//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"
//parse labels to save
istringstream iStringStream(label);
- m->binLabelsInFile.clear();
+ m->sharedBinLabelsInFile.clear();
while(!iStringStream.eof()){
if (m->control_pressed) { break; }
string temp;
iStringStream >> temp; m->gobble(iStringStream);
-
- m->binLabelsInFile.push_back(temp);
+
+ m->sharedBinLabelsInFile.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->sharedBinLabelsInFile.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->sharedBinLabelsInFile.push_back(binLabel);
+ }
+ }
+ }else {
+ label = m->saveNextLabel;
+
+ //read in first row since you know there is at least 1 group.
+ f >> groupN >> num;
+ }
//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
- m->currentBinLabels = m->binLabelsInFile;
+ m->currentSharedBinLabels = m->sharedBinLabelsInFile;
- //read in first row since you know there is at least 1 group.
- f >> groupN >> num;
-
holdLabel = label;
//add new vector to lookup
while ((nextLabel == holdLabel) && (f.eof() != true)) {
f >> groupN >> num;
- if (num != 1000) { break; }
count++;
allGroups.push_back(groupN);
m->saveNextLabel = nextLabel;
m->setAllGroups(allGroups);
-
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
return data[index].abundance;
}
/***********************************************************************/
+//returns vector of abundances
+vector<float> SharedRAbundFloatVector::getAbundances(){
+ vector<float> abunds;
+ for (int i = 0; i < data.size(); i++) {
+ abunds.push_back(data[i].abundance);
+ }
+
+ return abunds;
+}
+/***********************************************************************/
individualFloat SharedRAbundFloatVector::get(int index){
return data[index];
}
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
- if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+ if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; }
output << binLabel << '\t';
}
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
- if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+ if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; }
output << binLabel << '\t';
}
output << endl;
}
- m->printedHeaders = true;
+ m->printedSharedHeaders = true;
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundVector", "printHeaders");
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
- if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+ if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; }
newBinLabels.push_back(binLabel);
}
for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
thislookup = newLookup;
- m->currentBinLabels = newBinLabels;
+ m->currentSharedBinLabels = newBinLabels;
return 0;