X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=37cd28315a5c1928e965f7be8eef7ae0ef408692;hb=d945488119ad368b180537f36ed40298ff170f39;hp=6aeb4ce5ab19a655c832343cb601c715777c2534;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git diff --git a/sharedordervector.cpp b/sharedordervector.cpp index 6aeb4ce..37cd283 100644 --- a/sharedordervector.cpp +++ b/sharedordervector.cpp @@ -7,12 +7,8 @@ * */ -using namespace std; - - #include "sharedordervector.h" -#include "utilities.hpp" -#include +#include "sharedutilities.h" /***********************************************************************/ @@ -30,13 +26,13 @@ SharedOrderVector::SharedOrderVector(string id, vector ov) : //This function is used to read a .shared file for the collect.shared, rarefaction.shared and summary.shared commands //if you don't use a list and groupfile. -SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { +SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { //reads in a shared file try { - globaldata = GlobalData::getInstance(); - - if (globaldata->gGroupmap == NULL) { groupmap = new GroupMap(); } + maxRank = 0; numBins = 0; numSeqs = 0; + + groupmap = new GroupMap(); - int num, inputData, pos, count; + int num, inputData, count; count = 0; numSeqs = 0; string holdLabel, nextLabel, groupN; individual newguy; @@ -45,22 +41,22 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { f >> label >> groupN >> num; holdLabel = label; - if (globaldata->gGroupmap == NULL) { - //save group in groupmap - groupmap->namesOfGroups.push_back(groupN); - groupmap->groupIndex[groupN] = 0; - } + + //save group in groupmap + groupmap->namesOfGroups.push_back(groupN); + groupmap->groupIndex[groupN] = 0; + for(int i=0;i> inputData; + for (int j = 0; j < inputData; j++) { - push_back(i+1, i+1, groupN); + push_back(i, i, groupN); numSeqs++; } } - //save position in file in case next line is a new label. - pos = f.tellg(); + m->gobble(f); if (f.eof() != true) { f >> nextLabel; } @@ -69,61 +65,55 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() { f >> groupN >> num; count++; - if (globaldata->gGroupmap == NULL) { - //save group in groupmap - groupmap->namesOfGroups.push_back(groupN); - groupmap->groupIndex[groupN] = count; - } + + //save group in groupmap + groupmap->namesOfGroups.push_back(groupN); + groupmap->groupIndex[groupN] = count; + for(int i=0;i> inputData; + for (int j = 0; j < inputData; j++) { - push_back(i+1, i+1, groupN); + push_back(i, i, groupN); numSeqs++; } } - //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; } + for (int i = 0; i < nextLabel.length(); i++) { f.unget(); } + m->namesOfGroups = groupmap->namesOfGroups; + updateStats(); + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "SharedOrderVector"); exit(1); } } /***********************************************************************/ int SharedOrderVector::getNumBins(){ - if(needToUpdate == 1){ updateStats(); } return numBins; } /***********************************************************************/ int SharedOrderVector::getNumSeqs(){ - if(needToUpdate == 1){ updateStats(); } return numSeqs; } /***********************************************************************/ int SharedOrderVector::getMaxRank(){ - if(needToUpdate == 1){ updateStats(); } return maxRank; } @@ -137,8 +127,8 @@ void SharedOrderVector::set(int index, int binNumber, int abund, string groupNam data[index].group = groupName; data[index].bin = binNumber; data[index].abundance = abund; - needToUpdate = 1; - + //if (abund > maxRank) { maxRank = abund; } + updateStats(); } /***********************************************************************/ @@ -149,15 +139,18 @@ individual SharedOrderVector::get(int index){ /***********************************************************************/ - +//commented updateStats out to improve speed, but whoever calls this must remember to update when they are done with all the pushbacks they are doing void SharedOrderVector::push_back(int binNumber, int abund, string groupName){ individual newGuy; newGuy.group = groupName; newGuy.abundance = abund; newGuy.bin = binNumber; data.push_back(newGuy); - needToUpdate = 1; + //numSeqs++; + //numBins++; + //if (abund > maxRank) { maxRank = abund; } + //updateStats(); } /***********************************************************************/ @@ -172,20 +165,23 @@ void SharedOrderVector::print(ostream& output){ output << endl; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "print"); exit(1); } } +/***********************************************************************/ +void SharedOrderVector::clear(){ + numBins = 0; + maxRank = 0; + numSeqs = 0; + data.clear(); +} /***********************************************************************/ void SharedOrderVector::resize(int){ - cout << "resize() did nothing in class SharedOrderVector"; + m->mothurOut("resize() did nothing in class SharedOrderVector"); } /***********************************************************************/ @@ -228,13 +224,9 @@ RAbundVector SharedOrderVector::getRAbundVector(){ return rav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getRAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/ @@ -252,11 +244,7 @@ OrderVector SharedOrderVector::getOrderVector(map* nameMap = NULL) { return ov; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getOrderVector"); exit(1); } } @@ -286,14 +274,26 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) { return sharedRav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************************/ +vector SharedOrderVector::getSharedRAbundVector() { + try { + SharedUtil* util; + util = new SharedUtil(); + vector lookup; + + util->setGroups(m->Groups, m->namesOfGroups); + util->getSharedVectors(m->Groups, lookup, this); + + return lookup; + } + catch(exception& e) { + m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector"); exit(1); } - } /***********************************************************************/ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) { @@ -304,19 +304,15 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector"); exit(1); } - } /***********************************************************************/ SharedOrderVector SharedOrderVector::getSharedOrderVector(){ + random_shuffle(data.begin(), data.end()); return *this; } @@ -329,34 +325,23 @@ void SharedOrderVector::updateStats(){ numBins = 0; maxRank = 0; - for(int i=0;i hold(numSeqs); - + numSeqs = data.size(); + + vector hold(numSeqs, 0); for(int i=0;i numBins) { numBins = data[i].bin; } - if(data[i].abundance > maxRank) { maxRank = data[i].abundance; } + if(hold[i] > 0) { numBins++; } + if(hold[i] > maxRank) { maxRank = hold[i]; } } - numBins++; //if you have 10 bins largest .bin is 9 since we start at 0. + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedOrderVector", "updateStats"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SharedOrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/