adding current file class

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index eb00b59a324e5ef93850fa2a0aa16e1a0216a9dc..b334f909a7411d6dd00b3eda311740b7e93a80b8 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -258,7 +258,7 @@ int ChimeraSlayer::doPrep() {
                }else if (searchMethod == "blast") {
                
                        //generate blastdb
-                       databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch);
+                       databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
                        for (int i = 0; i < templateSeqs.size(); i++) {         databaseLeft->addSequence(*templateSeqs[i]);    }
                        databaseLeft->generateDB();
                        databaseLeft->setNumSeqs(templateSeqs.size());
@@ -384,7 +384,7 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q) {
                }else if (searchMethod == "blast") {
                        
                        //generate blastdb
-                       databaseLeft = new BlastDB(-2.0, -1.0, match, misMatch);
+                       databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
                        for (int i = 0; i < thisTemplate.size(); i++) { if (m->control_pressed) { return thisTemplate; }  databaseLeft->addSequence(*thisTemplate[i]);  }
                        databaseLeft->generateDB();
                        databaseLeft->setNumSeqs(thisTemplate.size());