SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
try {
- m->namesOfGroups.clear();
+ m->clearAllGroups();
+ vector<string> allGroups;
int num, count;
float inputData;
//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);
- f >> label;
- }
- }else { label = m->saveNextLabel; }
+
+ //parse labels to save
+ istringstream iStringStream(label);
+ m->sharedBinLabelsInFile.clear();
+ while(!iStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ iStringStream >> temp; m->gobble(iStringStream);
+
+ m->sharedBinLabelsInFile.push_back(temp);
+ }
+
+ 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->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
lookup[0]->setLabel(label);
lookup[0]->setGroup(groupN);
- m->namesOfGroups.push_back(groupN);
+ allGroups.push_back(groupN);
//fill vector. data = first sharedrabund in file
for(int i=0;i<num;i++){
//read the rest of the groups info in
while ((nextLabel == holdLabel) && (f.eof() != true)) {
f >> groupN >> num;
+
count++;
- m->namesOfGroups.push_back(groupN);
+ allGroups.push_back(groupN);
//add new vector to lookup
temp = new SharedRAbundFloatVector();
}
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];
}
/***********************************************************************/
void SharedRAbundFloatVector::printHeaders(ostream& output){
try {
+ string snumBins = toString(numBins);
output << "label\tGroup\tnumOtus\t";
if (m->sharedHeaderMode == "tax") {
- for (int i = 0; i < numBins; i++) { output << "PhyloType" << (i+1) << '\t'; }
+ for (int i = 0; i < numBins; i++) {
+
+ //if there is a bin label use it otherwise make one
+ string binLabel = "PhyloType";
+ 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;
+ if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; }
+
+ output << binLabel << '\t';
+ }
output << endl;
}else {
- for (int i = 0; i < numBins; i++) { output << "Otu" << (i+1) << '\t'; }
+ for (int i = 0; i < numBins; 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;
+ 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");
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
try {
SharedUtil* util;
util = new SharedUtil();
- util->setGroups(m->Groups, m->namesOfGroups);
+ vector<string> Groups = m->getGroups();
+ vector<string> allGroups = m->getAllGroups();
+ util->setGroups(Groups, allGroups);
+ m->setGroups(Groups);
bool remove = false;
for (int i = 0; i < lookup.size(); i++) {
//if this sharedrabund is not from a group the user wants then delete it.
- if (util->isValidGroup(lookup[i]->getGroup(), m->Groups) == false) {
+ if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) {
delete lookup[i]; lookup[i] = NULL;
lookup.erase(lookup.begin()+i);
i--;
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
SAbundVector SharedRAbundFloatVector::getSAbundVector() {
try {
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
//this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
try {
}
//for each bin
+ vector<string> newBinLabels;
+ string snumBins = toString(thislookup[0]->getNumBins());
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
for (int j = 0; j < thislookup.size(); j++) {
newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
}
+ //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;
+ 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->currentSharedBinLabels = newBinLabels;
return 0;
projects / mothur.git / blobdiff