added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 60bfb29a900dbabedcb49a23523b4b704e98352e..45e377c3cbe1ac1ad735cd9c4f47d4c4c37c30a5 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -13,6 +13,7 @@
 #include "command.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
+#include "counttable.h"
 
 
 class ClassifyOtuCommand : public Command {
@@ -20,32 +21,35 @@ class ClassifyOtuCommand : public Command {
 public:
        ClassifyOtuCommand(string);
        ClassifyOtuCommand();
-       ~ClassifyOtuCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ClassifyOtuCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.otu";                }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
+       string getDescription()         { return "find the concensus taxonomy for each OTU"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
 
 private:
-
+    GroupMap* groupMap;
+    CountTable* ct;
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
        bool abort, allLines, probs;
        int cutoff;
        set<string> labels; //holds labels to be used
        vector<string> outputNames;
        map<string, string> nameMap;
        map<string, string> taxMap;
-       map<string, vector<string> > outputTypes;
 
-       int readNamesFile();
-       int readTaxonomyFile();
-       void removeConfidences(string&);
        int process(ListVector*);
-       string findConsensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
+       string addUnclassifieds(string, int);
+       vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin
        
                                                                                                
 };