it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
}
//**********************************************************************************************************************
void ParseListCommand::help(){
try {
- m->mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile \n");
+ m->mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile. \n");
m->mothurOut("The parse.list command parameters are list, group and label.\n");
m->mothurOut("The list and group parameters are required.\n");
m->mothurOut("The label parameter is used to read specific labels in your input you want to use.\n");
if (abort == true) { return 0; }
//set fileroot
- string fileroot = outputDir + getRootName(getSimpleName(listfile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
vector<string> outputNames;
//fill filehandles with neccessary ofstreams
string filename = fileroot + groupMap->namesOfGroups[i] + ".list";
outputNames.push_back(filename);
- openOutputFile(filename, *temp);
+ m->openOutputFile(filename, *temp);
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
list = input->getListVector();
string lastLabel = list->getLabel();
+ if (m->control_pressed) {
+ delete input; delete list; delete groupMap;
+ for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ delete input; delete list; delete groupMap;
+ for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
- parse(list);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
-
+ parse(list);
+
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(lastLabel); //get new list vector to process
- parse(list);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ parse(list);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector(); //get new list vector to process
}
+ if (m->control_pressed) {
+ delete input; delete groupMap;
+ for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
}
+ if (m->control_pressed) {
+ delete input; delete groupMap;
+ for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close(); delete filehandles[groupMap->namesOfGroups[i]]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
list = input->getListVector(lastLabel); //get new list vector to process
- parse(list);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ parse(list);
delete list;
}
delete it3->second;
}
+
delete groupMap;
+ delete input;
+
+ if (m->control_pressed) {
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
/**********************************************************************************************************************/
-void ParseListCommand::parse(ListVector* thisList) {
+int ParseListCommand::parse(ListVector* thisList) {
try {
map<string, string> groupVector;
for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
map<string, string> groupBins;
string bin = list->get(i);
vector<string> names;
- splitAtComma(bin, names); //parses bin into individual sequence names
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
//parse bin into list of sequences in each group
for (int j = 0; j < names.size(); j++) {
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group
}
-
+
+ return 0;
}
catch(exception& e) {