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|
//
// createdatabasecommand.cpp
// Mothur
//
// Created by Sarah Westcott on 3/28/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "createdatabasecommand.h"
#include "inputdata.h"
//**********************************************************************************************************************
vector<string> CreateDatabaseCommand::setParameters(){
try {
CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("repname", "InputTypes", "", "", "NameCount", "NameCount", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pconstaxonomy);
CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(plist);
CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(pshared);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string CreateDatabaseCommand::getHelpString(){
try {
string helpString = "";
helpString += "The create.database command reads a list file or a shared file, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, or count file and creates a database file.\n";
helpString += "The create.database command parameters are repfasta, list, shared, repname, constaxonomy, group, count and label. List, repfasta, repnames or count, and constaxonomy are required.\n";
helpString += "The repfasta file is fasta file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
helpString += "The repname file is the name file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
helpString += "The count file is the count file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, count=yourCountFile). If it includes group info, mothur will give you the abundance breakdown by group. \n";
helpString += "The constaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile, name=yourNameFile).\n";
helpString += "The group file is optional and will just give you the abundance breakdown by group.\n";
helpString += "The label parameter allows you to specify a label to be used from your listfile.\n";
helpString += "NOTE: Make SURE the repfasta, repnames and contaxonomy are for the same label as the listfile.\n";
helpString += "The create.database command should be in the following format: \n";
helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, repname=final.an.0.03.rep.names, list=final.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string CreateDatabaseCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "database") { pattern = "[filename],database"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
CreateDatabaseCommand::CreateDatabaseCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["database"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
exit(1);
}
}
//**********************************************************************************************************************
CreateDatabaseCommand::CreateDatabaseCommand(string option) {
try{
abort = false; calledHelp = false;
//allow user to run help
if (option == "help") {
help(); abort = true; calledHelp = true;
}else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["database"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
it = parameters.find("repname");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["repname"] = inputDir + it->second; }
}
it = parameters.find("constaxonomy");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["constaxonomy"] = inputDir + it->second; }
}
it = parameters.find("repfasta");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["repfasta"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
it = parameters.find("count");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["count"] = inputDir + it->second; }
}
it = parameters.find("shared");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not found") { listfile = ""; }
else if (listfile == "not open") { listfile = ""; abort = true; }
else { m->setListFile(listfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not found") { sharedfile = ""; }
else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else { m->setSharedFile(sharedfile); }
if ((sharedfile == "") && (listfile == "")) {
//is there are current file available for either of these?
//give priority to list, then shared
listfile = m->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else {
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
abort = true;
}
}
}
else if ((sharedfile != "") && (listfile != "")) { m->mothurOut("When executing a create.database command you must enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true; }
if (sharedfile != "") { if (outputDir == "") { outputDir = m->hasPath(sharedfile); } }
else { if (outputDir == "") { outputDir = m->hasPath(listfile); } }
contaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
if (contaxonomyfile == "not found") { //if there is a current list file, use it
contaxonomyfile = ""; m->mothurOut("The constaxonomy parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
}
else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
repfastafile = validParameter.validFile(parameters, "repfasta", true);
if (repfastafile == "not found") { //if there is a current list file, use it
repfastafile = ""; m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
}
else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
repnamesfile = validParameter.validFile(parameters, "repname", true);
if (repnamesfile == "not found") { repnamesfile = ""; }
else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not found") { countfile = ""; }
else if (countfile == "not open") { countfile = ""; abort = true; }
if ((countfile == "") && (repnamesfile == "")) {
//if there is a current name file, use it, else look for current count file
string repnamesfile = m->getNameFile();
