PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
groupmap = g;
ct = NULL;
//check for necessary files
if (refTfile == "saved") { ReferenceDB* rdb = ReferenceDB::getInstance(); refTfile = rdb->getSavedTaxonomy(); }
string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
ifstream FileTest(taxFileNameTest.c_str());
if (!FileTest) {
m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
}else{
readTreeStruct(FileTest);
}
tree[0].rank = "0";
assignRank(0);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "PhyloSummary");
exit(1);
}
}
//***************************************************************************************************************
vector<Sequence*> MothurChimera::readSeqs(string file) {
try {
vector<Sequence*> container;
int count = 0;
length = 0;
unaligned = false;
ReferenceDB* rdb = ReferenceDB::getInstance();
if (file == "saved") {
m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine();
for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
Sequence* temp = new Sequence(rdb->referenceSeqs[i].getName(), rdb->referenceSeqs[i].getAligned());
if (count == 0) { length = temp->getAligned().length(); count++; } //gets first seqs length
else if (length != temp->getAligned().length()) { unaligned = true; }
if (temp->getName() != "") { container.push_back(temp); }
}
templateFileName = rdb->getSavedReference();
}else {
m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
ifstream in;
m->openInputFile(file, in);
//read in seqs and store in vector
while(!in.eof()){
if (m->control_pressed) { return container; }
Sequence* current = new Sequence(in); m->gobble(in);
if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
else if (length != current->getAligned().length()) { unaligned = true; }
if (current->getName() != "") {
container.push_back(current);
if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
}
}
in.close();
m->mothurOut("Done."); m->mothurOutEndLine();
filterString = (string(container[0]->getAligned().length(), '1'));
}
return container;
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "readSeqs");
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);
}
}
Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i, int tid, bool f, bool sh) :
Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
try {
ReferenceDB* rdb = ReferenceDB::getInstance();
threadID = tid;
flip = f;
shortcuts = sh;
string baseName = tempFile;
if (baseName == "saved") { baseName = rdb->getSavedReference(); }
string baseTName = tfile;
if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
/************calculate the probablity that each word will be in a specific taxonomy*************/
string tfileroot = m->getFullPathName(baseTName.substr(0,baseTName.find_last_of(".")+1));
string tempfileroot = m->getRootName(m->getSimpleName(baseName));
string phyloTreeName = tfileroot + "tree.train";
string phyloTreeSumName = tfileroot + "tree.sum";
string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
string probFileName2 = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.numNonZero";
ofstream out;
ofstream out2;
ifstream phyloTreeTest(phyloTreeName.c_str());
ifstream probFileTest2(probFileName2.c_str());
ifstream probFileTest(probFileName.c_str());
ifstream probFileTest3(phyloTreeSumName.c_str());
int start = time(NULL);
//if they are there make sure they were created after this release date
bool FilesGood = false;
if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
}
//if you want to save, but you dont need to calculate then just read
if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood && (tempFile != "saved")) {
ifstream saveIn;
m->openInputFile(tempFile, saveIn);
while (!saveIn.eof()) {
Sequence temp(saveIn);
m->gobble(saveIn);
rdb->referenceSeqs.push_back(temp);
}
saveIn.close();
}
if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){
if (tempFile == "saved") { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
m->mothurOut("Reading template taxonomy... "); cout.flush();
phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
m->mothurOut("DONE."); m->mothurOutEndLine();
genusNodes = phyloTree->getGenusNodes();
genusTotals = phyloTree->getGenusTotals();
if (tfile == "saved") {
m->mothurOutEndLine(); m->mothurOut("Using probabilties from " + rdb->getSavedTaxonomy() + " that are saved in memory... "); cout.flush();;
wordGenusProb = rdb->wordGenusProb;
WordPairDiffArr = rdb->WordPairDiffArr;
}else {
m->mothurOut("Reading template probabilities... "); cout.flush();
readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
}
//save probabilities
if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
}else{
//create search database and names vector
generateDatabaseAndNames(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0);
//prevents errors caused by creating shortcut files if you had an error in the sanity check.
