added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 0ac0288e5bcf1d8879105295e41ad632fce1bdf1..a0baf1849d92935fec3ca360a135805d3c41ddbc 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -19,15 +19,24 @@ class ClassifyOtuCommand : public Command {
 
 public:
        ClassifyOtuCommand(string);
-       ~ClassifyOtuCommand();
-       int execute();
-       void help();
+       ClassifyOtuCommand();
+       ~ClassifyOtuCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.otu";                }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       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:
 
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
        bool abort, allLines, probs;
        int cutoff;
        set<string> labels; //holds labels to be used
@@ -37,9 +46,9 @@ private:
 
        int readNamesFile();
        int readTaxonomyFile();
-       void removeConfidences(string&);
        int process(ListVector*);
-       string findConcensusTaxonomy(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
        
                                                                                                
 };