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//
// testoptimatrix.cpp
// Mothur
//
// Created by Sarah Westcott on 6/6/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#include "testoptimatrix.h"
#include "dataset.h"
/**************************************************************************************************/
TestOptiMatrix::TestOptiMatrix() { //setup
TestDataSet data;
filenames = data.getSubsetFNGFiles(); //Fasta, name, group returned
columnFile = data.getSubsetFNGDistFile();
phylipFile = data.getSubsetFNGPhylipDistFile();
}
/**************************************************************************************************/
TestOptiMatrix::~TestOptiMatrix() {}
/**************************************************************************************************/
////distfile, dupsFile, dupsFormat, distFormat, cutoff, sim
TEST(Test_Container_OptiMatrix, readColumn) {
TestOptiMatrix testOMatrix;
OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", 0.03, false);
//EXPECT_EQ(160,(matrix.print(cout)));
EXPECT_EQ(160,(matrix.getNumDists()));
}
TEST(Test_Container_OptiMatrix, readPhylip) {
TestOptiMatrix testOMatrix;
OptiMatrix pmatrix(testOMatrix.phylipFile, "", "", "phylip", 0.03, false);
//EXPECT_EQ(160,(pmatrix.print(cout)));
EXPECT_EQ(160,(pmatrix.getNumDists()));
}
TEST(Test_Container_OptiMatrix, getNumCLose) {
TestOptiMatrix testOMatrix;
OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", 0.03, false);
EXPECT_EQ(1,(matrix.getNumClose(0)));
EXPECT_EQ(2,(matrix.getNumClose(5)));
EXPECT_EQ(3,(matrix.getNumClose(10)));
EXPECT_EQ(7,(matrix.getNumClose(15)));
EXPECT_EQ(2,(matrix.getNumClose(20)));
}
TEST(Test_Container_OptiMatrix, isClose) {
TestOptiMatrix testOMatrix;
OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", 0.03, false);
//check closeness
EXPECT_EQ(true,(matrix.isClose(0, 8)));
EXPECT_EQ(true,(matrix.isClose(1, 28)));
EXPECT_EQ(true,(matrix.isClose(2, 44)));
EXPECT_EQ(true,(matrix.isClose(15, 42)));
EXPECT_EQ(true,(matrix.isClose(35, 36)));
//check not close
EXPECT_EQ(false,(matrix.isClose(57, 8)));
EXPECT_EQ(false,(matrix.isClose(47, 28)));
EXPECT_EQ(false,(matrix.isClose(32, 44)));
EXPECT_EQ(false,(matrix.isClose(23, 42)));
EXPECT_EQ(false,(matrix.isClose(12, 36)));
}
TEST(Test_Container_OptiMatrix, getCloseSeqs) {
TestOptiMatrix testOMatrix;
OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", 0.03, false);
//11 GQY1XT001B04KZ,GQY1XT001EBRFH 17 32 52 55 57
string Expected_ReturnResults = ""; Expected_ReturnResults += "17"; Expected_ReturnResults += "32"; Expected_ReturnResults += "52"; Expected_ReturnResults += "55"; Expected_ReturnResults += "57";
set<long long> temp = matrix.getCloseSeqs(11);
string ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//21 GQY1XT001BUMO0 26 42 46
Expected_ReturnResults = ""; Expected_ReturnResults += "26"; Expected_ReturnResults += "42"; Expected_ReturnResults += "46";
temp = matrix.getCloseSeqs(21);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//31 GQY1XT001CVCKG,GQY1XT001BO8Z9 20 27
Expected_ReturnResults = ""; Expected_ReturnResults += "20"; Expected_ReturnResults += "27";
temp = matrix.getCloseSeqs(31);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//41 GQY1XT001DY3E7 19 29
Expected_ReturnResults = ""; Expected_ReturnResults += "19"; Expected_ReturnResults += "29";
temp = matrix.getCloseSeqs(41);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//51 GQY1XT001EN363,GQY1XT001B0ZKY,GQY1XT001BCPXE,GQY1XT001BEKE1,GQY1XT001D25E1,GQY1XT001EWORZ,GQY1XT001AQB9P,GQY1XT001CEFI4 49
Expected_ReturnResults = ""; Expected_ReturnResults += "49";
temp = matrix.getCloseSeqs(51);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
}
TEST(Test_Container_OptiMatrix, getNameIndexMap) {
TestOptiMatrix testOMatrix;
OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", 0.03, false);
//maps names to index in closeness matrix
map<string, long long> nameIndexMap = matrix.getNameIndexMap();
//check nameMap
EXPECT_EQ(0,nameIndexMap["GQY1XT001A4DGI"]);
EXPECT_EQ(39,nameIndexMap["GQY1XT001DRYVA"]);
EXPECT_EQ(44,nameIndexMap["GQY1XT001E23UK"]);
EXPECT_EQ(52,nameIndexMap["GQY1XT001ENMKV"]);
EXPECT_EQ(48,nameIndexMap["GQY1XT001EJAUJ"]);
EXPECT_EQ("GQY1XT001A4DGI",(matrix.getName(0)));
EXPECT_EQ("GQY1XT001DRYVA",(matrix.getName(39)));
EXPECT_EQ("GQY1XT001E23UK",(matrix.getName(44)));
EXPECT_EQ("GQY1XT001ENMKV",(matrix.getName(52)));
EXPECT_EQ("GQY1XT001EJAUJ",(matrix.getName(48)));
}
TEST(Test_Container_OptiMatrix, getListSingle) {
TestOptiMatrix testOMatrix;
OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", 0.03, false);
//maps names to index in closeness matrix
ListVector* listSingle = matrix.getListSingle();
//check bin 0
string bin = listSingle->get(0);
EXPECT_EQ("GQY1XT001AD34Z", bin);
bin = listSingle->get(10);
EXPECT_EQ("GQY1XT001BRLCO", bin);
bin = listSingle->get(18);
EXPECT_EQ("GQY1XT001CKAUI", bin);
bin = listSingle->get(3);
EXPECT_EQ("GQY1XT001AOSH9,GQY1XT001BLJ4I,GQY1XT001BNIJQ,GQY1XT001CT9JB,GQY1XT001DCPGQ,GQY1XT001DY88Y,GQY1XT001AHO0L,GQY1XT001DRMZK,GQY1XT001DIXY7,GQY1XT001CDBZ1,GQY1XT001B8C47,GQY1XT001A71WZ,GQY1XT001D41QJ,GQY1XT001BAMTS", bin);
bin = listSingle->get(7);
EXPECT_EQ("GQY1XT001B8UKY", bin);
}
/**************************************************************************************************/
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