X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=a050ab3fe71998b5a8a6abf2b34b0e67f0083808;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=386017d9367f7eed2e5bfd984ffedb775a26a31a;hpb=6f9dc7ca71d7b8ed4aba2824f76ae6b29da89f3b;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 386017d..a050ab3 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -7,9 +7,6 @@ * */ - -using namespace std; - #include "sharedrabundvector.h" #include "sabundvector.hpp" #include "ordervector.hpp" @@ -18,11 +15,18 @@ using namespace std; /***********************************************************************/ -SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {}; +SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();} +/***********************************************************************/ + +SharedRAbundVector::~SharedRAbundVector() { + //for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + +} /***********************************************************************/ 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++) { @@ -30,7 +34,7 @@ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBin newGuy.abundance = 0; data.push_back(newGuy); } -}; +} /*********************************************************************** @@ -47,11 +51,7 @@ SharedRAbundVector::SharedRAbundVector(string id, vector rav) : Data } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); exit(1); } } @@ -65,16 +65,19 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } - int num, inputData, pos, count; + int num, inputData, count; count = 0; string holdLabel, nextLabel, groupN; individual newguy; - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } - lookup.clear(); + 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; } //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 @@ -93,19 +96,17 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), for(int i=0;i> inputData; - lookup[0]->push_back(inputData, i, groupN); //abundance, bin, group - push_back(inputData, i, groupN); - numSeqs += inputData; - numBins++; + lookup[0]->push_back(inputData, groupN); //abundance, bin, group + push_back(inputData, groupN); + //numSeqs += inputData; + //numBins++; if (inputData > maxRank) { maxRank = inputData; } - } - //save position in file in case next line is a new label. - pos = f.tellg(); - - if (f.eof() != true) { f >> nextLabel; } + m->gobble(f); + if (!(f.eof())) { f >> nextLabel; } + //read the rest of the groups info in while ((nextLabel == holdLabel) && (f.eof() != true)) { f >> groupN >> num; @@ -113,6 +114,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (globaldata->gGroupmap == NULL) { //save group in groupmap + groupmap->namesOfGroups.push_back(groupN); groupmap->groupIndex[groupN] = count; } @@ -126,39 +128,27 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), //fill vector. for(int i=0;i> inputData; - lookup[count]->push_back(inputData, i, groupN); //abundance, bin, group + lookup[count]->push_back(inputData, groupN); //abundance, bin, group } - //save position in file in case next line is a new label. - pos = f.tellg(); - + m->gobble(f); + if (f.eof() != true) { f >> nextLabel; } } - - //put file pointer back since you are now at a new distance label - f.seekg(pos, ios::beg); - if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } + globaldata->saveNextLabel = nextLabel; + + if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); exit(1); } } /***********************************************************************/ -SharedRAbundVector::~SharedRAbundVector() { - -} - -/***********************************************************************/ - void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){ try { int oldBinSize = data[binNumber].abundance; @@ -170,11 +160,7 @@ void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){ numSeqs += (newBinSize - oldBinSize); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "set"); exit(1); } } @@ -218,12 +204,22 @@ vector SharedRAbundVector::getData(){ } /***********************************************************************/ -void SharedRAbundVector::push_back(int binSize, int otu, string groupName){ +void SharedRAbundVector::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(); +} +/***********************************************************************/ + +void SharedRAbundVector::push_back(int binSize, string groupName){ try { individual newGuy; newGuy.abundance = binSize; newGuy.group = groupName; - newGuy.bin = otu; + newGuy.bin = data.size(); data.push_back(newGuy); numBins++; @@ -235,11 +231,7 @@ void SharedRAbundVector::push_back(int binSize, int otu, string groupName){ numSeqs += binSize; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "push_back"); exit(1); } } @@ -263,11 +255,7 @@ void SharedRAbundVector::insert(int binSize, int otu, string groupName){ numSeqs += binSize; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "insert"); exit(1); } } @@ -291,11 +279,7 @@ void SharedRAbundVector::push_front(int binSize, int otu, string groupName){ numSeqs += binSize; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "push_front"); exit(1); } } @@ -341,11 +325,7 @@ void SharedRAbundVector::print(ostream& output){ output << endl; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "print"); exit(1); } } @@ -391,24 +371,101 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ util = new SharedUtil(); util->setGroups(globaldata->Groups, globaldata->gGroupmap->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) { - delete lookup[i]; + remove = true; + delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); i--; } } - + + delete util; + + if (remove) { eliminateZeroOTUS(lookup); } + return lookup; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +int SharedRAbundVector::eliminateZeroOTUS(vector& thislookup) { + try { + + vector newLookup; + for (int i = 0; i < thislookup.size(); i++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(thislookup[i]->getLabel()); + temp->setGroup(thislookup[i]->getGroup()); + newLookup.push_back(temp); + } + + //for each bin + 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()); + } + } + } + + for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } + + thislookup = newLookup; + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "eliminateZeroOTUS"); + exit(1); + } + } + +/***********************************************************************/ +vector SharedRAbundVector::getSharedRAbundFloatVectors(vector thislookup){ + try { + vector newLookupFloat; + for (int i = 0; i < lookup.size(); i++) { + SharedRAbundFloatVector* temp = new SharedRAbundFloatVector(); + temp->setLabel(thislookup[i]->getLabel()); + temp->setGroup(thislookup[i]->getGroup()); + newLookupFloat.push_back(temp); + } + + for (int i = 0; i < thislookup.size(); i++) { + + for (int j = 0; j < thislookup[i]->getNumBins(); j++) { + + if (m->control_pressed) { return newLookupFloat; } + + int abund = thislookup[i]->getAbundance(j); + + float relabund = abund / (float) thislookup[i]->getNumSeqs(); + + newLookupFloat[i]->push_back(relabund, thislookup[i]->getGroup()); + } + } + + return newLookupFloat; + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); exit(1); } } @@ -416,20 +473,19 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ RAbundVector SharedRAbundVector::getRAbundVector() { try { - RAbundVector rav(data.size()); + RAbundVector rav; for (int i = 0; i < data.size(); i++) { - rav.set(i, data[i].abundance); + if(data[i].abundance != 0) { + rav.push_back(data[i].abundance); + } } - + + rav.setLabel(label); return rav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "getRAbundVector"); exit(1); } } @@ -444,11 +500,7 @@ RAbundVector SharedRAbundVector::getRAbundVector2() { return rav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "getRAbundVector2"); exit(1); } } @@ -470,11 +522,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){ return sav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "getSharedSAbundVector"); exit(1); } } @@ -493,11 +541,7 @@ SAbundVector SharedRAbundVector::getSAbundVector() { return sav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "getSAbundVector"); exit(1); } } @@ -521,11 +565,7 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { return ov; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedRAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedRAbundVector", "getSharedOrderVector"); exit(1); } } @@ -534,23 +574,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }