X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;h=cc3cd8df4205e2f37182a8a80037bc02bb37ca45;hb=cf9a187f89caf821e454d1547d9b3893e17a1e76;hp=3cb3e9e57c4da06f0589272cff4b3e97bd92eea4;hpb=301b61cb98aaa4641f8701f43cf830c0fa44fac1;p=mothur.git diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp index 3cb3e9e..cc3cd8d 100644 --- a/sharedlistvector.cpp +++ b/sharedlistvector.cpp @@ -44,11 +44,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function SharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "SharedListVector"); exit(1); } } @@ -67,11 +63,7 @@ void SharedListVector::set(int binNumber, string seqNames){ numSeqs += (nNames_new - nNames_old); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "set"); exit(1); } } @@ -96,11 +88,7 @@ void SharedListVector::push_back(string seqNames){ numSeqs += nNames; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector 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 SharedListVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "push_back"); exit(1); } } @@ -140,11 +128,7 @@ void SharedListVector::print(ostream& output){ output << endl; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "print"); exit(1); } } @@ -175,11 +159,7 @@ RAbundVector SharedListVector::getRAbundVector(){ return rav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getRAbundVector"); exit(1); } } @@ -200,11 +180,7 @@ SAbundVector SharedListVector::getSAbundVector(){ return sav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getSAbundVector"); exit(1); } } @@ -224,10 +200,14 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){ name = names.substr(0,names.find_first_of(',')); names = names.substr(names.find_first_of(',')+1, names.length()); groupName = groupmap->getGroup(name); + + if(groupName == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } + order->push_back(i, binSize, groupName); //i represents what bin you are in } //get last name groupName = groupmap->getGroup(names); + if(groupName == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } order->push_back(i, binSize, groupName); } @@ -237,14 +217,9 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){ return order; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getSharedOrderVector"); exit(1); } - } /***********************************************************************/ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) { @@ -258,6 +233,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) { name = names.substr(0,names.find_first_of(',')); names = names.substr(names.find_first_of(',')+1, names.length()); group = groupmap->getGroup(name); + if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } if (group == groupName) { //this name is in the group you want the vector for. rav.set(i, rav.getAbundance(i) + 1, group); //i represents what bin you are in } @@ -265,6 +241,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) { //get last name groupName = groupmap->getGroup(names); + if(groupName == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } if (group == groupName) { //this name is in the group you want the vector for. rav.set(i, rav.getAbundance(i) + 1, group); //i represents what bin you are in } @@ -277,11 +254,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getSharedRAbundVector"); exit(1); } } @@ -290,23 +263,23 @@ vector SharedListVector::getSharedRAbundVector() { try { SharedUtil* util; util = new SharedUtil(); - vector lookup; - map finder; + vector lookup; //contains just the groups the user selected + map finder; //contains all groups in groupmap string group, names, name; - + util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups); - delete util; - for (int i = 0; i < globaldata->Groups.size(); i++) { + for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { SharedRAbundVector* temp = new SharedRAbundVector(data.size()); - finder[globaldata->Groups[i]] = temp; - finder[globaldata->Groups[i]]->setLabel(label); - finder[globaldata->Groups[i]]->setGroup(globaldata->Groups[i]); - //*temp = getSharedRAbundVector(globaldata->Groups[i]); - lookup.push_back(finder[globaldata->Groups[i]]); + finder[globaldata->gGroupmap->namesOfGroups[i]] = temp; + finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label); + finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]); + if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) { //if this group is in user groups + lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]); + } } - + //fill vectors for(int i=0;i SharedListVector::getSharedRAbundVector() { name = names.substr(0,names.find_first_of(',')); names = names.substr(names.find_first_of(',')+1, names.length()); group = groupmap->getGroup(name); + if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in } //get last name group = groupmap->getGroup(names); + if(group == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); } finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in } @@ -326,14 +301,9 @@ vector SharedListVector::getSharedRAbundVector() { return lookup; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getSharedRAbundVector"); exit(1); } - } /***********************************************************************/ @@ -348,11 +318,7 @@ SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) { return sav; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getSharedSAbundVector"); exit(1); } } @@ -393,7 +359,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } else{ if(orderMap->count(seqName) == 0){ - cerr << seqName << " not found, check *.names file\n"; + m->mothurOut(seqName + " not found, check *.names file\n"); exit(1); } @@ -403,7 +369,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } if(orderMap->count(seqName) == 0){ - cerr << seqName << " not found, check *.names file\n"; + m->mothurOut(seqName + " not found, check *.names file\n"); exit(1); } ov.set((*orderMap)[seqName], i); @@ -416,11 +382,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SharedListVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the SharedListVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "SharedListVector", "getOrderVector"); exit(1); } }