//**********************************************************************************************************************
SummaryCommand::SummaryCommand(){
try {
+ abort = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
//open each groups summary file
string newLabel = "";
- ifstream* temp;
- map<string, ifstream*> filehandles;
+ map<string, vector<string> > files;
for (int i=0; i<outputNames.size(); i++) {
- temp = new ifstream;
- filehandles[outputNames[i]] = temp;
- m->openInputFile(outputNames[i], *(temp));
+ vector<string> thisFilesLines;
+
+ ifstream temp;
+ m->openInputFile(outputNames[i], temp);
//read through first line - labels
string tempLabel;
if (i == 0) { //we want to save the labels to output below
for (int j = 0; j < numCols+1; j++) {
- *(temp) >> tempLabel;
+ temp >> tempLabel;
if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
}else{ newLabel += tempLabel + '\t'; }
}
- }else{ for (int j = 0; j < numCols+1; j++) { *(temp) >> tempLabel; } }
+ }else{ for (int j = 0; j < numCols+1; j++) { temp >> tempLabel; } }
+
+ m->gobble(temp);
+
+ //for each label
+ for (int k = 0; k < numLines; k++) {
+
+ string thisLine = "";
+ string tempLabel;
+
+ for (int j = 0; j < numCols+1; j++) {
+ temp >> tempLabel;
+
+ //save for later
+ if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; }
+ else{ thisLine += tempLabel + "\t"; }
+ }
+
+ thisLine += "\n";
+
+ thisFilesLines.push_back(thisLine);
+
+ m->gobble(temp);
+ }
+
+ files[outputNames[i]] = thisFilesLines;
- m->gobble(*(temp));
+ temp.close();
+ remove(outputNames[i].c_str());
}
//output label line to new file
out << newLabel << endl;
//for each label
- for (int i = 0; i < numLines; i++) {
+ for (int k = 0; k < numLines; k++) {
//grab summary data for each group
for (int i=0; i<outputNames.size(); i++) {
- string tempLabel;
-
- for (int j = 0; j < numCols+1; j++) {
- *(filehandles[outputNames[i]]) >> tempLabel;
-
- //print to combined file
- if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t'; }
- else{ out << tempLabel << '\t'; }
- }
-
- out << endl;
- m->gobble(*(filehandles[outputNames[i]]));
+ out << files[outputNames[i]][k];
}
}
- //close each groups summary file
- for (int i=0; i<outputNames.size(); i++) { (*(filehandles[outputNames[i]])).close(); remove(outputNames[i].c_str()); }
outputNames.clear();
out.close();