added distance search method to classify.seqs

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index a305b5bfd09601220b15a44fd0ad18ee6b42a09d..5343ec2a58c8a043ae23ac7a58dbeae56744c1b6 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -26,7 +26,7 @@ class ChimeraSlayer : public Chimera {
                ChimeraSlayer(string, string);  
                ~ChimeraSlayer();
                
-               void getChimeras();
+               int getChimeras();
                void print(ostream&);
                
                void setCons(string){};
@@ -40,6 +40,7 @@ class ChimeraSlayer : public Chimera {
                vector<linePair*> lines;
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
+               vector< map<int, int> > spotMap;
                
                vector< vector<data_struct> > chimeraResults;
                vector<string> chimeraFlags;
@@ -47,8 +48,7 @@ class ChimeraSlayer : public Chimera {
                string fastafile, templateFile;
                
                Sequence* getSequence(string);  //find sequence from name
-                       
-                               
+               void printBlock(data_struct, ostream&, int i);
 };
 
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