}
-/***********************************************************************/
+***********************************************************************/
//reads a shared file
SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
//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"
m->binLabelsInFile.push_back(temp);
}
- f >> label;
- }
- }else { label = m->saveNextLabel; }
+ f >> label >> groupN >> num;
+ }else {
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+
+ //make binlabels because we don't have any
+ string snumBins = toString(num);
+ m->binLabelsInFile.clear();
+ for (int i = 0; i < num; i++) {
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ m->binLabelsInFile.push_back(binLabel);
+ }
+ }
+ }else {
+ label = m->saveNextLabel;
+
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
+ }
//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;
//add new vector to lookup
//fill vector. data = first sharedrabund in file
for(int i=0;i<num;i++){
f >> inputData;
+ if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
lookup[0]->push_back(inputData, groupN); //abundance, bin, group
push_back(inputData, groupN);
//read the rest of the groups info in
while ((nextLabel == holdLabel) && (f.eof() != true)) {
f >> groupN >> num;
+ if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); }
count++;
allGroups.push_back(groupN);
//fill vector.
for(int i=0;i<num;i++){
f >> inputData;
+ if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); }
lookup[count]->push_back(inputData, groupN); //abundance, bin, group
}
}
m->saveNextLabel = nextLabel;
m->setAllGroups(allGroups);
-
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
return data[index].abundance;
}
+/***********************************************************************/
+//returns vector of abundances
+vector<int> SharedRAbundVector::getAbundances(){
+ vector<int> abunds;
+ for (int i = 0; i < data.size(); i++) {
+ abunds.push_back(data[i].abundance);
+ }
+
+ return abunds;
+}
+
+
/***********************************************************************/
int SharedRAbundVector::numNZ(){