sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / formatmatrix.h

diff --git a/formatmatrix.h b/formatmatrix.h
index a02ef6cc27ac634eda25ec0c5b7cbc81b13c121a..859b78ab2b72569344ccf7c9485de76333ca5ae3 100644 (file)
--- a/formatmatrix.h
+++ b/formatmatrix.h
@@ -13,17 +13,56 @@
 #include "mothur.h"
 #include "listvector.hpp"
 #include "nameassignment.hpp"
+#include "counttable.h"
 
 
+//**********************************************************************************************************************
+//  This class takes a distance matrix file and converts it to a file where each row contains all distances below the cutoff
+//  for a given sequence.
+
+//  Example:
+       /*      5
+               A  
+               B  0.01 
+               C  0.015 0.03 
+               D  0.03 0.02 0.02  
+               E  0.04 0.05 0.03 0.02   
+               
+               becomes 
+               
+               0       4       1       0.01    2       0.015   3       0.03    4       0.04    
+               1       4       0       0.01    2       0.03    3       0.02    4       0.05    
+               2       4       0       0.015   1       0.03    3       0.02    4       0.03    
+               3       4       0       0.03    1       0.02    2       0.02    4       0.02    
+               4       4       0       0.04    1       0.05    2       0.03    3       0.02
+               
+               column 1 - sequence name converted to row number
+               column 2 - numDists under cutoff
+               rest of line - sequence row -> distance, sequence row -> distance
+               
+               if you had a cutoff of 0.03 then the file would look like,
+               
+               0       3       1       0.01    2       0.015   3       0.03    
+               1       3       0       0.01    2       0.03    3       0.02    
+               2       4       0       0.015   1       0.03    3       0.02    4       0.03    
+               3       4       0       0.03    1       0.02    2       0.02    4       0.02    
+               4       2       2       0.03    3       0.02    
+               
+               This class also creates a vector of ints, rowPos.
+               
+               rowPos[0] = position in the file of distances related to sequence 0.
+               If a sequence is excluded by the cutoff, it's rowPos = -1.
+*/
 //**********************************************************************************************************************
 
 class FormatMatrix {
 
 public:
-       FormatMatrix(){ }
+       FormatMatrix(){ m = MothurOut::getInstance(); }
        virtual ~FormatMatrix() {}
        
-       virtual void read(NameAssignment*){};
+       virtual int read(NameAssignment*){ return 1; }
+    virtual int read(CountTable*){ return 1; }
        
        void setCutoff(float c)                 {       cutoff = c;                     }
        ListVector* getListVector()             {       return list;            }
@@ -35,6 +74,7 @@ protected:
        float cutoff;
        string distFile;
        vector<int> rowPos;
+       MothurOut* m;
 };
 
 //**********************************************************************************************************************