//***************************************************************************************************************
ChimeraPerseusCommand::ChimeraPerseusCommand(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("chimera.uchime");
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; }
}
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = 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 = ""; }
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", false);
if (fastafile == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
}
//check for required parameters
bool hasName = true;
namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") {
//if there is a current fasta file, use it
string filename = m->getNameFile();
if (filename != "") { nameFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the name parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
hasName = false;
}else {
m->splitAtDash(namefile, nameFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < nameFileNames.size(); i++) {
bool ignore = false;
if (nameFileNames[i] == "current") {
nameFileNames[i] = m->getNameFile();
if (nameFileNames[i] != "") { m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
nameFileNames.erase(nameFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(nameFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
nameFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
nameFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
nameFileNames.erase(nameFileNames.begin()+i);
i--;
}else {
m->setNameFile(nameFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
}
if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
bool hasGroup = true;
groupfile = validParameter.validFile(parameters, "group", false);
if (groupfile == "not found") { groupfile = ""; hasGroup = false; }
else {
m->splitAtDash(groupfile, groupFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < groupFileNames.size(); i++) {
bool ignore = false;
if (groupFileNames[i] == "current") {
groupFileNames[i] = m->getGroupFile();
if (groupFileNames[i] != "") { m->mothurOut("Using " + groupFileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
groupFileNames.erase(groupFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(groupFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { groupFileNames[i] = inputDir + groupFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(groupFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(groupFileNames[i]);
m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
groupFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
groupFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
groupFileNames.erase(groupFileNames.begin()+i);
i--;
}else {
m->setGroupFile(groupFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (groupFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid group files."); m->mothurOutEndLine(); abort = true; }
}
if (hasGroup && (groupFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of groupfiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
//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 = ""; }
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.50"; }
m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found"){ temp = "-5.54"; }
m->mothurConvert(temp, alpha);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.33"; }
m->mothurConvert(temp, beta);
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraPerseusCommand", "ChimeraPerseusCommand");
exit(1);
}
}
SeqSummaryCommand::SeqSummaryCommand(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("summary.seqs");
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; }
}
//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("fasta");
//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["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//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["name"] = 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; }
}
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") {
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
//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 = "";
outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
if (countfile == "") {
if (namefile == "") {
vector<string> files; files.push_back(fastafile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
exit(1);
}
}
//***************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(string option) {
try {
abort = false; calledHelp = false;
ReferenceDB* rdb = ReferenceDB::getInstance();
//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("chimera.check");
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; }
}
vector<string> tempOutNames;
outputTypes["chimera"] = 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 {
it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
string path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["reference"] = inputDir + it->second; }
}
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", false);
if (fastafile == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
//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 = ""; }
namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }
else {
m->splitAtDash(namefile, nameFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < nameFileNames.size(); i++) {
bool ignore = false;
if (nameFileNames[i] == "current") {
nameFileNames[i] = m->getNameFile();
if (nameFileNames[i] != "") { m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
nameFileNames.erase(nameFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(nameFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
nameFileNames[i] = tryPath;
}
}
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
nameFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
nameFileNames.erase(nameFileNames.begin()+i);
i--;
}else {
m->setNameFile(nameFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (nameFileNames.size() != 0) {
if (nameFileNames.size() != fastaFileNames.size()) {
m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
abort = true;
}
}
}
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
rdb->save = save;
if (save) { //clear out old references
rdb->clearMemory();
}
//this has to go after save so that if the user sets save=t and provides no reference we abort
templatefile = validParameter.validFile(parameters, "reference", true);
if (templatefile == "not found") {
//check for saved reference sequences
