X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=9eeb0f21bf3626620806c49372ab36efd0ff0831;hp=f7405aefab95989d77bf3efec0ead7a44197b752;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=7ae40733a270f73ec8a331540cc7f28fd60b24fc diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp index f7405ae..9eeb0f2 100644 --- a/sharedrabundfloatvector.cpp +++ b/sharedrabundfloatvector.cpp @@ -12,14 +12,14 @@ /***********************************************************************/ -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++) { @@ -32,9 +32,9 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank( //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 allGroups; int num, count; float inputData; @@ -45,8 +45,62 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma 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 @@ -55,11 +109,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma 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> 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(); @@ -103,11 +150,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma 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"); @@ -128,16 +172,35 @@ void SharedRAbundFloatVector::set(int binNumber, float newBinSize, string groupn 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 SharedRAbundFloatVector::getAbundances(){ + vector 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]; } @@ -217,6 +280,52 @@ int SharedRAbundFloatVector::size(){ 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'; @@ -269,24 +378,31 @@ SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){ exit(1); } } -/***********************************************************************/ +***********************************************************************/ vector SharedRAbundFloatVector::getSharedRAbundFloatVectors(){ try { SharedUtil* util; util = new SharedUtil(); - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups); - + vector Groups = m->getGroups(); + vector 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; } @@ -333,7 +449,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){ exit(1); } } -/***********************************************************************/ +***********************************************************************/ SAbundVector SharedRAbundFloatVector::getSAbundVector() { try { @@ -375,7 +491,7 @@ SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() { 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* nameMap = NULL) { try { @@ -397,6 +513,61 @@ OrderVector SharedRAbundFloatVector::getOrderVector(map* nameMap = N exit(1); } } - +//********************************************************************************************************************** +int SharedRAbundFloatVector::eliminateZeroOTUS(vector& thislookup) { + try { + + vector 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 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); + } +} /***********************************************************************/