X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;h=cc3cd8df4205e2f37182a8a80037bc02bb37ca45;hb=83b5acbe3d6087a6cd73e80dde4b923387a01d01;hp=6cac9b1d9512a16d15eef553d351de0b16771b6e;hpb=f5023c911c377e5320c5110c78af98dd8841ef58;p=mothur.git diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp index 6cac9b1..cc3cd8d 100644 --- a/sharedlistvector.cpp +++ b/sharedlistvector.cpp @@ -44,7 +44,7 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB } catch(exception& e) { - errorOut(e, "SharedListVector", "SharedListVector"); + m->errorOut(e, "SharedListVector", "SharedListVector"); exit(1); } } @@ -63,7 +63,7 @@ void SharedListVector::set(int binNumber, string seqNames){ numSeqs += (nNames_new - nNames_old); } catch(exception& e) { - errorOut(e, "SharedListVector", "set"); + m->errorOut(e, "SharedListVector", "set"); exit(1); } } @@ -88,7 +88,7 @@ void SharedListVector::push_back(string seqNames){ numSeqs += nNames; } catch(exception& e) { - errorOut(e, "SharedListVector", "push_back"); + m->errorOut(e, "SharedListVector", "push_back"); exit(1); } } @@ -128,7 +128,7 @@ void SharedListVector::print(ostream& output){ output << endl; } catch(exception& e) { - errorOut(e, "SharedListVector", "print"); + m->errorOut(e, "SharedListVector", "print"); exit(1); } } @@ -159,7 +159,7 @@ RAbundVector SharedListVector::getRAbundVector(){ return rav; } catch(exception& e) { - errorOut(e, "SharedListVector", "getRAbundVector"); + m->errorOut(e, "SharedListVector", "getRAbundVector"); exit(1); } } @@ -180,7 +180,7 @@ SAbundVector SharedListVector::getSAbundVector(){ return sav; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSAbundVector"); + m->errorOut(e, "SharedListVector", "getSAbundVector"); exit(1); } } @@ -201,13 +201,13 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){ names = names.substr(names.find_first_of(',')+1, names.length()); groupName = groupmap->getGroup(name); - if(groupName == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } + 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") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } + 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); } @@ -217,7 +217,7 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){ return order; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSharedOrderVector"); + m->errorOut(e, "SharedListVector", "getSharedOrderVector"); exit(1); } } @@ -233,7 +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") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } + 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 } @@ -241,7 +241,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) { //get last name groupName = groupmap->getGroup(names); - if(groupName == "not found") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } + 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 } @@ -254,7 +254,7 @@ SharedRAbundVector SharedListVector::getSharedRAbundVector(string groupName) { } catch(exception& e) { - errorOut(e, "SharedListVector", "getSharedRAbundVector"); + m->errorOut(e, "SharedListVector", "getSharedRAbundVector"); exit(1); } } @@ -263,10 +263,8 @@ vector SharedListVector::getSharedRAbundVector() { try { SharedUtil* util; util = new SharedUtil(); - vector lookup; - vector lookup2; - map finder; - map::iterator it; + 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); @@ -277,10 +275,11 @@ vector SharedListVector::getSharedRAbundVector() { finder[globaldata->gGroupmap->namesOfGroups[i]] = temp; finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label); finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]); - //*temp = getSharedRAbundVector(globaldata->Groups[i]); - lookup.push_back(finder[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]]); + } } -//cout << "after blanks" << endl; + //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); -//cout << i << '\t' << name << '\t' << group << endl; - if(group == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } + 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); -//cout << i << '\t' << names << '\t' << group << endl; - if(group == "not found") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } + 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 } - if (globaldata->Groups.size() == globaldata->gGroupmap->namesOfGroups.size()) { //no groups specified - lookup2 = lookup; - }else{ //delete unwanted groups - for (int i = 0; i < globaldata->Groups.size(); i++) { - SharedRAbundVector* temp = new SharedRAbundVector(*finder[globaldata->Groups[i]]); - lookup2.push_back(temp); - delete finder[globaldata->Groups[i]]; //so we don't get dup memory - } - } - - return lookup2; + return lookup; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSharedRAbundVector"); + m->errorOut(e, "SharedListVector", "getSharedRAbundVector"); exit(1); } } @@ -331,7 +318,7 @@ SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) { return sav; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSharedSAbundVector"); + m->errorOut(e, "SharedListVector", "getSharedSAbundVector"); exit(1); } } @@ -372,7 +359,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } else{ if(orderMap->count(seqName) == 0){ - mothurOut(seqName + " not found, check *.names file\n"); + m->mothurOut(seqName + " not found, check *.names file\n"); exit(1); } @@ -382,7 +369,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } if(orderMap->count(seqName) == 0){ - mothurOut(seqName + " not found, check *.names file\n"); + m->mothurOut(seqName + " not found, check *.names file\n"); exit(1); } ov.set((*orderMap)[seqName], i); @@ -395,7 +382,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } } catch(exception& e) { - errorOut(e, "SharedListVector", "getOrderVector"); + m->errorOut(e, "SharedListVector", "getOrderVector"); exit(1); } }