if (rdb->referenceSeqs.size() != 0) {
templatefile = "saved";
}else {
m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
m->mothurOutEndLine();
abort = true;
}
}else if (templatefile == "not open") { abort = true; }
else { if (save) { rdb->setSavedReference(templatefile); } }
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
m->mothurConvert(temp, ksize);
temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; }
svg = m->isTrue(temp);
if (nameFileNames.size() != 0) { svg = true; }
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; }
m->mothurConvert(temp, increment);
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
exit(1);
}
}
//**********************************************************************************************************************
AlignCommand::AlignCommand(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("align.seqs");
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["fasta"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//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 = ""; }
//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("reference");
//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["reference"] = inputDir + it->second; }
}
}
candidateFileName = validParameter.validFile(parameters, "fasta", false);
if (candidateFileName == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
m->splitAtDash(candidateFileName, candidateFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < candidateFileNames.size(); i++) {
//candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
bool ignore = false;
if (candidateFileNames[i] == "current") {
candidateFileNames[i] = m->getFastaFile();
if (candidateFileNames[i] != "") { m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
candidateFileNames.erase(candidateFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(candidateFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
in.close();
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
candidateFileNames[i] = tryPath;
}
}
//if you can't open it, try output location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
candidateFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
candidateFileNames.erase(candidateFileNames.begin()+i);
i--;
}else {
m->setFastaFile(candidateFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
m->mothurConvert(temp, kmerSize);
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, misMatch);
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-5.0"; }
m->mothurConvert(temp, gapOpen);
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-2.0"; }
m->mothurConvert(temp, gapExtend);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
flip = m->isTrue(temp);
//this has to go after save so that if the user sets save=t and provides no reference we abort
templateFileName = validParameter.validFile(parameters, "reference", true);
if (templateFileName == "not found") { m->mothurOut("[ERROR]: The reference parameter is a required for the align.seqs command, aborting.\n"); abort = true;
}else if (templateFileName == "not open") { abort = true; }
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
m->mothurConvert(temp, threshold);
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
}
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "AlignCommand");
exit(1);
}
}
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) {
try {
abort = false; calledHelp = false;
Estimators.clear();
//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("dist.seqs");
map<string, string>::iterator it2;
//check to make sure all parameters are valid for command
for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = 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;
it2 = parameters.find("fasta");
//user has given a template file
if(it2 != parameters.end()){
path = m->hasPath(it2->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it2->second; }
}
it2 = parameters.find("oldfasta");
//user has given a template file
if(it2 != parameters.end()){
path = m->hasPath(it2->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["oldfasta"] = inputDir + it2->second; }
}
it2 = parameters.find("column");
//user has given a template file
if(it2 != parameters.end()){
path = m->hasPath(it2->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["column"] = inputDir + it2->second; }
}
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not found") {
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
ifstream inFASTA;
m->openInputFile(fastafile, inFASTA);
alignDB = SequenceDB(inFASTA);
inFASTA.close();
}else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else if (fastafile == "not open") { abort = true; }
else{
ifstream inFASTA;
m->openInputFile(fastafile, inFASTA);
alignDB = SequenceDB(inFASTA);
inFASTA.close();
m->setFastaFile(fastafile);
}
oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
if (oldfastafile == "not found") { oldfastafile = ""; }
else if (oldfastafile == "not open") { abort = true; }
column = validParameter.validFile(parameters, "column", true);
if (column == "not found") { column = ""; }
else if (column == "not open") { abort = true; }
else { m->setColumnFile(column); }
//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 = "";
outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "onegap"; }
else {
if (calc == "default") { calc = "onegap"; }
}
m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
convert(temp, countends);
temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
convert(temp, compress);
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
if (output == "phylip") { output = "lt"; }
if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so."); m->mothurOutEndLine(); abort=true; }
if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
}
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
}
FilterSeqsCommand::FilterSeqsCommand(string option) {
try {
abort = false; calledHelp = false; recalced = false;
filterFileName = "";
//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("filter.seqs");
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["fasta"] = tempOutNames;
outputTypes["filter"] = 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("fasta");
//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["fasta"] = inputDir + it->second; }
}
it = parameters.find("hard");
//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["hard"] = inputDir + it->second; }
}
}
//check for required parameters
