added out.hierarchy command

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index 7563c023d0b774917b25bbec62390b43d180922d..e885af5d171d24acd230748ff6a5783aa9952a5b 100644 (file)
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -14,8 +14,9 @@
 #include "chimera.h"
 #include "kmer.hpp"
 #include "kmerdb.hpp"
-#include "database.hpp"
+#include "alignmentdb.h"
 
+/***********************************************************/
 //This class was created using the algorythms described in 
 //CHIMERA_CHECK version 2.7 written by Niels Larsen. 
 
@@ -27,7 +28,7 @@ class ChimeraCheckRDP : public Chimera {
                ChimeraCheckRDP(string, string);        
                ~ChimeraCheckRDP();
                
-               void getChimeras();
+               int getChimeras();
                void print(ostream&);
                
                void setCons(string){};
@@ -38,7 +39,7 @@ class ChimeraCheckRDP : public Chimera {
                
                vector<linePair*> lines;
                vector<Sequence*> querySeqs;
-               Database* templateDB;
+               AlignmentDB* templateDB;
                Kmer* kmer;
                
                vector< vector<sim> > IS;  //IS[0] is the vector of IS values for each window for querySeqs[0]