int SharedCommand::execute(){
try {
globaldata = GlobalData::getInstance();
+ //lookup.clear();
+ int count = 1;
+ string errorOff = "no error";
//read in listfile
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
+
input = globaldata->ginput;
- list = globaldata->glist;
+ SharedList = globaldata->gSharedList;
+ SharedListVector* lastList = SharedList;
+ //lookup = SharedList->getSharedRAbundVector();
+ //vector<SharedRAbundVector*> lastLookup = lookup;
+
+ //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 = globaldata->labels;
+ set<int> userLines = globaldata->lines;
shared = new Shared();
- int i = 0;
- while(list != NULL){
- shared->getSharedVectors(i, list); //fills sharedGroups with new info and updates sharedVector
- list = input->getListVector(); //get new list vector to process
+
+ while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+
+ shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
+ printSharedData(); //prints info to the .shared file
+
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+ shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
+ printSharedData(); //prints info to the .shared file
+
+ processedLabels.insert(lastList->getLabel());
+ userLabels.erase(lastList->getLabel());
+ }
+
+ if (count != 1) { delete lastList; }
+ lastList = SharedList;
+ SharedList = input->getSharedListVector(); //get new list vector to process
+ count++;
+
+ //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ //lastLookup = lookup;
+ //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ //cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastList->getLabel()) != 1) {
+ //cout << ". I will use " << lastList->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
printSharedData(); //prints info to the .shared file
- i++;
}
+
+ delete lastList; globaldata->gSharedList = NULL;
+ delete shared;
+ out.close();
+
return 0;
}
catch(exception& e) {
//**********************************************************************************************************************
void SharedCommand::printSharedData() {
try {
+
+ ///for (int i = 0; i < thislookup.size(); i++) {
+ // out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+//cout << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
+ // thislookup[i]->print(out);
+ // }
//prints out horizontally
for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
SharedCommand::~SharedCommand(){
//delete list;
delete read;
+
}
//**********************************************************************************************************************