X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundvector.cpp;h=3901650cef965dc7a3c0126ecb54a8fb425e434d;hp=a050ab3fe71998b5a8a6abf2b34b0e67f0083808;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=37eac2026d91179acda0494c4dcca22f176551b9 diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index a050ab3..3901650 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -14,8 +14,7 @@ /***********************************************************************/ - -SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();} +SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {} /***********************************************************************/ SharedRAbundVector::~SharedRAbundVector() { @@ -26,7 +25,6 @@ SharedRAbundVector::~SharedRAbundVector() { /***********************************************************************/ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBins(n), numSeqs(0) { - globaldata = GlobalData::getInstance(); individual newGuy; //initialize data for (int i=0; i< n; i++) { @@ -57,13 +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 { - globaldata = GlobalData::getInstance(); - - if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } + m->clearAllGroups(); + vector allGroups; int num, inputData, count; count = 0; @@ -72,12 +69,62 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear(); - if (globaldata->saveNextLabel == "") { f >> label; } - else { label = globaldata->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; + } + + //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 @@ -86,11 +133,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), 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;ipush_back(inputData, groupN); //abundance, bin, group push_back(inputData, groupN); - //numSeqs += inputData; - //numBins++; + if (inputData > maxRank) { maxRank = inputData; } } @@ -112,12 +154,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), f >> 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 SharedRAbundVector(); @@ -128,6 +165,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //fill vector. for(int i=0;i> inputData; + lookup[count]->push_back(inputData, groupN); //abundance, bin, group } @@ -135,11 +173,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (f.eof() != true) { f >> nextLabel; } } - - globaldata->saveNextLabel = nextLabel; - - if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } - + m->saveNextLabel = nextLabel; + m->setAllGroups(allGroups); } catch(exception& e) { m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); @@ -316,8 +351,54 @@ 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'; @@ -345,7 +426,7 @@ int SharedRAbundVector::getGroupIndex() { return index; } void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; } /***********************************************************************/ int SharedRAbundVector::getNumBins(){ - return numBins; + return numBins; } /***********************************************************************/ @@ -370,12 +451,15 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ 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) { remove = true; delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); @@ -407,6 +491,8 @@ 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; } @@ -421,12 +507,25 @@ 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;