*/
#include "sharedcommand.h"
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSharedRabunds(SharedRAbundVector* left, SharedRAbundVector* right){
+ 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"));
}
}
string errorOff = "no error";
//errorOff = "";
+ //if user provided an order file containing the order the shared file should be in read it
+ if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
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;
if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
+
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
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());
void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
try {
- //initialize bin values
- for (int i = 0; i < thislookup.size(); i++) {
-//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
- out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(out);
+ 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();
+ m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ rav.print(*(filehandles[thislookup[i]->getGroup()]));
+ (*(filehandles[thislookup[i]->getGroup()])).close();
+ }
+ }else{
+ //create a map from groupName to each sharedrabund
+ map<string, SharedRAbundVector*> myMap;
+ map<string, SharedRAbundVector*>::iterator myIt;
- RAbundVector rav = thislookup[i]->getRAbundVector();
- openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
- rav.print(*(filehandles[thislookup[i]->getGroup()]));
- (*(filehandles[thislookup[i]->getGroup()])).close();
+ for (int i = 0; i < thislookup.size(); i++) {
+ 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++) {
+ myIt = myMap.find(order[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();
+ m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+ rav.print(*(filehandles[(myIt->second)->getGroup()]));
+ (*(filehandles[(myIt->second)->getGroup()])).close();
+ }else{
+ m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
+ }
+ }
+
}
}
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++) {
}
-
+//**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+ try {
+ //remove old names
+ order.clear();
+
+ ifstream in;
+ m->openInputFile(globaldata->getOrderGroupFile(), in);
+ string thisGroup;
+
+ while(!in.eof()){
+ in >> thisGroup; m->gobble(in);
+
+ order.push_back(thisGroup);
+
+ if (m->control_pressed) { order.clear(); break; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "readOrderFile");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
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