X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=9b2bb678ca7688777aa87a9f60015baba5d336d9;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=1440ee1135dfac48dfef52a7d47df39c56264eaa;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 1440ee1..9b2bb67 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -55,11 +55,12 @@ 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; @@ -68,12 +69,64 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear(); - if (m->saveNextLabel == "") { f >> label; } - else { label = m->saveNextLabel; } + //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->binLabelsInFile.clear(); + while(!iStringStream.eof()){ + if (m->control_pressed) { break; } + string temp; + iStringStream >> temp; m->gobble(iStringStream); + + m->binLabelsInFile.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->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; + + 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; - //read in first row since you know there is at least 1 group. - f >> groupN >> num; - holdLabel = label; //add new vector to lookup @@ -82,16 +135,16 @@ 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); - //numSeqs += inputData; - //numBins++; + if (inputData > maxRank) { maxRank = inputData; } } @@ -102,9 +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(); @@ -115,6 +169,8 @@ 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 } @@ -122,9 +178,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (f.eof() != true) { f >> nextLabel; } } - m->saveNextLabel = nextLabel; - + m->setAllGroups(allGroups); } catch(exception& e) { m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); @@ -161,6 +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(){ @@ -301,8 +368,54 @@ int SharedRAbundVector::size(){ return data.size(); } + /***********************************************************************/ -void SharedRAbundVector::print(ostream& output){ +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"; + 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'; + } + 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->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + + output << binLabel << '\t'; + } + + output << endl; + } + m->printedHeaders = true; + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "printHeaders"); + exit(1); + } +} +/***********************************************************************/ +void SharedRAbundVector::print(ostream& output) { try { output << numBins << '\t'; @@ -330,7 +443,7 @@ int SharedRAbundVector::getGroupIndex() { return index; } void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; } /***********************************************************************/ int SharedRAbundVector::getNumBins(){ - return numBins; + return numBins; } /***********************************************************************/ @@ -355,12 +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); @@ -392,6 +508,8 @@ 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; } @@ -406,12 +524,25 @@ int SharedRAbundVector::eliminateZeroOTUS(vector& thislooku 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->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + + newBinLabels.push_back(binLabel); } } for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } thislookup = newLookup; + m->currentBinLabels = newBinLabels; return 0;