exit(1);
}
}
+//**********************************************************************************************************************
+string RemoveRareCommand::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 == "rabund") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "sabund") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
+ else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
+ 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, "RemoveRareCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(){
try {
string temp = validParameter.validFile(parameters, "nseqs", false);
if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
- else { convert(temp, nseqs); }
+ else { m->mothurConvert(temp, nseqs); }
temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; }
byGroup = m->isTrue(temp);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
- string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
ofstream out, outGroup;
m->openOutputFile(outputFileName, out);
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
SharedUtil util;
- util.setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> namesGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesGroups);
m->openOutputFile(outputGroupFileName, outGroup);
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "pick" + m->getExtension(rabundfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
//**********************************************************************************************************************
int RemoveRareCommand::processShared(){
try {
- m->Groups = Groups;
+ m->setGroups(Groups);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "pick" + m->getExtension(sharedfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;