try {
m = MothurOut::getInstance();
maxLevel = 0;
+ ignore = false;
if (groupFile != "") {
groupmap = new GroupMap(groupFile);
exit(1);
}
}
+
+/**************************************************************************************************/
+
+PhyloSummary::PhyloSummary(string groupFile){
+ try {
+ m = MothurOut::getInstance();
+ maxLevel = 0;
+ ignore = true;
+
+ if (groupFile != "") {
+ groupmap = new GroupMap(groupFile);
+ groupmap->readMap();
+ }else{
+ groupmap = NULL;
+ }
+
+ tree.push_back(rawTaxNode("Root"));
+ tree[0].rank = "0";
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "PhyloSummary");
+ exit(1);
+ }
+}
/**************************************************************************************************/
void PhyloSummary::summarize(string userTfile){
tree[childPointer->second].total++;
currentNode = childPointer->second;
- }else{ //otherwise, error
- m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
- break;
+ }else{
+ if (ignore) {
+
+ tree.push_back(rawTaxNode(taxon));
+ int index = tree.size() - 1;
+
+ tree[index].parent = currentNode;
+ tree[index].level = (level+1);
+ tree[index].total = 1;
+ tree[currentNode].children[taxon] = index;
+
+ //initialize groupcounts
+ if (groupmap != NULL) {
+ for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
+ tree[index].groupCount[groupmap->namesOfGroups[j]] = 0;
+ }
+
+ //find out the sequences group
+ string group = groupmap->getGroup(seqName);
+
+ if (group == "not found") { m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+
+ //do you have a count for this group?
+ map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
+
+ //if yes, increment it - there should not be a case where we can't find it since we load group in read
+ if (itGroup != tree[index].groupCount.end()) {
+ tree[index].groupCount[group]++;
+ }
+ }
+
+ currentNode = index;
+
+ }else{ //otherwise, error
+ m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
+ break;
+ }
}
level++;
}
/**************************************************************************************************/
+int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
+ try {
+ numSeqs++;
+
+ map<string, int>::iterator childPointer;
+
+ int currentNode = 0;
+ string taxon;
+
+ int level = 0;
+
+ while (seqTaxonomy != "") {
+
+ if (m->control_pressed) { return 0; }
+
+ //somehow the parent is getting one too many accnos
+ //use print to reassign the taxa id
+ taxon = getNextTaxon(seqTaxonomy);
+
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, update count and move on
+ if (groupmap != NULL) {
+
+ map<string, bool> containsGroup;
+ for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
+ containsGroup[groupmap->namesOfGroups[j]] = false;
+ }
+
+ for (int k = 0; k < names.size(); k++) {
+ //find out the sequences group
+ string group = groupmap->getGroup(names[k]);
+
+ if (group == "not found") { m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+ else {
+ containsGroup[group] = true;
+ }
+ }
+
+ for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
+ if (itGroup->second == true) {
+ tree[childPointer->second].groupCount[itGroup->first]++;
+ }
+ }
+
+ }
+
+ tree[childPointer->second].total++;
+
+ currentNode = childPointer->second;
+ }else{
+ if (ignore) {
+
+ tree.push_back(rawTaxNode(taxon));
+ int index = tree.size() - 1;
+
+ tree[index].parent = currentNode;
+ tree[index].level = (level+1);
+ tree[index].total = 1;
+ tree[currentNode].children[taxon] = index;
+
+ //initialize groupcounts
+ if (groupmap != NULL) {
+ map<string, bool> containsGroup;
+ for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
+ tree[index].groupCount[groupmap->namesOfGroups[j]] = 0;
+ containsGroup[groupmap->namesOfGroups[j]] = false;
+ }
+
+
+ for (int k = 0; k < names.size(); k++) {
+ //find out the sequences group
+ string group = groupmap->getGroup(names[k]);
+
+ if (group == "not found") { m->mothurOut(names[k] + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+ else {
+ containsGroup[group] = true;
+ }
+ }
+
+ for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
+ if (itGroup->second == true) {
+ tree[index].groupCount[itGroup->first]++;
+ }
+ }
+ }
+
+ currentNode = index;
+
+ }else{ //otherwise, error
+ m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
+ break;
+ }
+ }
+
+ level++;
+
+ if ((seqTaxonomy == "") && (level < maxLevel)) { //if you think you are done and you are not.
+ for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "addSeqToTree");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
void PhyloSummary::assignRank(int index){
try {
map<string,int>::iterator it;
void PhyloSummary::print(ofstream& out){
try {
+
+ if (ignore) { assignRank(0); }
+
//print labels
out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
if (groupmap != NULL) {
projects / mothur.git / blobdiff