added warning about average neighbor merges around cutoff. fixed little bugs.

[mothur.git] / formatmatrix.h

diff --git a/formatmatrix.h b/formatmatrix.h
index a02ef6cc27ac634eda25ec0c5b7cbc81b13c121a..4ef36d95d6d8e11db5bf065a755fd0292e809c17 100644 (file)
--- a/formatmatrix.h
+++ b/formatmatrix.h
@@ -15,6 +15,43 @@
 #include "nameassignment.hpp"
 
 
+//**********************************************************************************************************************
+//  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 {