SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a shared file
try {
- globaldata = GlobalData::getInstance();
maxRank = 0; numBins = 0; numSeqs = 0;
-
- if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); }
+
+ groupmap = new GroupMap();
int num, inputData, count;
count = 0; numSeqs = 0;
individual newguy;
//read in first row since you know there is at least 1 group.
- f >> label >> groupN >> num;
+ //are we at the beginning of the file??
+ if (m->saveNextLabel == "") {
+ f >> label;
+
+ //is this a shared file that has headers
+ if (label == "label") {
+ //gets "group"
+ f >> label; m->gobble(f);
+
+ //gets "numOtus"
+ f >> label; m->gobble(f);
+
+ //eat rest of line
+ label = m->getline(f); m->gobble(f);
+
+ //parse labels to save
+ istringstream iStringStream(label);
+ m->binLabelsInFile.clear();
+ while(!iStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ iStringStream >> temp; m->gobble(iStringStream);
+
+ m->binLabelsInFile.push_back(temp);
+ }
+
+ f >> label;
+ }
+ }else { label = m->saveNextLabel; }
+
+ //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
+ m->currentBinLabels = m->binLabelsInFile;
+
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+
holdLabel = label;
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = 0;
- }
+
+ vector<string> allGroups;
+ //save group in groupmap
+ allGroups.push_back(groupN);
+ groupmap->groupIndex[groupN] = 0;
+
for(int i=0;i<num;i++){
f >> inputData;
m->gobble(f);
- if (f.eof() != true) { f >> nextLabel; }
+ if (!(f.eof())) { f >> nextLabel; }
//read the rest of the groups info in
while ((nextLabel == holdLabel) && (f.eof() != true)) {
f >> groupN >> num;
count++;
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = count;
- }
+
+ //save group in groupmap
+ allGroups.push_back(groupN);
+ groupmap->groupIndex[groupN] = count;
+
for(int i=0;i<num;i++){
f >> inputData;
}
- //put file pointer back since you are now at a new distance label
- for (int i = 0; i < nextLabel.length(); i++) { f.unget(); }
-
- if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
+ m->saveNextLabel = nextLabel;
+
+ groupmap->setNamesOfGroups(allGroups);
+ m->setAllGroups(allGroups);
updateStats();
}
}
+/***********************************************************************/
+void SharedOrderVector::clear(){
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+ data.clear();
+}
/***********************************************************************/
void SharedOrderVector::resize(int){
util = new SharedUtil();
vector<SharedRAbundVector*> lookup;
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
- util->getSharedVectors(globaldata->Groups, lookup, this);
+ vector<string> Groups = m->getGroups();
+ vector<string> allGroups = m->getAllGroups();
+ util->setGroups(Groups, allGroups);
+ util->getSharedVectors(Groups, lookup, this);
+ m->setGroups(Groups);
+ m->setAllGroups(allGroups);
return lookup;
}