if (repnamesfile != "") { m->mothurOut("Using " + repnamesfile + " as input file for the repname parameter."); m->mothurOutEndLine(); }
else {
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("[ERROR]: You must provide a count or repname file."); m->mothurOutEndLine(); abort = true; }
}
}
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your listfile.\n");}
}
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "CreateDatabaseCommand");
exit(1);
}
}
//**********************************************************************************************************************
int CreateDatabaseCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//taxonomies holds the taxonomy info for each Otu
//classifyOtuSizes holds the size info of each Otu to help with error checking
vector<string> taxonomies;
vector<string> otuLabels;
vector<int> classifyOtuSizes = readTax(taxonomies, otuLabels);
if (m->control_pressed) { return 0; }
vector<Sequence> seqs;
vector<int> repOtusSizes = readFasta(seqs);
if (m->control_pressed) { return 0; }
//names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
map<string, string> repNames;
map<string, int> nameMap;
int numUniqueNamesFile = 0;
CountTable ct;
if (countfile == "") {
numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
//the repnames file does not have the same order as the list file bins so we need to sort and reassemble for the search below
map<string, string> tempRepNames;
for (map<string, string>::iterator it = repNames.begin(); it != repNames.end();) {
string bin = it->first;
vector<string> temp;
m->splitAtChar(bin, temp, ',');
sort(temp.begin(), temp.end());
bin = "";
for (int i = 0; i < temp.size()-1; i++) {
bin += temp[i] + ',';
}
bin += temp[temp.size()-1];
tempRepNames[bin] = it->second;
repNames.erase(it++);
}
repNames = tempRepNames;
}else {
ct.readTable(countfile, true, false);
numUniqueNamesFile = ct.getNumUniqueSeqs();
nameMap = ct.getNameMap();
}
//are there the same number of otus in the fasta and name files
if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
if (m->control_pressed) { return 0; }
//are there the same number of OTUs in the tax and fasta file
if (classifyOtuSizes.size() != repOtusSizes.size()) { m->mothurOut("[ERROR]: you have " + toString(classifyOtuSizes.size()) + " taxonomies in your contaxonomy file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
if (m->control_pressed) { return 0; }
//at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
for (int i = 0; i < classifyOtuSizes.size(); i++) {
if (classifyOtuSizes[i] != repOtusSizes[i]) {
m->mothurOut("[ERROR]: OTU size info does not match for bin " + toString(i+1) + ". The contaxonomy file indicated the OTU represented " + toString(classifyOtuSizes[i]) + " sequences, but the repfasta file had " + toString(repOtusSizes[i]) + ". These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true;
}
}
if (m->control_pressed) { return 0; }
map<string, string> variables;
if (listfile != "") { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); }
else { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); }
string outputFileName = getOutputFileName("database", variables);
outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
string header = "OTUNumber\tAbundance\t";
if (listfile != "") {
//at this point we are fairly sure the repfasta, repnames and contaxonomy files match so lets proceed with the listfile
ListVector* list = getList();
if (otuLabels.size() != list->getNumBins()) {
m->mothurOut("[ERROR]: you have " + toString(otuLabels.size()) + " otus in your contaxonomy file, but your list file has " + toString(list->getNumBins()) + " otus. These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true; }
if (m->control_pressed) { delete list; return 0; }
GroupMap* groupmap = NULL;
if (groupfile != "") {
groupmap = new GroupMap(groupfile);
groupmap->readMap();
}
if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
if (groupfile != "") {
header = "OTUNumber\t";
for (int i = 0; i < groupmap->getNamesOfGroups().size(); i++) { header += (groupmap->getNamesOfGroups())[i] + '\t'; }
}else if (countfile != "") {
if (ct.hasGroupInfo()) {
header = "OTUNumber\t";
for (int i = 0; i < ct.getNamesOfGroups().size(); i++) { header += (ct.getNamesOfGroups())[i] + '\t'; }
}
}
header += "repSeqName\trepSeq\tOTUConTaxonomy";
out << header << endl;
vector<string> binLabels = list->getLabels();
for (int i = 0; i < list->getNumBins(); i++) {
int index = findIndex(otuLabels, binLabels[i]);
if (index == -1) { m->mothurOut("[ERROR]: " + binLabels[i] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
if (m->control_pressed) { break; }
out << otuLabels[index] << '\t';
vector<string> binNames;
string bin = list->get(i);
m->splitAtComma(bin, binNames);
string seqRepName = "";
int numSeqsRep = 0;
if (countfile == "") {
sort(binNames.begin(), binNames.end());
bin = "";
for (int j = 0; j < binNames.size()-1; j++) {
bin += binNames[j] + ',';
}
bin += binNames[binNames.size()-1];
map<string, string>::iterator it = repNames.find(bin);
if (it == repNames.end()) {
m->mothurOut("[ERROR: OTU " + otuLabels[index] + " is not in the repnames file. Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
}else { seqRepName = it->second; numSeqsRep = binNames.size(); }
//sanity check
if (binNames.size() != classifyOtuSizes[index]) {
m->mothurOut("[ERROR: OTU " + otuLabels[index] + " contains " + toString(binNames.size()) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
}
}else {
//find rep sequence in bin
for (int j = 0; j < binNames.size(); j++) {
map<string, int>::iterator itNameMap = nameMap.find(binNames[j]); //if you are in the counttable you must be the rep. because get.oturep with a countfile only includes the rep sequences in the rep.count file.
if (itNameMap != nameMap.end()) {
seqRepName = itNameMap->first;
numSeqsRep = itNameMap->second;
j += binNames.size();
}
}
if (seqRepName == "") {
m->mothurOut("[ERROR: OTU " + otuLabels[index] + " is not in the count file. Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
}
if (numSeqsRep != classifyOtuSizes[i]) {
m->mothurOut("[ERROR: OTU " + otuLabels[index] + " contains " + toString(numSeqsRep) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
}
}
//output abundances
if (groupfile != "") {
string groupAbunds = "";
map<string, int> counts;
//initialize counts to 0
for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { counts[(groupmap->getNamesOfGroups())[j]] = 0; }
//find abundances by group
bool error = false;
for (int j = 0; j < binNames.size(); j++) {
string group = groupmap->getGroup(binNames[j]);
if (group == "not found") {
m->mothurOut("[ERROR]: " + binNames[j] + " is not in your groupfile, please correct.\n");
error = true;
}else { counts[group]++; }
}
//output counts
for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << counts[(groupmap->getNamesOfGroups())[j]] << '\t'; }
if (error) { m->control_pressed = true; }
}else if (countfile != "") {
if (ct.hasGroupInfo()) {
vector<int> groupCounts = ct.getGroupCounts(seqRepName);
for (int j = 0; j < groupCounts.size(); j++) { out << groupCounts[j] << '\t'; }
}else { out << numSeqsRep << '\t'; }
}else { out << numSeqsRep << '\t'; }
//output repSeq
out << seqRepName << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
}
delete list;
if (groupfile != "") { delete groupmap; }
}else {
vector<SharedRAbundVector*> lookup = getShared();
header = "OTUNumber\t";
for (int i = 0; i < lookup.size(); i++) { header += lookup[i]->getGroup() + '\t'; }
header += "repSeqName\trepSeq\tOTUConTaxonomy";
out << header << endl;
for (int h = 0; h < lookup[0]->getNumBins(); h++) {
if (m->control_pressed) { break; }
int index = findIndex(otuLabels, m->currentSharedBinLabels[h]);
if (index == -1) { m->mothurOut("[ERROR]: " + m->currentSharedBinLabels[h] + " is not in your constaxonomy file, aborting.\n"); m->control_pressed = true; }
if (m->control_pressed) { break; }
out << otuLabels[index] << '\t';
int totalAbund = 0;
for (int i = 0; i < lookup.size(); i++) {
int abund = lookup[i]->getAbundance(h);
totalAbund += abund;
out << abund << '\t';
}
//sanity check
if (totalAbund != classifyOtuSizes[index]) {
m->mothurOut("[WARNING]: OTU " + m->currentSharedBinLabels[h] + " contains " + toString(totalAbund) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); //m->control_pressed = true; break;
}
//output repSeq
out << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
}
}
out.close();
if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int CreateDatabaseCommand::findIndex(vector<string>& otuLabels, string label){
try {
int index = -1;
for (int i = 0; i < otuLabels.size(); i++) {
if (m->isLabelEquivalent(otuLabels[i],label)) { index = i; break; }
}
return index;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "findIndex");
exit(1);
}
}
//**********************************************************************************************************************
vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<string>& otuLabels){
try {
vector<int> sizes;
ifstream in;
m->openInputFile(contaxonomyfile, in);
//read headers
m->getline(in);
while (!in.eof()) {
if (m->control_pressed) { break; }
string otu = ""; string tax = "unknown";
int size = 0;
in >> otu >> size >> tax; m->gobble(in);
sizes.push_back(size);
taxonomies.push_back(tax);
otuLabels.push_back(otu);
}
in.close();
return sizes;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "readTax");
exit(1);
}
}
//**********************************************************************************************************************
vector<int> CreateDatabaseCommand::readFasta(vector<Sequence>& seqs){
try {
vector<int> sizes;
ifstream in;
m->openInputFile(repfastafile, in);
set<int> sanity;
while (!in.eof()) {
