added classic parameter to cluster.split. working on make.contigs command. fixed...

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index eb0865c2744acfe120505a5a533cd482af8b9b19..2d01183479a504c798a18071df045f723643f850 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -123,7 +123,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                //create database
                                if(method == "kmer")                    {       database = new KmerDB(tempFile, kmerSize);                      }
                                else if(method == "suffix")             {       database = new SuffixDB(numSeqs);                                                               }
-                               else if(method == "blast")              {       database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");       }
+                               else if(method == "blast")              {       database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid);  }
                                else if(method == "distance")   {       database = new DistanceDB();    }
                                else {
                                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
@@ -238,7 +238,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
        }
 }
 /**************************************************************************************************/
-Classify::Classify() {         m = MothurOut::getInstance();   database = NULL;        }
+Classify::Classify() {         m = MothurOut::getInstance();   database = NULL;        flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {
@@ -296,7 +296,8 @@ int Classify::readTaxonomy(string file) {
                        delete buf4;
 
                        istringstream iss (tempBuf,istringstream::in);
-                       iss >> name >> taxInfo;
+                       iss >> name; m->gobble(iss);
+            iss >> taxInfo;
                        taxonomy[name] = taxInfo;
                        phyloTree->addSeqToTree(name, taxInfo);
                }
@@ -309,8 +310,9 @@ int Classify::readTaxonomy(string file) {
        
                //read template seqs and save
                while (!inTax.eof()) {
-                       inTax >> name >> taxInfo;
-                       
+                       inTax >> name; m->gobble(inTax);
+            inTax >> taxInfo;
+               
                        taxonomy[name] = taxInfo;
                        
                        phyloTree->addSeqToTree(name, taxInfo);