added summary.tax command and fixed bug with root level totals in tax.summary file

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 58274b3ec365c573eacc9644a446c209f35f63ff..47591f6a8ec577afe99fd21b0ab79b989023ce73 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -71,7 +71,7 @@ PhyloSummary::PhyloSummary(string groupFile){
 }
 /**************************************************************************************************/
 
-void PhyloSummary::summarize(string userTfile){
+int PhyloSummary::summarize(string userTfile){
        try {
                
                ifstream in;
@@ -79,14 +79,18 @@ void PhyloSummary::summarize(string userTfile){
                
                //read in users taxonomy file and add sequences to tree
                string name, tax;
+               int numSeqs = 0;
                while(!in.eof()){
                        in >> name >> tax; m->gobble(in);
                        
                        addSeqToTree(name, tax);
+                       numSeqs++;
                        
                        if (m->control_pressed) { break;  }
                }
                in.close();
+               
+               return numSeqs;
        }
        catch(exception& e) {
                m->errorOut(e, "PhyloSummary", "summarize");
@@ -126,6 +130,9 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
                
                int level = 0;
                
+               //are there confidence scores, if so remove them
+               if (seqTaxonomy.find_first_of('(') != -1) {  removeConfidences(seqTaxonomy);    }
+               
                while (seqTaxonomy != "") {
                        
                        if (m->control_pressed) { return 0; }
@@ -221,6 +228,9 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
                
                int level = 0;
                
+               //are there confidence scores, if so remove them
+               if (seqTaxonomy.find_first_of('(') != -1) {  removeConfidences(seqTaxonomy);    }
+               
                while (seqTaxonomy != "") {
                        
                        if (m->control_pressed) { return 0; }
@@ -361,16 +371,25 @@ void PhyloSummary::print(ofstream& out){
                out << endl;
                
                int totalChildrenInTree = 0;
+               map<string, int>::iterator itGroup;
                
                map<string,int>::iterator it;
                for(it=tree[0].children.begin();it!=tree[0].children.end();it++){   
-                       if (tree[it->second].total != 0)  {   totalChildrenInTree++; }
+                       if (tree[it->second].total != 0)  {   
+                               totalChildrenInTree++; 
+                               tree[0].total += tree[it->second].total;
+                               
+                               if (groupmap != NULL) {
+                                       vector<string> mGroups = groupmap->getNamesOfGroups();
+                                       for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } 
+                               }
+                       }
                }
                
                //print root
                out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
                
-               map<string, int>::iterator itGroup;
+               
                if (groupmap != NULL) {
                        //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
                        //      out << itGroup->second << '\t';
@@ -472,11 +491,39 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 
        }
        catch(exception& e) {
-               m->errorOut(e, "PhyloSummary", "print");
+               m->errorOut(e, "PhyloSummary", "readTreeStruct");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
+void PhyloSummary::removeConfidences(string& tax) {
+       try {
+               
+               string taxon;
+               string newTax = "";
+               
+               while (tax.find_first_of(';') != -1) {
+                       //get taxon
+                       taxon = tax.substr(0,tax.find_first_of(';'));
+                       
+                       int pos = taxon.find_first_of('(');
+                       if (pos != -1) {
+                               taxon = taxon.substr(0, pos); //rip off confidence 
+                       }
+                       
+                       taxon += ";";
+                       
+                       tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+                       newTax += taxon;
+               }
+               
+               tax = newTax;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PhyloSummary", "removeConfidences");
                exit(1);
        }
 }
-
 /**************************************************************************************************/