X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=a5e17c2454d615be3a1c75f8b57fbe54ef85acd8;hb=8742edef7a51b82834289e570d336f5a81ba1f2b;hp=f7405aefab95989d77bf3efec0ead7a44197b752;hpb=7ae40733a270f73ec8a331540cc7f28fd60b24fc;p=mothur.git diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp index f7405ae..a5e17c2 100644 --- a/sharedrabundfloatvector.cpp +++ b/sharedrabundfloatvector.cpp @@ -12,14 +12,14 @@ /***********************************************************************/ -SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {globaldata = GlobalData::getInstance();} +SharedRAbundFloatVector::SharedRAbundFloatVector() : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) {} /***********************************************************************/ SharedRAbundFloatVector::~SharedRAbundFloatVector() {} /***********************************************************************/ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank(0.0), numBins(n), numSeqs(0.0) { - globaldata = GlobalData::getInstance(); + individualFloat newGuy; //initialize data for (int i=0; i< n; i++) { @@ -32,9 +32,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(int n) : DataVector(), maxRank( //reads a shared file SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), maxRank(0.0), numBins(0), numSeqs(0.0) { try { - globaldata = GlobalData::getInstance(); - if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } + m->namesOfGroups.clear(); int num, count; float inputData; @@ -45,8 +44,42 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear(); + //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; + } + }else { label = m->saveNextLabel; } + + //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 >> label >> groupN >> num; + f >> groupN >> num; + holdLabel = label; //add new vector to lookup @@ -55,11 +88,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma 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; - } + m->namesOfGroups.push_back(groupN); //fill vector. data = first sharedrabund in file for(int i=0;i> groupN >> num; count++; - if (globaldata->gGroupmap == NULL) { - //save group in groupmap - groupmap->namesOfGroups.push_back(groupN); - groupmap->groupIndex[groupN] = count; - } + m->namesOfGroups.push_back(groupN); //add new vector to lookup temp = new SharedRAbundFloatVector(); @@ -103,11 +128,8 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma if (f.eof() != true) { f >> nextLabel; } } - //put file pointer back since you are now at a new distance label - for (int i = 0; i < nextLabel.length(); i++) { f.unget(); } + m->saveNextLabel = nextLabel; - if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } - } catch(exception& e) { m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector"); @@ -128,11 +150,20 @@ void SharedRAbundFloatVector::set(int binNumber, float newBinSize, string groupn numSeqs += (newBinSize - oldBinSize); } catch(exception& e) { - m->errorOut(e, "SharedRAbundVector", "set"); + m->errorOut(e, "SharedRAbundFloatVector", "set"); exit(1); } } +/***********************************************************************/ +void SharedRAbundFloatVector::clear(){ + numBins = 0; + maxRank = 0; + numSeqs = 0; + data.clear(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } + lookup.clear(); +} /***********************************************************************/ float SharedRAbundFloatVector::getAbundance(int index){ return data[index].abundance; @@ -217,6 +248,39 @@ int SharedRAbundFloatVector::size(){ return data.size(); } /***********************************************************************/ +void SharedRAbundFloatVector::printHeaders(ostream& output){ + try { + 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]; } + + 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" + toString(i+1); + 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 SharedRAbundFloatVector::print(ostream& output){ try { output << numBins << '\t'; @@ -275,18 +339,22 @@ vector SharedRAbundFloatVector::getSharedRAbundFloatVe SharedUtil* util; util = new SharedUtil(); - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups); - + util->setGroups(m->Groups, m->namesOfGroups); + + 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->Groups) == false) { delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); i--; + remove = true; } } delete util; + + if (remove) { eliminateZeroOTUS(lookup); } return lookup; } @@ -397,6 +465,54 @@ OrderVector SharedRAbundFloatVector::getOrderVector(map* nameMap = N exit(1); } } - +//********************************************************************************************************************** +int SharedRAbundFloatVector::eliminateZeroOTUS(vector& thislookup) { + try { + + vector newLookup; + for (int i = 0; i < thislookup.size(); i++) { + SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(); + temp->setLabel(thislookup[i]->getLabel()); + temp->setGroup(thislookup[i]->getGroup()); + newLookup.push_back(temp); + } + + //for each bin + vector newBinLabels; + 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; } + + //look at each sharedRabund and make sure they are not all zero + bool allZero = true; + for (int j = 0; j < thislookup.size(); j++) { + if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; } + } + + //if they are not all zero add this bin + if (!allZero) { + 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" + toString(i+1); + 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; + + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundFloatVector", "eliminateZeroOTUS"); + exit(1); + } +} /***********************************************************************/