fasta = validParameter.validFile(parameters, "fasta", false);
if (fasta == "not found") {
fasta = m->getFastaFile();
if (fasta != "") {
fastafileNames.push_back(fasta);
m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
string simpleName = m->getSimpleName(fasta);
filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
}
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
m->splitAtDash(fasta, fastafileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastafileNames.size(); i++) {
bool ignore = false;
if (fastafileNames[i] == "current") {
fastafileNames[i] = m->getFastaFile();
if (fastafileNames[i] != "") { m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastafileNames.erase(fastafileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastafileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; }
}
ifstream in;
int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastafileNames[i] = tryPath;
}
}
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastafileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastafileNames.erase(fastafileNames.begin()+i);
i--;
}else{
string simpleName = m->getSimpleName(fastafileNames[i]);
filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
m->setFastaFile(fastafileNames[i]);
}
in.close();
}
}
//make sure there is at least one valid file left
if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
if (!abort) {
//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 = "";
outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
}
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
else if (hard == "not open") { hard = ""; abort = true; }
temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
trump = temp[0];
temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
else { soft = (float)atoi(temp.c_str()) / 100.0; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
vertical = validParameter.validFile(parameters, "vertical", false);
if (vertical == "not found") {
if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
else { vertical = "F"; }
}
numSeqs = 0;
}
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
exit(1);
}
}
//***************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(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("chimera.bellerophon");
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["chimera"] = tempOutNames;
outputTypes["accnos"] = 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 = ""; }
fastafile = validParameter.validFile(parameters, "fasta", false);
if (fastafile == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
//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 = ""; }
string temp;
temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
filter = m->isTrue(temp);
temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
correction = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
m->mothurConvert(temp, increment);
}
}
catch(exception& e) {
m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
exit(1);
}
}
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(string option) {
try {
abort = false; calledHelp = false;
hasName = false; hasCount=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("classify.seqs");
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)) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
outputTypes["matchdist"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.valid(parameters, "outputdir"); if (outputDir == "not found"){ outputDir = ""; }
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.valid(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["reference"] = inputDir + it->second; }
}
it = parameters.find("taxonomy");
//user has given a template file
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
it = parameters.find("count");
//user has given a template file
if(it != parameters.end()){
path = util.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("fasta");
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
it = parameters.find("group");
if(it != parameters.end()){
path = util.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; }
}
}
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fasta file and the fasta parameter is required.\n"); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
else { current->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
if (namefile != "") { hasName = true; }
//check for required parameters
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if (countfile != "") { hasCount = true; }
//make sure there is at least one valid file left
if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name.\n"); abort = true; }
bool hasGroup = false;
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); hasGroup = true; }
if (hasGroup && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group.\n"); abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.valid(parameters, "outputdir"); if (outputDir == "not found"){ outputDir = ""; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
//this has to go after save so that if the user sets save=t and provides no reference we abort
templateFileName = validParameter.validFile(parameters, "reference");
if (templateFileName == "not found") {
m->mothurOut("[ERROR]: The reference parameter is a required for the classify.seqs command.\n"); abort = true;
}else if (templateFileName == "not open") { abort = true; }
//this has to go after save so that if the user sets save=t and provides no reference we abort
taxonomyFileName = validParameter.validFile(parameters, "taxonomy");
if (taxonomyFileName == "not found") { m->mothurOut("[ERROR]: The taxonomy parameter is a required for the classify.seqs command.\n"); abort = true;
}else if (taxonomyFileName == "not open") { abort = true; }
search = validParameter.valid(parameters, "search"); if (search == "not found"){ search = "kmer"; }
method = validParameter.valid(parameters, "method"); if (method == "not found"){ method = "wang"; }
temp = validParameter.valid(parameters, "ksize"); if (temp == "not found"){
temp = "8";
if (method == "zap") { temp = "7"; }
}
util.mothurConvert(temp, kmerSize);
temp = validParameter.valid(parameters, "match"); if (temp == "not found"){ temp = "1.0"; }
util.mothurConvert(temp, match);
temp = validParameter.valid(parameters, "printlevel"); if (temp == "not found"){ temp = "-1"; }
util.mothurConvert(temp, printlevel);
temp = validParameter.valid(parameters, "mismatch"); if (temp == "not found"){ temp = "-1.0"; }
