/***********************************************************************/
-SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {globaldata = GlobalData::getInstance();}
+SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {}
/***********************************************************************/
SharedRAbundFloatVector::~SharedRAbundFloatVector() {}
/***********************************************************************/
SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(0.0), numBins(n), numSeqs(0.0) {
- globaldata = GlobalData::getInstance();
+
individualFloat newGuy;
//initialize data
for (int i=0; i< n; i++) {
//reads a shared file
SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {
try {
- globaldata = GlobalData::getInstance();
- if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); }
+ m->clearAllGroups();
+ vector<string> allGroups;
int num, count;
float inputData;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
lookup.clear();
- //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->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;
+
holdLabel = label;
//add new vector to lookup
lookup[0]->setLabel(label);
lookup[0]->setGroup(groupN);
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = 0;
- }
+ 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++;
- if (globaldata->gGroupmap == NULL) {
- //save group in groupmap
- groupmap->namesOfGroups.push_back(groupN);
- groupmap->groupIndex[groupN] = count;
- }
+ allGroups.push_back(groupN);
//add new vector to lookup
temp = new SharedRAbundFloatVector();
if (f.eof() != true) { f >> nextLabel; }
}
- //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;
+ m->setAllGroups(allGroups);
}
catch(exception& e) {
m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
numSeqs += (newBinSize - oldBinSize);
}
catch(exception& e) {
- m->errorOut(e, "SharedRAbundVector", "set");
+ m->errorOut(e, "SharedRAbundFloatVector", "set");
exit(1);
}
}
+/***********************************************************************/
+void SharedRAbundFloatVector::clear(){
+ numBins = 0;
+ maxRank = 0;
+ numSeqs = 0;
+ data.clear();
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+ lookup.clear();
+}
/***********************************************************************/
float SharedRAbundFloatVector::getAbundance(int index){
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];
}
return data.size();
}
/***********************************************************************/
+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++) {
+
+ //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++) {
+ //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->printedSharedHeaders = true;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "printHeaders");
+ exit(1);
+ }
+}
+/***********************************************************************/
void SharedRAbundFloatVector::print(ostream& output){
try {
output << numBins << '\t';
exit(1);
}
}
-/***********************************************************************/
+***********************************************************************/
vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
try {
SharedUtil* util;
util = new SharedUtil();
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->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(), globaldata->Groups) == false) {
+ if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) {
delete lookup[i]; lookup[i] = NULL;
lookup.erase(lookup.begin()+i);
i--;
+ remove = true;
}
}
delete util;
+
+ if (remove) { eliminateZeroOTUS(lookup); }
return lookup;
}
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 {
exit(1);
}
}
-
+//**********************************************************************************************************************
+int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //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; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ 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;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
/***********************************************************************/
projects / mothur.git / blobdiff