if (m->control_pressed) { m->mothurRemove(phyloTreeName); m->mothurRemove(probFileName); m->mothurRemove(probFileName2); }
else{
genusNodes = phyloTree->getGenusNodes();
genusTotals = phyloTree->getGenusTotals();
m->mothurOut("Calculating template taxonomy tree... "); cout.flush();
phyloTree->printTreeNodes(phyloTreeName);
m->mothurOut("DONE."); m->mothurOutEndLine();
m->mothurOut("Calculating template probabilities... "); cout.flush();
numKmers = database->getMaxKmer() + 1;
//initialze probabilities
wordGenusProb.resize(numKmers);
WordPairDiffArr.resize(numKmers);
for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
ofstream out;
ofstream out2;
#ifdef USE_MPI
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) {
#endif
if (shortcuts) {
m->openOutputFile(probFileName, out);
//output mothur version
out << "#" << m->getVersion() << endl;
out << numKmers << endl;
m->openOutputFile(probFileName2, out2);
//output mothur version
out2 << "#" << m->getVersion() << endl;
}
#ifdef USE_MPI
}
#endif
//for each word
for (int i = 0; i < numKmers; i++) {
//m->mothurOut("[DEBUG]: kmer = " + toString(i) + "\n");
if (m->control_pressed) { break; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) {
#endif
if (shortcuts) { out << i << '\t'; }
#ifdef USE_MPI
}
#endif
vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
//for each sequence with that word
vector<int> count; count.resize(genusNodes.size(), 0);
for (int j = 0; j < seqsWithWordi.size(); j++) {
int temp = phyloTree->getGenusIndex(names[seqsWithWordi[j]]);
count[temp]++; //increment count of seq in this genus who have this word
}
//probabilityInTemplate = (# of seqs with that word in template + 0.50) / (total number of seqs in template + 1);
float probabilityInTemplate = (seqsWithWordi.size() + 0.50) / (float) (names.size() + 1);
diffPair tempProb(log(probabilityInTemplate), 0.0);
WordPairDiffArr[i] = tempProb;
int numNotZero = 0;
for (int k = 0; k < genusNodes.size(); k++) {
//probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
wordGenusProb[i][k] = log((count[k] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
if (count[k] != 0) {
#ifdef USE_MPI
int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) {
#endif
if (shortcuts) { out << k << '\t' << wordGenusProb[i][k] << '\t' ; }
#ifdef USE_MPI
}
#endif
numNotZero++;
}
}
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) {
#endif
if (shortcuts) {
out << endl;
out2 << probabilityInTemplate << '\t' << numNotZero << '\t' << log(probabilityInTemplate) << endl;
}
#ifdef USE_MPI
}
#endif
}
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) {
#endif
if (shortcuts) {
out.close();
out2.close();
}
#ifdef USE_MPI
}
#endif
//read in new phylotree with less info. - its faster
ifstream phyloTreeTest(phyloTreeName.c_str());
delete phyloTree;
phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
//save probabilities
if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
}
}
if (m->debug) { m->mothurOut("[DEBUG]: about to generateWordPairDiffArr\n"); }
generateWordPairDiffArr();
if (m->debug) { m->mothurOut("[DEBUG]: done generateWordPairDiffArr\n"); }
//save probabilities
if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
m->mothurOut("DONE."); m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); m->mothurOutEndLine();
}
catch(exception& e) {
m->errorOut(e, "Bayesian", "Bayesian");
exit(1);
}
}
//**********************************************************************************************************************
AlignCommand::AlignCommand(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("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 = "-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, "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);
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
templateFileName = validParameter.validFile(parameters, "reference", true);
if (templateFileName == "not found") {
//check for saved reference sequences
if (rdb->referenceSeqs.size() != 0) {
templateFileName = "saved";
}else {
m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
m->mothurOutEndLine();
abort = true;
}
}else if (templateFileName == "not open") { abort = true; }
else { if (save) { rdb->setSavedReference(templateFileName); } }
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);
}
}