if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { remove(listFileNames[i].c_str()); } return 0; }
//****************** merge list file and create rabund and sabund files ******************************//
-
- mergeLists(listFileNames, singletonName, labels);
+ ListVector* listSingle;
+ map<float, int> labelBins = completeListFile(listFileNames, singletonName, labels, listSingle); //returns map of label to numBins
+
+ if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ mergeLists(listFileNames, labelBins, listSingle);
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}
}
//**********************************************************************************************************************
-int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton, set<string> userLabels){
+map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames, string singleton, set<string> userLabels, ListVector*& listSingle){
try {
- if (outputDir == "") { outputDir += hasPath(distfile); }
- fileroot = outputDir + getRootName(getSimpleName(distfile));
-
- openOutputFile(fileroot+ tag + ".sabund", outSabund);
- openOutputFile(fileroot+ tag + ".rabund", outRabund);
- openOutputFile(fileroot+ tag + ".list", outList);
- outputNames.push_back(fileroot+ tag + ".sabund");
- outputNames.push_back(fileroot+ tag + ".rabund");
- outputNames.push_back(fileroot+ tag + ".list");
+ map<float, int> labelBin;
+ vector<float> orderFloat;
+ int numSingleBins;
//read in singletons
- ListVector* listSingle = NULL;
if (singleton != "none") {
ifstream in;
openInputFile(singleton, in);
listSingle->push_back(secondCol);
}
in.close();
- }
+ remove(singleton.c_str());
+
+ numSingleBins = listSingle->getNumBins();
+ }else{ listSingle = NULL; numSingleBins = 0; }
- vector<float> orderFloat;
-
//go through users set and make them floats so we can sort them
for(set<string>::iterator it = userLabels.begin(); it != userLabels.end(); ++it) {
- float temp;
+ float temp = -10.0;
- if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
- convert(*it, temp);
- orderFloat.push_back(temp);
- }else if (*it == "unique") { orderFloat.push_back(-1.0); }
- else {
- userLabels.erase(*it);
- it--;
- }
+ if ((*it != "unique") && (convertTestFloat(*it, temp) == true)) { convert(*it, temp); }
+ else if (*it == "unique") { temp = -1.0; }
+
+ orderFloat.push_back(temp);
+ labelBin[temp] = numSingleBins; //initialize numbins
}
//sort order
sort(orderFloat.begin(), orderFloat.end());
-
- vector<InputData*> inputs;
- vector<string> lastLabels;
- for (int i = 0; i < listNames.size(); i++) {
- InputData* input = new InputData(listNames[i], "list");
- inputs.push_back(input);
+ userLabels.clear();
- ifstream in;
- openInputFile(listNames[i], in);
- ListVector tempList(in);
- lastLabels.push_back(tempList.getLabel());
- in.close();
- }
+ //get the list info from each file
+ for (int k = 0; k < listNames.size(); k++) {
- ListVector* merged = NULL;
-
- //for each label needed
- for(int l = 0; l < orderFloat.size(); l++){
+ if (m->control_pressed) {
+ if (listSingle != NULL) { delete listSingle; listSingle = NULL; remove(singleton.c_str()); }
+ for (int i = 0; i < listNames.size(); i++) { remove(listNames[i].c_str()); }
+ return labelBin;
+ }
- string thisLabel;
- if (orderFloat[l] == -1) { thisLabel = "unique"; }
- else { thisLabel = toString(orderFloat[l], length-1); }
-
- //get the list info from each file
- for (int k = 0; k < listNames.size(); k++) {
+ InputData* input = new InputData(listNames[k], "list");
+ ListVector* list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ string filledInList = listNames[k] + "filledInTemp";
+ ofstream outFilled;
+ openOutputFile(filledInList, outFilled);
- if (m->control_pressed) {
- if (listSingle != NULL) { delete listSingle; remove(singleton.c_str()); }
- for (int i = 0; i < listNames.size(); i++) { delete inputs[i]; remove(listNames[i].c_str()); }
- delete merged; merged = NULL;
- return 0;
- }
-
- ListVector* list = inputs[k]->getListVector();
-
+ //for each label needed
+ for(int l = 0; l < orderFloat.size(); l++){
+
+ string thisLabel;
+ if (orderFloat[l] == -1) { thisLabel = "unique"; }
+ else { thisLabel = toString(orderFloat[l], length-1); }
+
//this file has reached the end
- if (list == NULL) { list = inputs[k]->getListVector(lastLabels[k], true); }
+ if (list == NULL) {
+ list = input->getListVector(lastLabel, true);
