}
}
//**********************************************************************************************************************
+string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(){
try {
abort = true; calledHelp = true;
else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not found") {
else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (listfile == "not open") { listfile = ""; abort = true; }
+ else { m->setListFile(listfile); }
//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"){
}
namesfile = validParameter.validFile(parameters, "name", true);
- if (namesfile == "not open") { abort = true; }
+ if (namesfile == "not open") { namesfile = ""; abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
+ else { m->setNameFile(namesfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ if (namesfile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 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++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ 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());
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ 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());
list = input->getListVector();
}
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 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; }
//output error messages about any remaining user labels
set<string>::iterator it;
list = input->getListVector(lastLabel);
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+ 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 fasta;
if (groupfile != "") { delete groupMap; }
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ 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();
try {
string binnames, name, sequence;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
- m->openOutputFile(outputFileName, out);
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
+ m->openOutputFile(outputFileName, out);
//save to output list of output file names
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);