if (m->control_pressed) { break; }
string binInfo;
Sequence seq(in, binInfo, true); m->gobble(in);
//the binInfo should look like - binNumber|size ie. 1|200 if it is binNumber|size|group then the user gave us the wrong repfasta file
vector<string> info;
m->splitAtChar(binInfo, info, '|');
//if (info.size() != 2) { m->mothurOut("[ERROR]: your repfasta file is not the right format. The create database command is designed to be used with the output from get.oturep. When running get.oturep you can not use a group file, because mothur is only expecting one representative sequence per OTU and when you use a group file with get.oturep a representative is found for each group.\n"); m->control_pressed = true; break;}
int size = 0;
m->mothurConvert(info[1], size);
int binNumber = 0;
string temp = "";
for (int i = 0; i < info[0].size(); i++) { if (isspace(info[0][i])) {;}else{temp +=info[0][i]; } }
m->mothurConvert(m->getSimpleLabel(temp), binNumber);
set<int>::iterator it = sanity.find(binNumber);
if (it != sanity.end()) {
m->mothurOut("[ERROR]: your repfasta file is not the right format. The create database command is designed to be used with the output from get.oturep. When running get.oturep you can not use a group file, because mothur is only expecting one representative sequence per OTU and when you use a group file with get.oturep a representative is found for each group.\n"); m->control_pressed = true; break;
}else { sanity.insert(binNumber); }
sizes.push_back(size);
seqs.push_back(seq);
}
in.close();
return sizes;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
ListVector* CreateDatabaseCommand::getList(){
try {
InputData* input = new InputData(listfile, "list");
ListVector* list = input->getListVector();
string lastLabel = list->getLabel();
if (label == "") { label = lastLabel; delete input; return list; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> labels; labels.insert(label);
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && (userLabels.size() != 0)) {
if (m->control_pressed) { delete input; return list; }
if(labels.count(list->getLabel()) == 1){
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
break;
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(lastLabel);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
break;
}
lastLabel = list->getLabel();
//get next line to process
//prevent memory leak
delete list;
list = input->getListVector();
}
if (m->control_pressed) { delete input; return list; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
delete list;
list = input->getListVector(lastLabel);
}
delete input;
return list;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "getList");
exit(1);
}
}
//**********************************************************************************************************************
vector<SharedRAbundVector*> CreateDatabaseCommand::getShared(){
try {
InputData input(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
if (label == "") { label = lastLabel; return lookup; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> labels; labels.insert(label);
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && (userLabels.size() != 0)) {
if (m->control_pressed) { return lookup; }
if(labels.count(lookup[0]->getLabel()) == 1){
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
break;
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundVectors(lastLabel);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
break;
}
lastLabel = lookup[0]->getLabel();
//get next line to process
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundVectors();
}
if (m->control_pressed) { return lookup; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundVectors(lastLabel);
}
return lookup;
}
catch(exception& e) {
m->errorOut(e, "CreateDatabaseCommand", "getShared");
exit(1);
}
}
//**********************************************************************************************************************
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