major change to the tree class to use the count table class instead of tree map....

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index acee70c5cb474dee4e25eea4a6dcf6b5bd55fa06..6d43dcb9dd2067bab91f46d42ff8afa238a4a191 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -41,6 +41,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.seqs";               }
        string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
        string getDescription()         { return "classify sequences"; }
@@ -61,6 +62,7 @@ private:
        vector<linePair*> lines;
        vector<string> fastaFileNames;
        vector<string> namefileNames;
+    vector<string> countfileNames;
        vector<string> groupfileNames;
        vector<string> outputNames;
        map<string, vector<string> > nameMap;
@@ -69,13 +71,12 @@ private:
        Classify* classify;
        ReferenceDB* rdb;
        
-       string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
+       string fastaFileName, templateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
-       bool abort, probs, save, flip;
+       bool abort, probs, save, flip, hasName, hasCount;
        
        int driver(linePair*, string, string, string, string);
-       void appendTaxFiles(string, string);
        int createProcesses(string, string, string, string); 
        string addUnclassifieds(string, int);