//**********************************************************************************************************************
int SharedCommand::createSharedFromListGroup() {
try {
GroupMap* groupMap = NULL;
CountTable* countTable = NULL;
pickedGroups = false;
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
int groupError = groupMap->readMap();
if (groupError == 1) { delete groupMap; return 0; }
vector<string> allGroups = groupMap->getNamesOfGroups();
if (Groups.size() == 0) { Groups = allGroups; }
else { pickedGroups = true; }
}else{
countTable = new CountTable();
countTable->readTable(countfile, true, false);
vector<string> allGroups = countTable->getNamesOfGroups();
if (Groups.size() == 0) { Groups = allGroups; }
else { pickedGroups = true; }
}
int numGroups = Groups.size();
if (m->getControl_pressed()) { return 0; }
ofstream out;
string filename = "";
if (!pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
util.openOutputFile(filename, out);
}
//set fileroot
fileroot = outputDir + util.getRootName(util.getSimpleName(listfile));
map<string, string> variables;
variables["[filename]"] = fileroot;
string errorOff = "no error";
InputData input(listfile, "shared", Groups);
SharedListVector* SharedList = input.getSharedListVector();
string lastLabel = SharedList->getLabel();
SharedRAbundVectors* lookup;
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
out.close(); if (!pickedGroups) { util.mothurRemove(filename); }
return 0;
}
//sanity check
vector<string> namesSeqs;
int numGroupNames = 0;
if (current->getGroupMode() == "group") { namesSeqs = groupMap->getNamesSeqs(); numGroupNames = groupMap->getNumSeqs(); }
else { namesSeqs = countTable->getNamesOfSeqs(); numGroupNames = countTable->getNumUniqueSeqs(); }
int error = ListGroupSameSeqs(namesSeqs, SharedList);
if ((!pickedGroups) && (SharedList->getNumSeqs() != numGroupNames)) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(numGroupNames) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct.\n"); m->setControl_pressed(true);
out.close(); if (!pickedGroups) { util.mothurRemove(filename); } //remove blank shared file you made
//delete memory
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
return 0;
}
if (error == 1) { m->setControl_pressed(true); }
//if user has specified groups make new groupfile for them
if ((pickedGroups) && (current->getGroupMode() == "group")) { //make new group file
string groups = "";
if (numGroups < 4) {
for (int i = 0; i < numGroups-1; i++) {
groups += Groups[i] + ".";
}
groups+=Groups[numGroups-1];
}else { groups = "merge"; }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(listfile));
variables["[group]"] = groups;
string newGroupFile = getOutputFileName("group",variables);
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
util.openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
if (isValidGroup(groupName, Groups)) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
outGroups.close();
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
bool printHeaders = true;
while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
delete lookup;
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
}
if ((util.anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) ) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
SharedList = input.getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
delete lookup;
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
//restore real lastlabel to save below
SharedList->setLabel(saveLabel);
}
lastLabel = SharedList->getLabel();
delete SharedList;
SharedList = input.getSharedListVector(); //get new list vector to process
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
}
}
//run last label if you need to
if (needToRun ) {
if (SharedList != NULL) { delete SharedList; }
SharedList = input.getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
delete SharedList;
}
if (!pickedGroups) { out.close(); }
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (m->getControl_pressed()) {
if (!pickedGroups) { util.mothurRemove(filename); }
return 0;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "createSharedFromListGroup");
exit(1);
}
}
int SeqSummaryCommand::execute(){
try{
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
//set current fasta to fastafile
m->setFastaFile(fastafile);
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
string summaryFile = getOutputFileName("summary",variables);
long long numSeqs = 0;
long long size = 0;
long long numUniques = 0;
map<int, long long> startPosition;
map<int, long long> endPosition;
map<int, long long> seqLength;
map<int, long long> ambigBases;
map<int, long long> longHomoPolymer;
if (namefile != "") { nameMap = m->readNames(namefile); numUniques = nameMap.size(); }
else if (countfile != "") {
CountTable ct;
ct.readTable(countfile, false, false);
nameMap = ct.getNameMap();
size = ct.getNumSeqs();
numUniques = ct.getNumUniqueSeqs();
}
if (m->control_pressed) { return 0; }
