X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=9eeb0f21bf3626620806c49372ab36efd0ff0831;hp=a5e17c2454d615be3a1c75f8b57fbe54ef85acd8;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=8742edef7a51b82834289e570d336f5a81ba1f2b diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp index a5e17c2..9eeb0f2 100644 --- a/sharedrabundfloatvector.cpp +++ b/sharedrabundfloatvector.cpp @@ -33,7 +33,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank( SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) { try { - m->namesOfGroups.clear(); + m->clearAllGroups(); + vector allGroups; int num, count; float inputData; @@ -47,7 +48,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma //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" @@ -61,25 +62,45 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma //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 @@ -88,7 +109,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma 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> groupN >> num; + count++; - m->namesOfGroups.push_back(groupN); + allGroups.push_back(groupN); //add new vector to lookup temp = new SharedRAbundFloatVector(); @@ -129,7 +151,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma } m->saveNextLabel = nextLabel; - + m->setAllGroups(allGroups); } catch(exception& e) { m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector"); @@ -169,6 +191,16 @@ 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]; } @@ -250,13 +282,20 @@ int SharedRAbundFloatVector::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" + toString(i+1); - if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + 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'; } @@ -264,8 +303,14 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){ }else { for (int i = 0; i < numBins; i++) { //if there is a bin label use it otherwise make one - string binLabel = "Otu" + toString(i+1); - if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + 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'; } @@ -273,7 +318,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){ output << endl; } - m->printedHeaders = true; + m->printedSharedHeaders = true; } catch(exception& e) { m->errorOut(e, "SharedRAbundVector", "printHeaders"); @@ -333,18 +378,21 @@ SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){ exit(1); } } -/***********************************************************************/ +***********************************************************************/ vector SharedRAbundFloatVector::getSharedRAbundFloatVectors(){ try { SharedUtil* util; util = new SharedUtil(); - util->setGroups(m->Groups, m->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(), m->Groups) == false) { + if (util->isValidGroup(lookup[i]->getGroup(), m->getGroups()) == false) { delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); i--; @@ -401,7 +449,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){ exit(1); } } -/***********************************************************************/ +***********************************************************************/ SAbundVector SharedRAbundFloatVector::getSAbundVector() { try { @@ -443,7 +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 { @@ -479,6 +527,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector& //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; } @@ -494,8 +543,14 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector& 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" + toString(i+1); - if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + 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); } @@ -504,7 +559,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector& for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } thislookup = newLookup; - m->currentBinLabels = newBinLabels; + m->currentSharedBinLabels = newBinLabels; return 0;