X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=sharedrabundvector.cpp;h=a050ab3fe71998b5a8a6abf2b34b0e67f0083808;hb=e6c4a7223199d800d496356604eb34dfe273673d;hp=846f9cdb705c7a801097feaeca59272d4001d361;hpb=eb1c88346fb246e95a6b38935b103f95e38b82ca;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 846f9cd..a050ab3 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -7,23 +7,26 @@ * */ - -using namespace std; - #include "sharedrabundvector.h" -#include "utilities.hpp" #include "sabundvector.hpp" #include "ordervector.hpp" -#include +#include "sharedutilities.h" /***********************************************************************/ -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++) { @@ -31,7 +34,7 @@ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBin newGuy.abundance = 0; data.push_back(newGuy); } -}; +} /*********************************************************************** @@ -48,55 +51,100 @@ 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); } } -/*********************************************************************** - - +/***********************************************************************/ +//reads a shared file SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) { try { - int i, num; - string holdLabel, group - individual newGuy; + globaldata = GlobalData::getInstance(); - f >> label >> group >> num; + if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } - //initialize data - for (i=0; isaveNextLabel == "") { f >> label; } + else { label = globaldata->saveNextLabel; } + + //read in first row since you know there is at least 1 group. + f >> groupN >> num; + + holdLabel = label; + + //add new vector to lookup + SharedRAbundVector* temp = new SharedRAbundVector(); + lookup.push_back(temp); + 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; } - int inputData; - - for(int i=0;i> inputData; - set(i, inputData); + + lookup[0]->push_back(inputData, groupN); //abundance, bin, group + push_back(inputData, groupN); + //numSeqs += inputData; + //numBins++; + if (inputData > maxRank) { maxRank = inputData; } + } + + 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; + count++; + + if (globaldata->gGroupmap == NULL) { + //save group in groupmap + + groupmap->namesOfGroups.push_back(groupN); + groupmap->groupIndex[groupN] = count; + } + + //add new vector to lookup + temp = new SharedRAbundVector(); + lookup.push_back(temp); + lookup[count]->setLabel(label); + lookup[count]->setGroup(groupN); + + //fill vector. + for(int i=0;i> inputData; + lookup[count]->push_back(inputData, groupN); //abundance, bin, group + } + + m->gobble(f); + + if (f.eof() != true) { f >> nextLabel; } } + + 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"; + m->errorOut(e, "SharedRAbundVector", "SharedRAbundVector"); 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"; - exit(1); - } -} - -/***********************************************************************/ - -SharedRAbundVector::~SharedRAbundVector() { - } /***********************************************************************/ @@ -112,11 +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); } } @@ -160,12 +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++; @@ -177,19 +231,63 @@ 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"; + m->errorOut(e, "SharedRAbundVector", "push_back"); 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"; +} + +/***********************************************************************/ + +void SharedRAbundVector::insert(int binSize, int otu, string groupName){ + try { + individual newGuy; + newGuy.abundance = binSize; + newGuy.group = groupName; + newGuy.bin = otu; + + data.insert(data.begin()+otu, newGuy); + numBins++; + + if(binSize > maxRank){ + maxRank = binSize; + } + + numSeqs += binSize; + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "insert"); exit(1); } } /***********************************************************************/ -void SharedRAbundVector::pop_back(){ +void SharedRAbundVector::push_front(int binSize, int otu, string groupName){ + try { + individual newGuy; + newGuy.abundance = binSize; + newGuy.group = groupName; + newGuy.bin = otu; + + data.insert(data.begin(), newGuy); + numBins++; + + if(binSize > maxRank){ + maxRank = binSize; + } + + numSeqs += binSize; + } + catch(exception& e) { + m->errorOut(e, "SharedRAbundVector", "push_front"); + exit(1); + } +} +/***********************************************************************/ +void SharedRAbundVector::pop_back(){ + numSeqs -= data[data.size()-1].abundance; + numBins--; return data.pop_back(); } @@ -223,15 +321,11 @@ void SharedRAbundVector::print(ostream& output){ try { output << numBins << '\t'; - for(int i=0;ierrorOut(e, "SharedRAbundVector", "print"); exit(1); } } @@ -271,23 +365,127 @@ SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){ return *this; } /***********************************************************************/ +vector SharedRAbundVector::getSharedRAbundVectors(){ + try { + SharedUtil* util; + 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) { + 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) { + m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); + exit(1); + } +} +//********************************************************************************************************************** +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); + } +} +/***********************************************************************/ 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); } } @@ -302,11 +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); } } @@ -328,11 +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); } } @@ -351,11 +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); } } @@ -374,14 +560,12 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { random_shuffle(ov.begin(), ov.end()); ov.setLabel(label); + ov.updateStats(); + 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); } } @@ -390,23 +574,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }