X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=9276b7bfdc0ae441a883f42ddd0aabcddf1f04bd;hb=2e77272b6f5987bd2bde592bb15262a8c69ea9e0;hp=9634613ded396633062188934cab9f1f4a40e9dc;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 9634613..9276b7b 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -7,21 +7,26 @@ * */ - -using namespace std; - #include "sharedrabundvector.h" #include "sabundvector.hpp" #include "ordervector.hpp" +#include "sharedutilities.h" + +/***********************************************************************/ +SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();} /***********************************************************************/ -SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {}; +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++) { @@ -29,7 +34,7 @@ SharedRAbundVector::SharedRAbundVector(int n) : DataVector(), maxRank(0), numBin newGuy.abundance = 0; data.push_back(newGuy); } -}; +} /*********************************************************************** @@ -46,59 +51,105 @@ 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"; - 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; @@ -110,11 +161,7 @@ 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 +205,22 @@ 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 +232,7 @@ 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 +256,7 @@ 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 +280,7 @@ 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); } } @@ -281,11 +326,7 @@ 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); } } @@ -325,23 +366,48 @@ SharedRAbundVector SharedRAbundVector::getSharedRAbundVector(){ return *this; } /***********************************************************************/ +vector SharedRAbundVector::getSharedRAbundVectors(){ + try { + SharedUtil* util; + util = new SharedUtil(); + + util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups); + + 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]; lookup[i] = NULL; + lookup.erase(lookup.begin()+i); + i--; + } + } + + delete util; + + return lookup; + } + 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 +422,7 @@ 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 +444,7 @@ 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 +463,7 @@ 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 +482,12 @@ 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 +496,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }