X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=0f2e48e8ac7bbdc18b10f15f1b764aed7ee58890;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=74fb1c51ebb37d10185dced775be0af3829a7c41;hpb=1bf53bca7e26bf091588bc8ca6e68cbfae1df6fe;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 74fb1c5..0f2e48e 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" @@ -85,25 +86,47 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //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; + + if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(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 @@ -112,11 +135,12 @@ 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> inputData; + if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); } lookup[0]->push_back(inputData, groupN); //abundance, bin, group push_back(inputData, groupN); @@ -131,9 +155,10 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //read the rest of the groups info in while ((nextLabel == holdLabel) && (f.eof() != true)) { f >> groupN >> num; + if (m->debug) { m->mothurOut("[DEBUG]: "+ groupN + '\t' + toString(num)); } count++; - m->namesOfGroups.push_back(groupN); + allGroups.push_back(groupN); //add new vector to lookup temp = new SharedRAbundVector(); @@ -144,6 +169,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //fill vector. for(int i=0;i> inputData; + if (m->debug) { m->mothurOut("[DEBUG]: OTU" + toString(i+1)+ '\t' +toString(inputData)); } lookup[count]->push_back(inputData, groupN); //abundance, bin, group } @@ -152,8 +178,8 @@ 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 +216,18 @@ 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(){ @@ -334,14 +372,20 @@ 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); - 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'; } @@ -349,15 +393,21 @@ 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->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; } - output << mybinLabel << '\t'; + output << binLabel << '\t'; } output << endl; } - m->printedHeaders = true; + m->printedSharedHeaders = true; } catch(exception& e) { m->errorOut(e, "SharedRAbundVector", "printHeaders"); @@ -393,7 +443,7 @@ int SharedRAbundVector::getGroupIndex() { return index; } void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; } /***********************************************************************/ int SharedRAbundVector::getNumBins(){ - return numBins; + return numBins; } /***********************************************************************/ @@ -418,12 +468,15 @@ 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 +509,7 @@ 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; } @@ -472,8 +526,14 @@ int SharedRAbundVector::eliminateZeroOTUS(vector& thislooku } //if there is a bin label use it otherwise make one - string binLabel = "Otu" + (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); } @@ -482,7 +542,7 @@ int SharedRAbundVector::eliminateZeroOTUS(vector& thislooku for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } thislookup = newLookup; - m->currentBinLabels = newBinLabels; + m->currentSharedBinLabels = newBinLabels; return 0;