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//
// dataset.cpp
// Mothur
//
// Created by Sarah Westcott on 3/24/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#include "dataset.h"
#include "inputdata.h"
/***********************************************************************/
TestDataSet::TestDataSet() {
m = MothurOut::getInstance();
gMap = NULL;
testDir = "/Users/sarahwestcott/Desktop/mothur/TestMothur/TestFiles/";
}
/***********************************************************************/
void TestDataSet::createCountTable() {
fillGroup();
fillNames();
ct = new CountTable();
for (map<string, string>::iterator itNameMap = nameMap.begin(); itNameMap !=nameMap.end(); itNameMap++) {
string firstCol = itNameMap->first;
string secondCol = itNameMap->second;
vector<string> names;
util.splitAtChar(secondCol, names, ',');
//set to 0
map<string, int> groupCounts;
int total = 0;
vector<string> Groups = gMap->getNamesOfGroups();
ct->setNamesOfGroups(Groups);
for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
//get counts for each of the users groups
for (int i = 0; i < names.size(); i++) {
string group = gMap->getGroup(names[i]);
map<string, int>::iterator it = groupCounts.find(group);
//if not found, then this sequence is not from a group we care about
if (it != groupCounts.end()) {
it->second++;
total++;
}
}
if (total != 0) {
vector<int> abunds;
for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) { abunds.push_back(it->second); }
ct->push_back(firstCol, abunds);
}
}
delete gMap; gMap = NULL;
nameMap.clear();
}
/***********************************************************************/
vector<string> TestDataSet::getSubsetFNGFiles() {
vector<string> filenames;
filenames.push_back(testDir+"test.fasta");
filenames.push_back(testDir+"test.names");
filenames.push_back(testDir+"test.groups");
return filenames;
}
/***********************************************************************/
string TestDataSet::getCountTableFile() {
return testDir+"test.count_table";
}
/***********************************************************************/
string TestDataSet::getSharedFile() {
return testDir+"test.opti_mcc.shared";
}
/***********************************************************************/
string TestDataSet::getRelabundFile() {
return testDir+"test.opti_mcc.relabund";
}
/***********************************************************************/
vector<string> TestDataSet::getOptiRefFiles() {
vector<string> filenames;
filenames.push_back(testDir+"silva.v4.unique.fasta");
filenames.push_back(testDir+"silva.v4.count_table");
filenames.push_back(testDir+"silva.v4.unique.dist");
filenames.push_back(testDir+"silva.v4.unique.phylip.dist");
filenames.push_back(testDir+"silva.v4.unique.opti_mcc.list");
filenames.push_back(testDir+"test.fit.dist");
return filenames;
}
/***********************************************************************/
vector<string> TestDataSet::getOligosFiles() {
vector<string> filenames;
filenames.push_back(testDir+"GQY1XT001.oligos"); //single
filenames.push_back(testDir+"Undetermined.oligos"); //paired
filenames.push_back(testDir+"bo.oligos"); //index "NONE"
filenames.push_back(testDir+"comboNames.oligos"); //named primers and named barcodes
return filenames;
}
/***********************************************************************/
string TestDataSet::getSubsetFNGDistFile() {
return (testDir+"test.dist");
}
/***********************************************************************/
string TestDataSet::getSubsetFNGPhylipDistFile() {
return (testDir+"test.phylip.dist");
}
/***********************************************************************/
void TestDataSet::fillSeqs() {
seqs.clear();
//read info from stable file
//string testfile = m->getTestFilePath() + "testFile.fasta";
string testfile = testDir+"test.fasta";
ifstream in;
util.openInputFile(testfile, in);
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
Sequence read(in); util.gobble(in);
seqs.push_back(read);
}
in.close();
}
/***********************************************************************/
void TestDataSet::fillNames() {
nameMap.clear();
//read info from stable file
string testfile = testDir+"test.names";
util.readNames(testfile, nameMap);
}
/***********************************************************************/
void TestDataSet::fillGroup() {
if (gMap != NULL) { delete gMap; gMap = NULL; }
//read info from stable file
string testfile = testDir+"test.groups";
gMap = new GroupMap();
gMap->readMap(testfile);
}
/***********************************************************************/
void TestDataSet::fillLookup() {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
lookup.clear();
//read info from stable file
string testfile = testDir+"test.opti_mcc.shared";
InputData input(testfile, "sharedfile", nullVector);
SharedRAbundVectors* shared = input.getSharedRAbundVectors();
lookup = shared->getSharedRAbundVectors();
}
/***********************************************************************/
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