working on removing pointers from chimera.slayer to eliminate pesky memory leaks

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index ded0f89b1cb57c88c66777405d1c0d8de9df088d..304ea108f3ce76790b5bfa2e3946289eb8d97720 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,6 +15,8 @@
 #include "maligner.h"
 #include "slayer.h"
 
+
+
 //***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
@@ -28,21 +30,21 @@ class ChimeraSlayer : public Chimera {
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
-               Sequence* print(ostream&, ostream&);
-               Sequence* print(ostream&, ostream&, data_results, data_results);
+               Sequence print(ostream&, ostream&);
+               Sequence print(ostream&, ostream&, data_results, data_results);
                void printHeader(ostream&);
                int doPrep();
                data_results getResults() { return printResults; }
                
                #ifdef USE_MPI
-               Sequence* print(MPI_File&, MPI_File&);
-               Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
+               Sequence print(MPI_File&, MPI_File&);
+               Sequence print(MPI_File&, MPI_File&, data_results, data_results);
                #endif
                
        private:
-               Sequence* querySeq;
+               Sequence querySeq;
                Sequence trimQuery;
-               DeCalculator* decalc;
+               DeCalculator decalc;
                Database* databaseRight;
                Database* databaseLeft;
                map<string, int> priority; //for template=self, seqname, seqAligned, abundance
@@ -60,10 +62,10 @@ class ChimeraSlayer : public Chimera {
                string getBlock(data_struct, string);
                string getBlock(data_results, data_results, bool, bool, string);
                //int readNameFile(string);
-               vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
-               vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
-               vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
-               vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);
+               vector<Sequence*> getTemplate(Sequence, vector<Sequence*>&);
+               vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
+               vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
+               vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
                
 };