X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.cpp;h=9276b7bfdc0ae441a883f42ddd0aabcddf1f04bd;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=246712824907240690d86c07632ed1cc58966182;hpb=016a30dacbe75869aef5fdb58d2d1bf9eb8f9b33;p=mothur.git diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp index 2467128..9276b7b 100644 --- a/sharedrabundvector.cpp +++ b/sharedrabundvector.cpp @@ -51,11 +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); } } @@ -74,11 +70,15 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(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(); + if (globaldata->saveNextLabel == "") { f >> label; } + else { label = globaldata->saveNextLabel; } + //read in first row since you know there is at least 1 group. - f >> label >> groupN >> num; + f >> groupN >> num; + holdLabel = label; //add new vector to lookup @@ -97,16 +97,17 @@ 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; } - } - if (f.eof() != true) { f >> nextLabel; } + 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; @@ -114,6 +115,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0), if (globaldata->gGroupmap == NULL) { //save group in groupmap + groupmap->namesOfGroups.push_back(groupN); groupmap->groupIndex[groupN] = count; } @@ -127,25 +129,21 @@ 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 } + m->gobble(f); if (f.eof() != true) { f >> nextLabel; } } - - //put file pointer back since you are now at a new distance label - for (int i = 0; i < nextLabel.length(); i++) { f.unget(); } + + 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); } } @@ -163,11 +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); } } @@ -211,12 +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++; @@ -228,11 +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); } } @@ -256,11 +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); } } @@ -284,11 +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); } } @@ -334,11 +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); } } @@ -388,7 +376,7 @@ 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--; } @@ -399,11 +387,7 @@ vector SharedRAbundVector::getSharedRAbundVectors(){ 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); } } @@ -411,20 +395,19 @@ 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); } } @@ -439,11 +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); } } @@ -465,11 +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); } } @@ -488,11 +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); } } @@ -516,11 +487,7 @@ 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); } } @@ -529,23 +496,19 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() { OrderVector SharedRAbundVector::getOrderVector(map* nameMap = NULL) { try { OrderVector ov; - - for(int i=0;ierrorOut(e, "SharedRAbundVector", "getOrderVector"); exit(1); } }