added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 0bf4a9154412080d28fa065ab33789279832fbeb..4965642e7f77f0d8638bceb177bd79788c8e39ad 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -10,7 +10,7 @@
  *
  */
 
-#include "mothur.h"
+
 #include "command.hpp"
 #include "classify.h"
 #include "referencedb.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"; }
@@ -75,7 +76,6 @@ private:
        bool abort, probs, save, flip;
        
        int driver(linePair*, string, string, string, string);
-       void appendTaxFiles(string, string);
        int createProcesses(string, string, string, string); 
        string addUnclassifieds(string, int);
        
@@ -130,7 +130,7 @@ struct classifyData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){ 
        classifyData* pDataArray;
@@ -163,7 +163,7 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                //make classify
                Classify* myclassify;
                if(pDataArray->method == "bayesian"){   myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID, pDataArray->flip);         }
-               else if(pDataArray->method == "knn"){   myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID, pDataArray->flipThreshold);                                }
+               else if(pDataArray->method == "knn"){   myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID);                           }
                else {
                        pDataArray->m->mothurOut(pDataArray->search + " is not a valid method option. I will run the command using bayesian.");
                        pDataArray->m->mothurOutEndLine();