int BinSeqCommand::execute(){
try {
int count = 1;
- string binnames, name, sequence;
+ int error = 0;
//read fastafile
fasta->readFastaFile(in);
input = globaldata->ginput;
list = globaldata->gListVector;
+ ListVector* lastList = list;
+
+ //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;
+
- while(list != NULL){
+ while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
+ error = process(list, count);
+ if (error == 1) { return 0; }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ }
+
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+
+ error = process(lastList, count);
+ if (error == 1) { return 0; }
+
+ processedLabels.insert(lastList->getLabel());
+ userLabels.erase(lastList->getLabel());
+
+ }
+
+ if (count != 1) { delete lastList; }
+ lastList = list;
+
+ list = input->getListVector();
+ 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;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ error = process(lastList, count);
+ if (error == 1) { return 0; }
+ }
+
+ delete lastList;
+ return 0;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+void BinSeqCommand::readNamesFile() {
+ try {
+ vector<string> dupNames;
+ openInputFile(namesfile, inNames);
+
+ string name, names, sequence;
+
+ while(inNames){
+ inNames >> name; //read from first column A
+ inNames >> names; //read from second column A,B,C,D
+
+ dupNames.clear();
+
+ //parse names into vector
+ splitAtComma(names, dupNames);
+
+ //store names in fasta map
+ sequence = fasta->getSequence(name);
+ for (int i = 0; i < dupNames.size(); i++) {
+ fasta->push_back(dupNames[i], sequence);
+ }
+
+ gobble(inNames);
+ }
+ inNames.close();
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+int BinSeqCommand::process(ListVector* list, int count) {
+ try {
+ string binnames, name, sequence;
string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
openOutputFile(outputFileName, out);
if (group == "not found") {
cout << name << " is missing from your group file. Please correct. " << endl;
remove(outputFileName.c_str());
- return 0;
+ return 1;
}else{
name = name + "|" + group + "|" + toString(i+1);
out << ">" << name << endl;
}else {
cout << name << " is missing from your fasta or name file. Please correct. " << endl;
remove(outputFileName.c_str());
- return 0;
+ return 1;
}
}
if (group == "not found") {
cout << binnames << " is missing from your group file. Please correct. " << endl;
remove(outputFileName.c_str());
- return 0;
+ return 1;
}else{
binnames = binnames + "|" + group + "|" + toString(i+1);
out << ">" << binnames << endl;
}else {
cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
remove(outputFileName.c_str());
- return 0;
+ return 1;
}
-
}
+
out.close();
- }
-
- delete list;
- list = input->getListVector();
- count++;
- }
-
- return 0;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-void BinSeqCommand::readNamesFile() {
- try {
- vector<string> dupNames;
- openInputFile(namesfile, inNames);
-
- string name, names, sequence;
-
- while(inNames){
- inNames >> name; //read from first column A
- inNames >> names; //read from second column A,B,C,D
-
- dupNames.clear();
-
- //parse names into vector
- splitAtComma(names, dupNames);
-
- //store names in fasta map
- sequence = fasta->getSequence(name);
- for (int i = 0; i < dupNames.size(); i++) {
- fasta->push_back(dupNames[i], sequence);
- }
-
- gobble(inNames);
- }
- inNames.close();
+ return 0;
}
catch(exception& e) {
//**********************************************************************************************************************
-
projects / mothur.git / blobdiff