X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=7bc333bc02e737f7caab1f4b4d34ec0c131dc2dd;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=74fb1c51ebb37d10185dced775be0af3829a7c41;hpb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 74fb1c5..7bc333b 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -55,12 +55,13 @@ SharedRAbundVector::SharedRAbundVector(string id, vector rav) : Data } -/***********************************************************************/ +***********************************************************************/ //reads a shared file SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) { try { - m->namesOfGroups.clear(); - + m->clearAllGroups(); + vector allGroups; + int num, inputData, count; count = 0; string holdLabel, nextLabel, groupN; @@ -71,7 +72,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //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" @@ -94,16 +95,36 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), m->binLabelsInFile.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->binLabelsInFile.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->binLabelsInFile.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; - //read in first row since you know there is at least 1 group. - f >> groupN >> num; - holdLabel = label; //add new vector to lookup @@ -112,7 +133,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), 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 SharedRAbundVector(); @@ -152,8 +173,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (f.eof() != true) { f >> nextLabel; } } - m->saveNextLabel = nextLabel; - + m->saveNextLabel = nextLabel; + m->setAllGroups(allGroups); } catch(exception& e) { m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); @@ -190,6 +211,18 @@ int SharedRAbundVector::getAbundance(int index){ return data[index].abundance; } +/***********************************************************************/ +//returns vector of abundances +vector SharedRAbundVector::getAbundances(){ + vector abunds; + for (int i = 0; i < data.size(); i++) { + abunds.push_back(data[i].abundance); + } + + return abunds; +} + + /***********************************************************************/ int SharedRAbundVector::numNZ(){ @@ -334,13 +367,19 @@ int SharedRAbundVector::size(){ /***********************************************************************/ void SharedRAbundVector::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); + 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->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } output << binLabel << '\t'; @@ -349,10 +388,16 @@ void SharedRAbundVector::printHeaders(ostream& output){ }else { for (int i = 0; i < numBins; i++) { //if there is a bin label use it otherwise make one - string mybinLabel = "Otu" + toString(i+1); - if (i < m->currentBinLabels.size()) { mybinLabel = 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->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } - output << mybinLabel << '\t'; + output << binLabel << '\t'; } output << endl; @@ -393,7 +438,7 @@ int SharedRAbundVector::getGroupIndex() { return index; } void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; } /***********************************************************************/ int SharedRAbundVector::getNumBins(){ - return numBins; + return numBins; } /***********************************************************************/ @@ -418,12 +463,15 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ 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) { remove = true; delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); @@ -456,6 +504,7 @@ int SharedRAbundVector::eliminateZeroOTUS(vector& thislooku //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; } @@ -472,7 +521,13 @@ int SharedRAbundVector::eliminateZeroOTUS(vector& thislooku } //if there is a bin label use it otherwise make one - string binLabel = "Otu" + (i+1); + 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->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } newBinLabels.push_back(binLabel);