTable();
ct.readTable(testData.countfile, false, true);
EXPECT_EQ(ct.getNumGroups(), 0);
EXPECT_EQ(ct.getNumSeqs(), 200);
//int readTable(string, string); //filename, format - if format=fasta, read fasta file and create unique table
ct.clearTable();
ct.readTable(testData.fastafile, "fasta");
EXPECT_EQ(ct.getNumGroups(), 0);
EXPECT_EQ(ct.getNumSeqs(), 93);
EXPECT_EQ(ct.getHardCodedHeaders()[0], "Representative_Sequence");
EXPECT_EQ(ct.getHardCodedHeaders()[1], "total");
}
/**************************************************************************************************/
//Testing testGroups functions
TEST(Test_Container_CountTable, testGroups) {
TestCountTable testData;
CountTable ct;
EXPECT_EQ(ct.testGroups(testData.countfile), true);
vector<string> groups;
ct.testGroups(testData.countfile, groups);
EXPECT_EQ(groups[0], "F003D000");
EXPECT_EQ(groups[1], "F003D002");
EXPECT_EQ(groups[2], "F003D004");
EXPECT_EQ(groups[3], "F003D006");
EXPECT_EQ(groups[4], "F003D008");
EXPECT_EQ(groups[5], "F003D142");
ct.createTable(testData.namefile, testData.groupfile, false);
CountTable ct2; ct2.copy(&ct);
EXPECT_EQ(ct2.getNumGroups(), 10);
EXPECT_EQ(ct2.getNumSeqs(), 200);
EXPECT_EQ(ct2.hasGroupInfo(), true);
groups = ct2.getNamesOfGroups();
EXPECT_EQ(groups[0], "F003D000");
EXPECT_EQ(groups[1], "F003D002");
EXPECT_EQ(groups[2], "F003D004");
EXPECT_EQ(groups[3], "F003D006");
EXPECT_EQ(groups[4], "F003D008");
EXPECT_EQ(groups[5], "F003D142");
groups.clear();
groups.push_back("group1"); groups.push_back("group2"); groups.push_back("group3");
ct2.setNamesOfGroups(groups);
groups = ct2.getNamesOfGroups();
EXPECT_EQ(groups[0], "group1");
EXPECT_EQ(groups[1], "group2");
EXPECT_EQ(groups[2], "group3");
ct2.addGroup("group4");
ct2.removeGroup("group2");
groups = ct2.getNamesOfGroups();
EXPECT_EQ(groups[0], "group1");
EXPECT_EQ(groups[1], "group3");
EXPECT_EQ(groups[2], "group4");
}
/**************************************************************************************************/
//Testing testGroups functions
TEST(Test_Container_CountTable, push_backs) {
TestCountTable testData;
CountTable ct;
ct.push_back("seq1");
EXPECT_EQ(ct.getNamesOfSeqs()[0], "seq1");
ct.push_back("seq2", 15);
EXPECT_EQ(ct.getNumSeqs(), 16);
EXPECT_EQ(ct.size(), 2);
ct.renameSeq("seq1", "mySeq");
EXPECT_EQ(ct.getNamesOfSeqs()[0], "mySeq");
ct.remove("mySeq");
EXPECT_EQ(ct.getNamesOfSeqs()[0], "seq2");
ct.push_back("seq3", 10);
EXPECT_EQ(ct.get("seq2"), 0);
EXPECT_EQ(ct.get("seq3"), 1);
ct.setNumSeqs("seq3", 100);
EXPECT_EQ(ct.getNumSeqs("seq3"), 100);
}
/**************************************************************************************************/
//Testing testGroups functions
TEST(Test_Container_CountTable, push_backGroups) {
TestCountTable testData;
CountTable ct;
ct.createTable(testData.namefile, testData.groupfile, false);
ct.setAbund("GQY1XT001B1CEF", "F003D000", 50);
EXPECT_EQ(ct.getGroupCount("GQY1XT001B1CEF", "F003D000"), 50);
vector<int> abunds; abunds.resize(10, 100);
ct.push_back("mySeq", abunds);
EXPECT_EQ(ct.getGroupCount("mySeq", "F003D000"), 100);
}
/**************************************************************************************************/
TEST(Test_Container_CountTable, getSets) {
TestCountTable testData;
CountTable ct;
ct.createTable(testData.namefile, testData.groupfile, false);
vector<string> thisSeqsGroups = ct.getGroups("GQY1XT001B1CEF");
EXPECT_EQ(thisSeqsGroups[0], "F003D148");
vector<int> thisSeqsAbunds = ct.getGroupCounts("GQY1XT001B1CEF");
EXPECT_EQ(thisSeqsAbunds[0], 0);
EXPECT_EQ(thisSeqsAbunds[8], 1);
EXPECT_EQ(ct.getGroupCount("GQY1XT001B1CEF", "F003D148"), 1);
EXPECT_EQ(ct.getGroupCount("F003D148"), 21);
//EXPECT_EQ(ct.getNumSeqs("fakeSeq"), 0);
EXPECT_EQ(ct.getNumSeqs("GQY1XT001CO8VD"), 16);
EXPECT_EQ(ct.getNumUniqueSeqs(), 93);
}
/**************************************************************************************************/
TEST(Test_Container_CountTable, dataStructures) {
TestCountTable testData;
CountTable ct;
ct.createTable(testData.namefile, testData.groupfile, false);
EXPECT_EQ(ct.getNamesOfSeqs().size(), 93);
EXPECT_EQ(ct.getNamesOfSeqs("F003D148").size(), 19);
EXPECT_EQ(ct.getNamesOfSeqs("F003D004").size(), 11);
EXPECT_EQ(ct.getNumSeqs("GQY1XT001B1CEF"), 1);
EXPECT_EQ(ct.getNumSeqs("GQY1XT001CO8VD"), 16);
ct.mergeCounts("GQY1XT001B1CEF", "GQY1XT001CO8VD");
EXPECT_EQ(ct.getNumSeqs("GQY1XT001B1CEF"), 17);
}
/**************************************************************************************************/
//ListVector getListVector();
//SharedRAbundVectors* getShared();
//SharedRAbundVectors* getShared(vector<string>); //set of groups selected
//map<string, int> getNameMap(); //sequenceName -> total number of sequences it represents
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