return (left->getGroup() < right->getGroup());
}
//**********************************************************************************************************************
+vector<string> SharedCommand::getValidParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(){
+ try {
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "SharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
SharedCommand::SharedCommand(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
//getting output filename
filename = globaldata->inputFileName;
- if (outputDir == "") { outputDir += hasPath(filename); }
+ if (outputDir == "") { outputDir += m->hasPath(filename); }
- filename = outputDir + getRootName(getSimpleName(filename));
+ filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
+ outputTypes["shared"].push_back(filename);
- openOutputFile(filename, out);
+ m->openOutputFile(filename, out);
pickedGroups = false;
groupMap = globaldata->gGroupmap;
}
//set fileroot
- fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
+ fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile()));
//clears file before we start to write to it below
for (int i=0; i<groups.size(); i++) {
remove((fileroot + groups[i] + ".rabund").c_str());
outputNames.push_back((fileroot + groups[i] + ".rabund"));
+ outputTypes["rabund"].push_back((fileroot + groups[i] + ".rabund"));
}
}
groups += globaldata->Groups[i] + ".";
}
- string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
ofstream outGroups;
- openOutputFile(newGroupFile, outGroups);
+ m->openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
userLabels.erase(SharedList->getLabel());
}
- if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
globaldata->setGroupFile("");
globaldata->setSharedFile(filename);
+
if (m->control_pressed) {
delete input; globaldata->ginput = NULL;
remove(filename.c_str());
if (order.size() == 0) { //user has not specified an order so do aplabetically
sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+ globaldata->Groups.clear();
+
//initialize bin values
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
+ globaldata->Groups.push_back(thislookup[i]->getGroup());
+
RAbundVector rav = thislookup[i]->getRAbundVector();
- openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
rav.print(*(filehandles[thislookup[i]->getGroup()]));
(*(filehandles[thislookup[i]->getGroup()])).close();
}
myMap[thislookup[i]->getGroup()] = thislookup[i];
}
+ globaldata->Groups.clear();
//loop through ordered list and print the rabund
for (int i = 0; i < order.size(); i++) {
if(myIt != myMap.end()) { //we found it
out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
(myIt->second)->print(out);
+
+ globaldata->Groups.push_back((myIt->second)->getGroup());
RAbundVector rav = (myIt->second)->getRAbundVector();
- openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+ m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
rav.print(*(filehandles[(myIt->second)->getGroup()]));
(*(filehandles[(myIt->second)->getGroup()])).close();
}else{
int SharedCommand::createMisMatchFile() {
try {
ofstream outMisMatch;
- string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+ string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
//you have sequences in your list file that are not in your group file
if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
outputMisMatchName += "missing.group";
m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
- openOutputFile(outputMisMatchName, outMisMatch);
+ m->openOutputFile(outputMisMatchName, outMisMatch);
map<string, string> listNames;
map<string, string>::iterator itList;
map<string, string>::iterator itMatch;
- openOutputFile(outputMisMatchName, outMisMatch);
+ m->openOutputFile(outputMisMatchName, outMisMatch);
//loop through names in seqNames and if they aren't in namesIn list output them
for (int i = 0; i < seqNames.size(); i++) {
order.clear();
ifstream in;
- openInputFile(globaldata->getOrderGroupFile(), in);
+ m->openInputFile(globaldata->getOrderGroupFile(), in);
string thisGroup;
while(!in.eof()){
- in >> thisGroup; gobble(in);
+ in >> thisGroup; m->gobble(in);
order.push_back(thisGroup);