int BinSeqCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int error = 0;
fasta = new FastaMap();
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
groupMap->readMap();
}
//read fastafile
fasta->readFastaFile(fastafile);
//if user gave a namesfile then use it
if (namesfile != "") {
readNamesFile();
}
input = new InputData(listfile, "list");
list = input->getListVector();
string lastLabel = list->getLabel();
if (m->control_pressed) { delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
//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;
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
error = process(list);
if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(lastLabel);
error = process(list);
if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
delete list;
list = input->getListVector();
}
if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
error = process(list);
if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
delete list;
}
delete input;
delete fasta;
if (groupfile != "") { delete groupMap; }
if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "BinSeqCommand", "execute");
exit(1);
}
}
int DeUniqueSeqsCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filenames and open files
ofstream out;
string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));
int pos = outFastaFile.find("unique");
if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
else { outFastaFile = outputDir + outFastaFile; }
map<string, string> variables;
variables["[filename]"] = outFastaFile;
outFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outFastaFile, out);
readNamesFile();
if (m->control_pressed) { out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
ifstream in;
m->openInputFile(fastaFile, in);
while (!in.eof()) {
if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
//look for sequence name in nameMap
map<string, string>::iterator it = nameMap.find(seq.getName());
if (it == nameMap.end()) { m->mothurOut("[ERROR]: Your namefile does not contain " + seq.getName() + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
else {
vector<string> names;
m->splitAtComma(it->second, names);
//output sequences
for (int i = 0; i < names.size(); i++) {
out << ">" << names[i] << endl;
out << seq.getAligned() << endl;
}
//remove seq from name map so we can check for seqs in namefile not in fastafile later
nameMap.erase(it);
}
}
}
in.close();
out.close();
if (nameMap.size() != 0) { //then there are names in the namefile not in the fastafile
for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
m->mothurOut(it->first + " is not in your fasta file, but is in your name file. Please correct."); m->mothurOutEndLine();
}
}
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outFastaFile); m->mothurOutEndLine();
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "execute");
exit(1);
}
}
int main( const int argc, const char *argv[] )
{
fileplayer_s *playersFile;
names_s *nameList;
int next_name;
srand( time( NULL ) );
if ( argc < 4 )
{
printf( "Usage: %s <names file> <input file> <output file>\n", argv[0] );
return EXIT_SUCCESS;
}
if ( (nameList = readNamesFile( argv[1] )) == NULL )
{
printf( "Unable to load names file <%s>.\n", argv[1] );
return EXIT_SUCCESS;
}
if ( (playersFile = readPlayersFile( argv[2] )) == NULL )
{
printf( "Unable to load players file <%s>.\n", argv[2] );
free( nameList );
return EXIT_SUCCESS;
}
srand( time( NULL ) );
next_name = 0;
for ( int i = 0; i < TOTAL_TEAMS; ++i )
{
for ( int j = 0; j < PLAYERS_PER_TEAM; ++j )
{
position2_e pos = positions[j];
int idx = (i * PLAYERS_PER_TEAM) + j;
if ( pos == pos2_Pitcher ) generatePitcher( &playersFile[idx], &nameList[next_name] );
else if ( pos == pos2_Closer ) generateCloser( &playersFile[idx], &nameList[next_name] );
else generateBatter( &playersFile[idx], &nameList[next_name], pos );
next_name++;
}
}
if ( ! writePlayersFile( argv[3], playersFile ) )
{
printf( "Cannot save player changes.\n" );
free( nameList );
free( playersFile );
return EXIT_FAILURE;
}
free( nameList );
free( playersFile );
return EXIT_SUCCESS;
}
