X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedlistvector.cpp;h=6dfcb97f0aff013d15c1c641e93a24b0d7b229a3;hb=15b252e317fde72ce0a5de8776cb88112e0ed2b6;hp=4303cfde13d3c4250c8f952c7a6eeb4bd9a2553d;hpb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e;p=mothur.git diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp index 4303cfd..6dfcb97 100644 --- a/sharedlistvector.cpp +++ b/sharedlistvector.cpp @@ -16,35 +16,33 @@ /***********************************************************************/ -SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance(); groupmap = NULL; } +SharedListVector::SharedListVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; } /***********************************************************************/ -SharedListVector::SharedListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){globaldata = GlobalData::getInstance(); groupmap = NULL; } +SharedListVector::SharedListVector(int n): DataVector(), data(n, "") , maxRank(0), numBins(0), numSeqs(0){ groupmap = NULL; } /***********************************************************************/ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) { try { - globaldata = GlobalData::getInstance(); - //set up groupmap for later. - groupmap = new GroupMap(globaldata->getGroupFile()); - groupmap->readMap(); + groupmap = new GroupMap(m->getGroupFile()); + groupmap->readMap(); int hold; string inputData; f >> label >> hold; data.assign(hold, ""); - + for(int i=0;i> inputData; set(i, inputData); } - + } catch(exception& e) { - errorOut(e, "SharedListVector", "SharedListVector"); + m->errorOut(e, "SharedListVector", "SharedListVector"); exit(1); } } @@ -52,18 +50,20 @@ SharedListVector::SharedListVector(ifstream& f) : DataVector(), maxRank(0), numB /***********************************************************************/ void SharedListVector::set(int binNumber, string seqNames){ try { - int nNames_old = getNumNames(data[binNumber]); + int nNames_old = m->getNumNames(data[binNumber]); data[binNumber] = seqNames; - int nNames_new = getNumNames(seqNames); + int nNames_new = m->getNumNames(seqNames); if(nNames_old == 0) { numBins++; } if(nNames_new == 0) { numBins--; } if(nNames_new > maxRank) { maxRank = nNames_new; } numSeqs += (nNames_new - nNames_old); + + } catch(exception& e) { - errorOut(e, "SharedListVector", "set"); + m->errorOut(e, "SharedListVector", "set"); exit(1); } } @@ -79,7 +79,7 @@ string SharedListVector::get(int index){ void SharedListVector::push_back(string seqNames){ try { data.push_back(seqNames); - int nNames = getNumNames(seqNames); + int nNames = m->getNumNames(seqNames); numBins++; @@ -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); } } @@ -141,7 +141,7 @@ RAbundVector SharedListVector::getRAbundVector(){ RAbundVector rav; for(int i=0;igetNumNames(data[i]); rav.push_back(binSize); } @@ -159,7 +159,7 @@ RAbundVector SharedListVector::getRAbundVector(){ return rav; } catch(exception& e) { - errorOut(e, "SharedListVector", "getRAbundVector"); + m->errorOut(e, "SharedListVector", "getRAbundVector"); exit(1); } } @@ -171,7 +171,7 @@ SAbundVector SharedListVector::getSAbundVector(){ SAbundVector sav(maxRank+1); for(int i=0;igetNumNames(data[i]); sav.set(binSize, sav.get(binSize) + 1); } sav.set(0, 0); @@ -180,7 +180,7 @@ SAbundVector SharedListVector::getSAbundVector(){ return sav; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSAbundVector"); + m->errorOut(e, "SharedListVector", "getSAbundVector"); exit(1); } } @@ -194,20 +194,20 @@ SharedOrderVector* SharedListVector::getSharedOrderVector(){ order->setLabel(label); for(int i=0;igetNumNames(get(i)); //find number of individual in given bin names = get(i); while (names.find_first_of(',') != -1) { 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") { 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); } } @@ -266,42 +266,66 @@ vector SharedListVector::getSharedRAbundVector() { 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); + + vector Groups = m->getGroups(); + vector allGroups = groupmap->getNamesOfGroups(); + util->setGroups(Groups, allGroups); + m->setGroups(Groups); delete util; - for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) { + for (int i = 0; i < allGroups.size(); i++) { SharedRAbundVector* temp = new SharedRAbundVector(data.size()); - 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]]); + finder[allGroups[i]] = temp; + finder[allGroups[i]]->setLabel(label); + finder[allGroups[i]]->setGroup(allGroups[i]); + if (m->inUsersGroups(allGroups[i], m->getGroups())) { //if this group is in user groups + lookup.push_back(finder[allGroups[i]]); } } //fill vectors for(int i=0;igetGroup(name); - if(group == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } - finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in + int nameLength = names.size(); + string seqName = ""; + + for(int j=0;jgetGroup(seqName); + if(group == "not found") { m->mothurOut("Error: Sequence '" + seqName + "' 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 + + seqName = ""; + } + else{ + seqName += names[j]; + } } + group = groupmap->getGroup(seqName); + if(group == "not found") { m->mothurOut("Error: Sequence '" + seqName + "' 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 + + + +// while (names.find_first_of(',') != -1) { +// 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") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); } - finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in +// 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 } - + return lookup; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSharedRAbundVector"); + m->errorOut(e, "SharedListVector", "getSharedRAbundVector"); exit(1); } } @@ -318,7 +342,7 @@ SharedSAbundVector SharedListVector::getSharedSAbundVector(string groupName) { return sav; } catch(exception& e) { - errorOut(e, "SharedListVector", "getSharedSAbundVector"); + m->errorOut(e, "SharedListVector", "getSharedSAbundVector"); exit(1); } } @@ -331,7 +355,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ OrderVector ov; for(int i=0;igetNumNames(data[i]); for(int j=0;j* 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); } @@ -369,7 +393,7 @@ 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); @@ -382,7 +406,7 @@ OrderVector SharedListVector::getOrderVector(map* orderMap = NULL){ } } catch(exception& e) { - errorOut(e, "SharedListVector", "getOrderVector"); + m->errorOut(e, "SharedListVector", "getOrderVector"); exit(1); } }