X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=b637000fe688920ac89097358cc50e9ac5ca2fc8;hb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;hp=57528b4026e538f4b9ad85b706182e162bca2567;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 57528b4..b637000 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -14,7 +14,7 @@
 
 //***************************************************************************************************************
 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string mode, int k, int ms, int mms, int win, float div, 
-int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera()  {  	
+int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera()  {  	
 	try {
 		fastafile = file;
 		templateFileName = temp; templateSeqs = readSeqs(temp);
@@ -35,6 +35,8 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 		realign = r; 
 		trimChimera = trim;
 		numNoParents = 0;
+		blastlocation = blas;
+		threadID = tid;
 	
 		doPrep();
 	}
@@ -46,7 +48,7 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 //***************************************************************************************************************
 //template=self
 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& prior, string mode, int k, int ms, int mms, int win, float div, 
-							 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera()  {  	
+							 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera()  {  	
 	try {
 		fastafile = file; templateSeqs = readSeqs(fastafile);
 		templateFileName = temp; 
@@ -68,6 +70,8 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
 		trimChimera = trim;
 		priority = prior;
 		numNoParents = 0;
+		blastlocation = blas;
+		threadID = tid;
 		
 		createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
 		
@@ -216,7 +220,7 @@ int ChimeraSlayer::doPrep() {
 		}else if (searchMethod == "blast") {
 		
 			//generate blastdb
-			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
+			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3, blastlocation, threadID);
 			
 			if (m->control_pressed) { return 0; }
 
@@ -330,7 +334,7 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence q, vector<Sequence*>& user
 		}else if (searchMethod == "blast") {
 			
 			//generate blastdb
-			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
+			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3, blastlocation, threadID);
 			
 			if (m->control_pressed) { return userTemplate; }