changes while testing

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 15ef0aa75dfc5793d1d1bef68996f477134e99a3..5f97c7ec693a97997554683188a013b1054eb3d7 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -236,7 +236,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
        }
 }
 /**************************************************************************************************/
-Classify::Classify() {         m = MothurOut::getInstance();   database = NULL;        flipped=false; }
+Classify::Classify() {         m = MothurOut::getInstance();   database = NULL;        phyloTree=NULL; flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {
@@ -309,16 +309,19 @@ int Classify::readTaxonomy(string file) {
         
         taxonomy.clear(); 
         m->readTax(file, taxonomy);
-        map<string, string> tempTaxonomy;
+        
+        //commented out to save time with large templates. 6/12/13
+        //map<string, string> tempTaxonomy;
         for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {  
-            if (m->inUsersGroups(itTax->first, names)) {
-                phyloTree->addSeqToTree(itTax->first, itTax->second); 
-                tempTaxonomy[itTax->first] = itTax->second;
-            }else {
-                m->mothurOut("[WARNING]: " + itTax->first + " is in your taxonomy file and not in your reference file, ignoring.\n");
-            }
+            //if (m->inUsersGroups(itTax->first, names)) {
+                phyloTree->addSeqToTree(itTax->first, itTax->second);
+            if (m->control_pressed) { break; }
+                //tempTaxonomy[itTax->first] = itTax->second;
+           // }else {
+            //    m->mothurOut("[WARNING]: " + itTax->first + " is in your taxonomy file and not in your reference file, ignoring.\n");
+            //}
         }
-        taxonomy = tempTaxonomy;
+        //taxonomy = tempTaxonomy;
 #endif 
                phyloTree->assignHeirarchyIDs(0);
                
@@ -340,21 +343,8 @@ int Classify::readTaxonomy(string file) {
 vector<string> Classify::parseTax(string tax) {
        try {
                vector<string> taxons;
-               
-               tax = tax.substr(0, tax.length()-1);  //get rid of last ';'
-       
-               //parse taxonomy
-               string individual;
-               while (tax.find_first_of(';') != -1) {
-                       individual = tax.substr(0,tax.find_first_of(';'));
-                       tax = tax.substr(tax.find_first_of(';')+1, tax.length());
-                       taxons.push_back(individual);
-                       
-               }
-               //get last one
-               taxons.push_back(tax);
-               
-               return taxons;
+               m->splitAtChar(tax, taxons, ';');
+        return taxons;
        }
        catch(exception& e) {
                m->errorOut(e, "Classify", "parseTax");