util.mothurConvert(temp, misMatch);
temp = validParameter.valid(parameters, "gapopen"); if (temp == "not found"){ temp = "-2.0"; }
util.mothurConvert(temp, gapOpen);
temp = validParameter.valid(parameters, "gapextend"); if (temp == "not found"){ temp = "-1.0"; }
util.mothurConvert(temp, gapExtend);
temp = validParameter.valid(parameters, "numwanted"); if (temp == "not found"){ temp = "10"; }
util.mothurConvert(temp, numWanted);
temp = validParameter.valid(parameters, "cutoff"); if (temp == "not found"){ temp = "80"; }
util.mothurConvert(temp, cutoff);
temp = validParameter.valid(parameters, "probs"); if (temp == "not found"){ temp = "true"; }
probs = util.isTrue(temp);
temp = validParameter.valid(parameters, "relabund"); if (temp == "not found"){ temp = "false"; }
relabund = util.isTrue(temp);
temp = validParameter.valid(parameters, "shortcuts"); if (temp == "not found"){ temp = "true"; }
writeShortcuts = util.isTrue(temp);
flip = true;
temp = validParameter.valid(parameters, "iters"); if (temp == "not found") { temp = "100"; }
util.mothurConvert(temp, iters);
output = validParameter.valid(parameters, "output"); if(output == "not found"){ output = "detail"; }
if ((output != "simple") && (output != "detail")) { m->mothurOut(output + " is not a valid output form. Options are simple and detail. I will use detail."); m->mothurOutEndLine(); output = "detail"; }
if ((method == "wang") && (search != "kmer")) {
m->mothurOut("The wang method requires the kmer search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
if ((method == "zap") && ((search != "kmer") && (search != "align"))) {
m->mothurOut("The zap method requires the kmer or align search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
if (!abort) {
if (!hasCount) {
if (namefile == ""){
if (fastafile != "") {
vector<string> files; files.push_back(fastafile);
if (!current->getMothurCalling()) { parser.getNameFile(files); }
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
AlignCommand::AlignCommand(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("align.seqs");
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)) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.valid(parameters, "outputdir"); if (outputDir == "not found"){ outputDir = ""; }
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.valid(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
//user has given a template file
it = parameters.find("reference");
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["reference"] = inputDir + it->second; }
}
it = parameters.find("fasta");
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
}
templateFileName = validParameter.validFile(parameters, "reference");
if (templateFileName == "not found") { m->mothurOut("[ERROR]: The reference parameter is a required for the align.seqs command, aborting.\n"); abort = true;
}else if (templateFileName == "not open") { abort = true; }
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fasta file and the fasta parameter is required.\n"); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
else { current->setFastaFile(fastafile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.valid(parameters, "ksize"); if (temp == "not found"){ temp = "8"; }
util.mothurConvert(temp, kmerSize);
temp = validParameter.valid(parameters, "match"); if (temp == "not found"){ temp = "1.0"; }
util.mothurConvert(temp, match);
temp = validParameter.valid(parameters, "mismatch"); if (temp == "not found"){ temp = "-1.0"; }
util.mothurConvert(temp, misMatch);
temp = validParameter.valid(parameters, "gapopen"); if (temp == "not found"){ temp = "-5.0"; }
util.mothurConvert(temp, gapOpen);
temp = validParameter.valid(parameters, "gapextend"); if (temp == "not found"){ temp = "-2.0"; }
util.mothurConvert(temp, gapExtend);
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "flip"); if (temp == "not found"){ temp = "t"; }
flip = util.isTrue(temp);
temp = validParameter.valid(parameters, "threshold"); if (temp == "not found"){ temp = "0.50"; }
util.mothurConvert(temp, threshold);
search = validParameter.valid(parameters, "search"); if (search == "not found"){ search = "kmer"; }
if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
align = validParameter.valid(parameters, "align"); if (align == "not found"){ align = "needleman"; }
if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
}
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "AlignCommand");
exit(1);
}
}
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(string option) {
try {
abort = false; calledHelp = false;
hasName = false; hasCount=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("classify.seqs");
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["taxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
outputTypes["matchdist"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//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 = ""; }
//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("reference");
//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["reference"] = inputDir + it->second; }
}
it = parameters.find("taxonomy");
//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["taxonomy"] = inputDir + it->second; }
}
}
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") {
//if there is a current fasta file, use it
string filename = m->getFastaFile();
if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
m->splitAtDash(fastaFileName, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
bool ignore = false;
if (fastaFileNames[i] == "current") {
fastaFileNames[i] = m->getFastaFile();
if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
fastaFileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
}else {
m->setFastaFile(fastaFileNames[i]);
}
}
}
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }
else {
m->splitAtDash(namefile, namefileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < namefileNames.size(); i++) {
bool ignore = false;
if (namefileNames[i] == "current") {
namefileNames[i] = m->getNameFile();
if (namefileNames[i] != "") { m->mothurOut("Using " + namefileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
namefileNames.erase(namefileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(namefileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { namefileNames[i] = inputDir + namefileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(namefileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
namefileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
namefileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
//erase from file list
namefileNames.erase(namefileNames.begin()+i);
i--;
}else {
m->setNameFile(namefileNames[i]);
}
}
}
}
if (namefileNames.size() != 0) { hasName = true; }
if (namefile != "") {
if (namefileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a name file, you must have one for each fasta file."); m->mothurOutEndLine(); }
}
//check for required parameters
countfile = validParameter.validFile(parameters, "count", false);
if (countfile == "not found") {
countfile = "";
}else {
m->splitAtDash(countfile, countfileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < countfileNames.size(); i++) {
bool ignore = false;
if (countfileNames[i] == "current") {
countfileNames[i] = m->getCountTableFile();
if (countfileNames[i] != "") { m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
countfileNames.erase(countfileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(countfileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { countfileNames[i] = inputDir + countfileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
countfileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
countfileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
countfileNames.erase(countfileNames.begin()+i);
i--;
}else {
m->setCountTableFile(countfileNames[i]);
}
}
}
}
if (countfileNames.size() != 0) { hasCount = true; if (countfileNames.size() != fastaFileNames.size()) {m->mothurOut("If you provide a count file, you must have one for each fasta file."); m->mothurOutEndLine(); } }
//make sure there is at least one valid file left
if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
groupfile = validParameter.validFile(parameters, "group", false);
if (groupfile == "not found") { groupfile = ""; }
else {
m->splitAtDash(groupfile, groupfileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < groupfileNames.size(); i++) {
bool ignore = false;
if (groupfileNames[i] == "current") {
groupfileNames[i] = m->getGroupFile();
if (groupfileNames[i] != "") { m->mothurOut("Using " + groupfileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current group file, ignoring current."); m->mothurOutEndLine(); ignore=true;
//erase from file list
groupfileNames.erase(groupfileNames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = m->hasPath(groupfileNames[i]);
//cout << path << '\t' << inputDir << endl;
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
}
int ableToOpen;
ifstream in;
ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
groupfileNames[i] = tryPath;
}
}
if (ableToOpen == 1) {
if (m->getOutputDir() != "") { //default path is set
string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
ifstream in2;
ableToOpen = m->openInputFile(tryPath, in2, "noerror");
in2.close();
groupfileNames[i] = tryPath;
}
}
in.close();
if (ableToOpen == 1) {
m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
groupfileNames.erase(groupfileNames.begin()+i);
i--;
}else {
m->setGroupFile(groupfileNames[i]);
}
}
}
}
if (groupfile != "") {
if (groupfileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each fasta file."); m->mothurOutEndLine(); }
if (hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
}else {
for (int i = 0; i < fastaFileNames.size(); i++) { groupfileNames.push_back(""); }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
//this has to go after save so that if the user sets save=t and provides no reference we abort
templateFileName = validParameter.validFile(parameters, "reference", true);
if (templateFileName == "not found") {
m->mothurOut("[ERROR]: The reference parameter is a required for the classify.seqs command.\n"); abort = true;
}else if (templateFileName == "not open") { abort = true; }
//this has to go after save so that if the user sets save=t and provides no reference we abort
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
if (taxonomyFileName == "not found") { m->mothurOut("[ERROR]: The taxonomy parameter is a required for the classify.seqs command.\n"); abort = true;
}else if (taxonomyFileName == "not open") { abort = true; }
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "wang"; }
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){
temp = "8";
if (method == "zap") { temp = "7"; }
}
m->mothurConvert(temp, kmerSize);
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "printlevel", false); if (temp == "not found"){ temp = "-1"; }
m->mothurConvert(temp, printlevel);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, misMatch);
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
m->mothurConvert(temp, gapOpen);
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
m->mothurConvert(temp, gapExtend);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found"){ temp = "10"; }
m->mothurConvert(temp, numWanted);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "80"; }
m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
probs = m->isTrue(temp);
temp = validParameter.validFile(parameters, "relabund", false); if (temp == "not found"){ temp = "false"; }
relabund = m->isTrue(temp);
temp = validParameter.validFile(parameters, "shortcuts", false); if (temp == "not found"){ temp = "true"; }
writeShortcuts = m->isTrue(temp);
//temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "T"; }
//flip = m->isTrue(temp);
flip = true;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
m->mothurConvert(temp, iters);
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "detail"; }
if ((output != "simple") && (output != "detail")) { m->mothurOut(output + " is not a valid output form. Options are simple and detail. I will use detail."); m->mothurOutEndLine(); output = "detail"; }
if ((method == "wang") && (search != "kmer")) {
m->mothurOut("The wang method requires the kmer search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
if ((method == "zap") && ((search != "kmer") && (search != "align"))) {
m->mothurOut("The zap method requires the kmer or align search. " + search + " will be disregarded, and kmer will be used." ); m->mothurOutEndLine();
search = "kmer";
}
if (!abort) {
if (!hasCount) {
if (namefileNames.size() == 0){
if (fastaFileNames.size() != 0) {
vector<string> files; files.push_back(fastaFileNames[fastaFileNames.size()-1]);
parser.getNameFile(files);
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
exit(1);
}
}
