//clears file before we start to write to it below
for (int i=0; i<groupMap->getNumGroups(); i++) {
- openOutputFile(fileroot + groupMap->namesOfGroups[i] + ".list", *(filehandles[groupMap->namesOfGroups[i]]));
- (*(filehandles[groupMap->namesOfGroups[i]])).close();
+ remove((fileroot + groupMap->namesOfGroups[i] + ".list").c_str());
}
-
-
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function ParseListCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function ParseListCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "ParseListCommand");
exit(1);
}
+
}
/***********************************************************************/
void ParseListCommand::parse(int index, SharedListVector* list) {
if (groupName != "not found") {
listGroups[groupName] = listGroups[groupName] + "," + member; //adds prefix to the correct group.
}else {
- cerr << "Error: Sequence '" << member << "' was not found in the group file, please correct\n";
+ mothurOut("Error: Sequence '" + toString(member) + "' was not found in the group file, please correct\n");
}
}
if (groupName != "not found") {
listGroups[groupName] = listGroups[groupName] + "," + bin; //adds prefix to the correct group.
}else {
- cerr << "Error: Sequence '" << bin << "' was not found in the group file, please correct\n";
+ mothurOut("Error: Sequence '" + toString(bin) + "' was not found in the group file, please correct\n");
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function parse. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function parse. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "parse");
exit(1);
}
}
read->read(&*globaldata);
input = globaldata->ginput;
list = globaldata->gSharedList;
- SharedListVector* lastList = list;
+ string lastLabel = list->getLabel();
//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;
-
+
//parses and sets each groups listvector
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
- cout << list->getLabel() << '\t' << count << endl;
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lastLabel) == 1){
+ mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
process(list);
processedLabels.insert(list->getLabel());
userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- cout << lastList->getLabel() << '\t' << count << endl;
- process(lastList);
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getSharedListVector(lastLabel);
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = list;
-
+
+ lastLabel = list->getLabel();
+
+ delete list;
list = input->getSharedListVector();
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;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastList->getLabel() << '\t' << count << endl;
- process(lastList);
+ delete list;
+ list = input->getSharedListVector(lastLabel);
+
+ mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(list);
+ delete list;
}
- delete lastList; globaldata->gSharedList = NULL;
+ globaldata->gSharedList = NULL;
//delete list vectors to fill with parsed data
for (it2 = mapOfLists.begin(); it2 != mapOfLists.end(); it2++) {
delete it2->second;
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff