X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=sharedrabundvector.cpp;h=d135091c3301ed428a8e8e0391a2120643a21520;hb=86b6cc7ce1ec7fce12cdfdd6225de4dee7cfbdbf;hp=f60562a75a5202a366a6bf9cbd831421133feab0;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index f60562a..d135091 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -16,6 +16,12 @@ /***********************************************************************/ 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]; } + +} /***********************************************************************/ @@ -45,11 +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); } } @@ -63,12 +65,12 @@ 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]; } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear(); //read in first row since you know there is at least 1 group. @@ -91,16 +93,15 @@ 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(); + gobble(f); if (f.eof() != true) { f >> nextLabel; } @@ -124,27 +125,22 @@ 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(); - + 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); + for (int i = 0; i < nextLabel.length(); i++) { f.unget(); } 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); } } @@ -162,11 +158,7 @@ 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); } } @@ -210,12 +202,12 @@ vector SharedRAbundVector::getData(){ } /***********************************************************************/ -void SharedRAbundVector::push_back(int binSize, int otu, string groupName){ +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++; @@ -227,11 +219,7 @@ 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); } } @@ -255,11 +243,7 @@ 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); } } @@ -283,11 +267,7 @@ 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); } } @@ -333,11 +313,7 @@ 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); } } @@ -387,20 +363,18 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ 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]; + delete lookup[i]; lookup[i] = NULL; lookup.erase(lookup.begin()+i); i--; } } - + + delete util; + 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"; - 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"; + m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors"); exit(1); } } @@ -408,20 +382,19 @@ 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); } } @@ -436,11 +409,7 @@ 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); } } @@ -462,11 +431,7 @@ 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); } } @@ -485,11 +450,7 @@ 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); } } @@ -513,11 +474,7 @@ 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); } } @@ -538,11 +495,7 @@ OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) 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", "getOrderVector"); exit(1); } }