vector<unsigned long long> positions;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
#else
positions = m->setFilePosFasta(fastafile, numSeqs);
if (numSeqs < processors) { processors = numSeqs; }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
}
#endif
if(processors == 1){
numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
}else{
numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
}
if (m->control_pressed) { return 0; }
//set size
if (countfile != "") {}//already set
else if (namefile == "") { size = numSeqs; }
else { for (map<int, long long>::iterator it = startPosition.begin(); it != startPosition.end(); it++) { size += it->second; } }
if ((namefile != "") || (countfile != "")) {
string type = "count";
if (namefile != "") { type = "name"; }
if (numSeqs != numUniques) { // do fasta and name/count files match
m->mothurOut("[ERROR]: Your " + type + " file contains " + toString(numUniques) + " unique sequences, but your fasta file contains " + toString(numSeqs) + ". File mismatch detected, quitting command.\n"); m->control_pressed = true;
}
}
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
long long ptile0_25 = 1+(long long)(size * 0.025); //number of sequences at 2.5%
long long ptile25 = 1+(long long)(size * 0.250); //number of sequences at 25%
long long ptile50 = 1+(long long)(size * 0.500);
long long ptile75 = 1+(long long)(size * 0.750);
long long ptile97_5 = 1+(long long)(size * 0.975);
long long ptile100 = (long long)(size);
vector<int> starts; starts.resize(7,0); vector<int> ends; ends.resize(7,0); vector<int> ambigs; ambigs.resize(7,0); vector<int> lengths; lengths.resize(7,0); vector<int> homops; homops.resize(7,0);
//find means
long long meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
//minimum
if ((startPosition.begin())->first == -1) { starts[0] = 0; }
else {starts[0] = (startPosition.begin())->first; }
long long totalSoFar = 0;
//set all values to min
starts[1] = starts[0]; starts[2] = starts[0]; starts[3] = starts[0]; starts[4] = starts[0]; starts[5] = starts[0];
int lastValue = 0;
for (map<int, long long>::iterator it = startPosition.begin(); it != startPosition.end(); it++) {
int value = it->first; if (value == -1) { value = 0; }
meanStartPosition += (value*it->second);
totalSoFar += it->second;
if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ starts[1] = value; } //save value
if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { starts[2] = value; } //save value
if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { starts[3] = value; } //save value
if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { starts[4] = value; } //save value
if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { starts[5] = value; } //save value
if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { starts[6] = value; } //save value
lastValue = totalSoFar;
}
starts[6] = (startPosition.rbegin())->first;
if ((endPosition.begin())->first == -1) { ends[0] = 0; }
else {ends[0] = (endPosition.begin())->first; }
totalSoFar = 0;
//set all values to min
ends[1] = ends[0]; ends[2] = ends[0]; ends[3] = ends[0]; ends[4] = ends[0]; ends[5] = ends[0];
lastValue = 0;
for (map<int, long long>::iterator it = endPosition.begin(); it != endPosition.end(); it++) {
int value = it->first; if (value == -1) { value = 0; }
meanEndPosition += (value*it->second);
totalSoFar += it->second;
if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ ends[1] = value; } //save value
if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { ends[2] = value; } //save value
if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { ends[3] = value; } //save value
if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { ends[4] = value; } //save value
if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { ends[5] = value; } //save value
if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { ends[6] = value; } //save value
lastValue = totalSoFar;
}
ends[6] = (endPosition.rbegin())->first;
if ((seqLength.begin())->first == -1) { lengths[0] = 0; }
else {lengths[0] = (seqLength.begin())->first; }
//set all values to min
lengths[1] = lengths[0]; lengths[2] = lengths[0]; lengths[3] = lengths[0]; lengths[4] = lengths[0]; lengths[5] = lengths[0];
totalSoFar = 0;
lastValue = 0;
for (map<int, long long>::iterator it = seqLength.begin(); it != seqLength.end(); it++) {
int value = it->first;
meanSeqLength += (value*it->second);
totalSoFar += it->second;
if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ lengths[1] = value; } //save value
if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { lengths[2] = value; } //save value
if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { lengths[3] = value; } //save value
if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { lengths[4] = value; } //save value
if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { lengths[5] = value; } //save value
if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { lengths[6] = value; } //save value
