X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundvector.cpp;h=3901650cef965dc7a3c0126ecb54a8fb425e434d;hp=9634613ded396633062188934cab9f1f4a40e9dc;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445 diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 9634613..3901650 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -7,17 +7,20 @@ * */ - -using namespace std; - #include "sharedrabundvector.h" #include "sabundvector.hpp" #include "ordervector.hpp" +#include "sharedutilities.h" /***********************************************************************/ +SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {} +/***********************************************************************/ + +SharedRAbundVector::~SharedRAbundVector() { + //for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } -SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {}; +} /***********************************************************************/ @@ -29,7 +32,7 @@ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBin newGuy.abundance = 0; data.push_back(newGuy); } -}; +} /*********************************************************************** @@ -46,55 +49,137 @@ 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; + m->clearAllGroups(); + vector allGroups; - f >> label >> group >> num; + int num, inputData, count; + count = 0; + string holdLabel, nextLabel, groupN; + individual newguy; - //initialize data - for (i=0; isaveNextLabel == "") { + f >> label; - for(int i=0;i> 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; + + holdLabel = label; + + //add new vector to lookup + SharedRAbundVector* temp = new SharedRAbundVector(); + lookup.push_back(temp); + lookup[0]->setLabel(label); + lookup[0]->setGroup(groupN); + + allGroups.push_back(groupN); + + //fill vector. data = first sharedrabund in file + for(int i=0;i> inputData; - set(i, inputData); + + lookup[0]->push_back(inputData, groupN); //abundance, bin, group + push_back(inputData, groupN); + + 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++; + + allGroups.push_back(groupN); + + //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; } } + m->saveNextLabel = nextLabel; + m->setAllGroups(allGroups); } 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() { - } /***********************************************************************/ @@ -110,11 +195,7 @@ 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); } } @@ -158,12 +239,22 @@ 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++; @@ -175,11 +266,7 @@ 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); } } @@ -203,11 +290,7 @@ 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); } } @@ -231,11 +314,7 @@ 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); } } @@ -272,8 +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'; @@ -281,11 +406,7 @@ 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); } } @@ -305,7 +426,7 @@ int SharedRAbundVector::getGroupIndex() { return index; } void SharedRAbundVector::setGroupIndex(int vIndex) { index = vIndex; } /***********************************************************************/ int SharedRAbundVector::getNumBins(){ - return numBins; + return numBins; } /***********************************************************************/ @@ -325,23 +446,145 @@ SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){ return *this; } /***********************************************************************/ +vector SharedRAbundVector::getSharedRAbundVectors(){ + try { + SharedUtil* util; + util = new SharedUtil(); + + 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->getGroups()) == 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 + 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; } + + //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"; + 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; + + } + 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); } } @@ -356,11 +599,7 @@ 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); } } @@ -382,11 +621,7 @@ 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); } } @@ -405,11 +640,7 @@ 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); } } @@ -428,14 +659,12 @@ 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); } } @@ -444,23 +673,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }