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";
+ errorOut(e, "SharedCommand", "SharedCommand");
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";
- exit(1);
- }
-
}
//**********************************************************************************************************************
int SharedCommand::execute(){
try {
- globaldata = GlobalData::getInstance();
+
//lookup.clear();
int count = 1;
string errorOff = "no error";
input = globaldata->ginput;
SharedList = globaldata->gSharedList;
- SharedListVector* lastList = SharedList;
- //lookup = SharedList->getSharedRAbundVector();
- //vector<SharedRAbundVector*> lastLookup = lookup;
-
+ 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.
set<string> processedLabels;
set<string> userLabels = globaldata->labels;
set<int> userLines = globaldata->lines;
- shared = new Shared();
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
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
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 ((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()); mothurOutEndLine();
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ 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++;
- //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- //lastLookup = lookup;
- //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
+ count++;
}
//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;
+ 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) {
- shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
+ if (SharedList != NULL) { delete SharedList; }
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel()); 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;
- delete shared;
+ globaldata->gSharedList = NULL;
+ delete read;
+
out.close();
+ 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";
+ errorOut(e, "SharedCommand", "execute");
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";
- exit(1);
- }
-
}
//**********************************************************************************************************************
-void SharedCommand::printSharedData() {
+void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
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
- it->second->print(out); // prints sharedrabundvector
+
+ //initialize bin values
+ for (int i = 0; i < thislookup.size(); i++) {
+ out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(out);
+
+ 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();
}
+
}
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";
+ errorOut(e, "SharedCommand", "printSharedData");
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";
- exit(1);
- }
-
}
//**********************************************************************************************************************
SharedCommand::~SharedCommand(){
//delete list;
- delete read;
+
}
projects / mothur.git / blobdiff