+ }else{ //do you have the distance, or do you need to fill in
- float labelFloat;
- if (list->getLabel() == "unique") { labelFloat = -1.0; }
- else { convert(list->getLabel(), labelFloat); }
-
- //check for missing labels
- if (labelFloat > orderFloat[l]) { //you are missing the label, get the next smallest one
- //if its bigger get last label, otherwise keep it
- delete list;
- list = inputs[k]->getListVector(lastLabels[k], true); //get last list vector to use, you actually want to move back in the file
- }
- lastLabels[k] = list->getLabel();
+ float labelFloat;
+ if (list->getLabel() == "unique") { labelFloat = -1.0; }
+ else { convert(list->getLabel(), labelFloat); }
- //is this the first file
- if (merged == NULL) { merged = new ListVector(); merged->setLabel(thisLabel); }
-
- for (int j = 0; j < list->getNumBins(); j++) {
- merged->push_back(list->get(j));
+ //check for missing labels
+ if (labelFloat > orderFloat[l]) { //you are missing the label, get the next smallest one
+ //if its bigger get last label, otherwise keep it
+ delete list;
+ list = input->getListVector(lastLabel, true); //get last list vector to use, you actually want to move back in the file
+ }
+ lastLabel = list->getLabel();
}
+ //print to new file
+ list->setLabel(thisLabel);
+ list->print(outFilled);
+
+ //update labelBin
+ labelBin[orderFloat[l]] += list->getNumBins();
+
delete list;
+
+ list = input->getListVector();
}
+ if (list != NULL) { delete list; }
+ delete input;
+
+ outFilled.close();
+ remove(listNames[k].c_str());
+ rename(filledInList.c_str(), listNames[k].c_str());
+ }
+
+ return labelBin;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterSplitCommand", "completeListFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> userLabels, ListVector* listSingle){
+ try {
+ if (outputDir == "") { outputDir += hasPath(distfile); }
+ fileroot = outputDir + getRootName(getSimpleName(distfile));
+
+ openOutputFile(fileroot+ tag + ".sabund", outSabund);
+ openOutputFile(fileroot+ tag + ".rabund", outRabund);
+ openOutputFile(fileroot+ tag + ".list", outList);
+
+ outputNames.push_back(fileroot+ tag + ".sabund");
+ outputNames.push_back(fileroot+ tag + ".rabund");
+ outputNames.push_back(fileroot+ tag + ".list");
+
+ map<float, int>::iterator itLabel;
+
+ //for each label needed
+ for(itLabel = userLabels.begin(); itLabel != userLabels.end(); itLabel++) {
+
+ string thisLabel;
+ if (itLabel->first == -1) { thisLabel = "unique"; }
+ else { thisLabel = toString(itLabel->first, length-1); }
+
+ outList << thisLabel << '\t' << itLabel->second << '\t';
+
+ RAbundVector* rabund = new RAbundVector();
+ rabund->setLabel(thisLabel);
+
//add in singletons
if (listSingle != NULL) {
for (int j = 0; j < listSingle->getNumBins(); j++) {
- merged->push_back(listSingle->get(j));
+ outList << listSingle->get(j) << '\t';
+ rabund->push_back(getNumNames(listSingle->get(j)));
}
}
- //print to files
- printData(merged);
+ //get the list info from each file
+ for (int k = 0; k < listNames.size(); k++) {
+
+ if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < listNames.size(); i++) { remove(listNames[i].c_str()); } delete rabund; return 0; }
+
+ InputData* input = new InputData(listNames[k], "list");
+ ListVector* list = input->getListVector(thisLabel);
+
+ //this file has reached the end
+ if (list == NULL) { m->mothurOut("Error merging listvectors in file " + listNames[k]); m->mothurOutEndLine(); }
+ else {
+ for (int j = 0; j < list->getNumBins(); j++) {
+ outList << list->get(j) << '\t';
+ rabund->push_back(getNumNames(list->get(j)));
+ }
+ delete list;
+ }
+ delete input;
+ }
+
+ SAbundVector sabund = rabund->getSAbundVector();
+
+ sabund.print(outSabund);
+ rabund->print(outRabund);
+ outList << endl;
- delete merged; merged = NULL;
+ delete rabund;
}
- if (listSingle != NULL) { delete listSingle; remove(singleton.c_str()); }
+ outList.close();
+ outRabund.close();
+ outSabund.close();
- for (int i = 0; i < listNames.size(); i++) { delete inputs[i]; remove(listNames[i].c_str()); }
+ if (listSingle != NULL) { delete listSingle; }
+
+ for (int i = 0; i < listNames.size(); i++) { remove(listNames[i].c_str()); }
return 0;
}
exit(1);
}
}
+
//**********************************************************************************************************************
void ClusterSplitCommand::printData(ListVector* oldList){
projects / mothur.git / blobdiff