added more descriptive error messages to sharedlist

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
index a4860dcb83ee16ddaca43afd6cc4adb4a1973adc..cced0b7d404b4145a437b677f37fa869bb8abb3f 100644 (file)
--- a/ccode.h
+++ b/ccode.h
@@ -46,10 +46,20 @@ class Ccode : public Chimera {
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
                
-               vector< vector<Sequence*> > closest;  //bestfit[0] is a vector of sequence at are closest to queryseqs[0]...
+               vector<int> windows;
+               vector< vector<Sequence*> > closest;  //closest[0] is a vector of sequence at are closest to queryseqs[0]...
+               vector< vector<float> > averageRef;  //averageRef[0] is the average distance at each window for the references for querySeqs[0]
+               vector< vector<float> > averageQuery;  //averageQuery[0] is the average distance at each winow for the query for querySeqs[0]
                
                vector< vector<Sequence*> > findClosest(int, int, int); 
-               void removeSeqs(vector<Sequence*>);  //removes sequences from closest that are to different of too similar to eachother. 
+               void removeBadReferenceSeqs(vector<Sequence*>&, int);  //removes sequences from closest that are to different of too similar to eachother. 
+               void trimSequences();
+               vector<int> findWindows();
+               vector<float> getAverageRef(vector<Sequence*>);
+               vector<float> getAverageQuery (vector<Sequence*>, int);
+               
+               
+               int getDiff(string, string);  //return number of mismatched bases, a gap to base is not counted as a mismatch
                
                void createProcessesClosest();