lastValue = totalSoFar;
}
lengths[6] = (seqLength.rbegin())->first;
if ((ambigBases.begin())->first == -1) { ambigs[0] = 0; }
else {ambigs[0] = (ambigBases.begin())->first; }
//set all values to min
ambigs[1] = ambigs[0]; ambigs[2] = ambigs[0]; ambigs[3] = ambigs[0]; ambigs[4] = ambigs[0]; ambigs[5] = ambigs[0];
totalSoFar = 0;
lastValue = 0;
for (map<int, long long>::iterator it = ambigBases.begin(); it != ambigBases.end(); it++) {
int value = it->first;
meanAmbigBases += (value*it->second);
totalSoFar += it->second;
if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ ambigs[1] = value; } //save value
if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { ambigs[2] = value; } //save value
if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { ambigs[3] = value; } //save value
if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { ambigs[4] = value; } //save value
if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { ambigs[5] = value; } //save value
if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { ambigs[6] = value; } //save value
lastValue = totalSoFar;
}
ambigs[6] = (ambigBases.rbegin())->first;
if ((longHomoPolymer.begin())->first == -1) { homops[0] = 0; }
else {homops[0] = (longHomoPolymer.begin())->first; }
//set all values to min
homops[1] = homops[0]; homops[2] = homops[0]; homops[3] = homops[0]; homops[4] = homops[0]; homops[5] = homops[0];
totalSoFar = 0;
lastValue = 0;
for (map<int, long long>::iterator it = longHomoPolymer.begin(); it != longHomoPolymer.end(); it++) {
int value = it->first;
meanLongHomoPolymer += (it->first*it->second);
totalSoFar += it->second;
if (((totalSoFar <= ptile0_25) && (totalSoFar > 1)) || ((lastValue < ptile0_25) && (totalSoFar > ptile0_25))){ homops[1] = value; } //save value
if (((totalSoFar <= ptile25) && (totalSoFar > ptile0_25)) || ((lastValue < ptile25) && (totalSoFar > ptile25))) { homops[2] = value; } //save value
if (((totalSoFar <= ptile50) && (totalSoFar > ptile25)) || ((lastValue < ptile50) && (totalSoFar > ptile50))) { homops[3] = value; } //save value
if (((totalSoFar <= ptile75) && (totalSoFar > ptile50)) || ((lastValue < ptile75) && (totalSoFar > ptile75))) { homops[4] = value; } //save value
if (((totalSoFar <= ptile97_5) && (totalSoFar > ptile75)) || ((lastValue < ptile97_5) && (totalSoFar > ptile97_5))) { homops[5] = value; } //save value
if ((totalSoFar <= ptile100) && (totalSoFar > ptile97_5)) { homops[6] = value; } //save value
lastValue = totalSoFar;
}
homops[6] = (longHomoPolymer.rbegin())->first;
double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer;
meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size;
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
m->mothurOut("Minimum:\t" + toString(starts[0]) + "\t" + toString(ends[0]) + "\t" + toString(lengths[0]) + "\t" + toString(ambigs[0]) + "\t" + toString(homops[0]) + "\t" + toString(1)); m->mothurOutEndLine();
m->mothurOut("2.5%-tile:\t" + toString(starts[1]) + "\t" + toString(ends[1]) + "\t" + toString(lengths[1]) + "\t" + toString(ambigs[1]) + "\t" + toString(homops[1]) + "\t" + toString(ptile0_25)); m->mothurOutEndLine();
m->mothurOut("25%-tile:\t" + toString(starts[2]) + "\t" + toString(ends[2]) + "\t" + toString(lengths[2]) + "\t" + toString(ambigs[2]) + "\t" + toString(homops[2]) + "\t" + toString(ptile25)); m->mothurOutEndLine();
m->mothurOut("Median: \t" + toString(starts[3]) + "\t" + toString(ends[3]) + "\t" + toString(lengths[3]) + "\t" + toString(ambigs[3]) + "\t" + toString(homops[3]) + "\t" + toString(ptile50)); m->mothurOutEndLine();
m->mothurOut("75%-tile:\t" + toString(starts[4]) + "\t" + toString(ends[4]) + "\t" + toString(lengths[4]) + "\t" + toString(ambigs[4]) + "\t" + toString(homops[4]) + "\t" + toString(ptile75)); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(starts[5]) + "\t" + toString(ends[5]) + "\t" + toString(lengths[5]) + "\t" + toString(ambigs[5]) + "\t" + toString(homops[5]) + "\t" + toString(ptile97_5)); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(starts[6]) + "\t" + toString(ends[6]) + "\t" + toString(lengths[6]) + "\t" + toString(ambigs[6]) + "\t" + toString(homops[6]) + "\t" + toString(ptile100)); m->mothurOutEndLine();
m->mothurOut("Mean:\t" + toString(meanstartPosition) + "\t" + toString(meanendPosition) + "\t" + toString(meanseqLength) + "\t" + toString(meanambigBases) + "\t" + toString(meanlongHomoPolymer)); m->mothurOutEndLine();
if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
m->mothurOutEndLine();
if ((namefile == "") && (countfile == "")) { m->mothurOut("It took " + toString(time(NULL) - start) + " secs to summarize " + toString(numSeqs) + " sequences.\n"); }
else{ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to summarize " + toString(size) + " sequences.\n"); }
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("summary");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "execute");
exit(1);
}
}