fixed get.lienage and remove.lineage bug with confidence scores that are floats....

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index eee0ccad08a84f448ea47a42213673b0dd05254f..2a5505f149241c88b0591f1622a50d6a2fc89577 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -257,6 +257,33 @@ int GetLineageCommand::execute(){
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
+                       
+                       //set fasta file as new current fastafile
+                       string current = "";
+                       itTypes = outputTypes.find("fasta");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("name");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("group");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("list");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+                       }
+                       
+                       itTypes = outputTypes.find("taxonomy");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+                       }                       
                }
                
                return 0;               
@@ -544,7 +571,7 @@ int GetLineageCommand::readTax(){
                //bool wroteSomething = false;
                
                bool taxonsHasConfidence = false;
-               vector< map<string, int> > searchTaxons;
+               vector< map<string, float> > searchTaxons;
                string noConfidenceTaxons = taxons;
                int hasConPos = taxons.find_first_of('(');
                if (hasConPos != string::npos) {  
@@ -602,7 +629,7 @@ int GetLineageCommand::readTax(){
                                        if (pos != string::npos) { //if yes, then are the confidences okay
                                                
                                                bool good = true;
-                                               vector< map<string, int> > usersTaxon = getTaxons(newtax);
+                                               vector< map<string, float> > usersTaxon = getTaxons(newtax);
                                                
                                                //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
                                                //we want to "line them up", so we will find the the index where the searchstring starts
@@ -664,10 +691,10 @@ int GetLineageCommand::readTax(){
        }
 }
 /**************************************************************************************************/
-vector< map<string, int> > GetLineageCommand::getTaxons(string tax) {
+vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
        try {
                
-               vector< map<string, int> > t;
+               vector< map<string, float> > t;
                string taxon = "";
                int taxLength = tax.length();
                for(int i=0;i<taxLength;i++){
@@ -684,10 +711,10 @@ vector< map<string, int> > GetLineageCommand::getTaxons(string tax) {
                                        newtaxon = taxon;
                                        confidence = "0";
                                } 
-                               int con = 0;
+                               float con = 0;
                                convert(confidence, con);
                                
-                               map<string, int> temp;
+                               map<string, float> temp;
                                temp[newtaxon] = con;
                                t.push_back(temp);