filename = getRootName(filename);
filename = filename + "shared";
openOutputFile(filename, out);
+
+ groupMap = globaldata->gGroupmap;
+
+ //fill filehandles with neccessary ofstreams
+ int i;
+ ofstream* temp;
+ for (i=0; i<groupMap->getNumGroups(); i++) {
+ temp = new ofstream;
+ filehandles[groupMap->namesOfGroups[i]] = temp;
+ }
+
+ //set fileroot
+ fileroot = getRootName(globaldata->getListFile());
+
+ //clears file before we start to write to it below
+ for (int i=0; i<groupMap->getNumGroups(); i++) {
+ remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+ }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
-
}
//**********************************************************************************************************************
int SharedCommand::execute(){
try {
- cout << "creating sharedfile...";
//lookup.clear();
int count = 1;
string errorOff = "no error";
input = globaldata->ginput;
SharedList = globaldata->gSharedList;
- SharedListVector* lastList = SharedList;
+ string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+
lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
userLines.erase(count);
}
- if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- lookup = lastList->getSharedRAbundVector();
+ if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete SharedList;
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = SharedList;
-
+
+ lastLabel = SharedList->getLabel();
+
+ delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
count++;
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;
+ if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
- }else {
- //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- lookup = lastList->getSharedRAbundVector();
+ delete SharedList;
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
+ delete SharedList;
}
- delete lastList; globaldata->gSharedList = NULL;
+ globaldata->gSharedList = NULL;
delete read;
out.close();
- cout << "complete." << endl;
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedCommand", "execute");
exit(1);
}
-
}
//**********************************************************************************************************************
void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
+
+ openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ (*filehandles[thislookup[i]->getGroup()]) << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(*(filehandles[thislookup[i]->getGroup()]));
+ (*(filehandles[thislookup[i]->getGroup()])).close();
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedCommand", "printSharedData");
exit(1);
}
-
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff