changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 0bf4a9154412080d28fa065ab33789279832fbeb..1316a250cc8418843e542dd446e021769d6f6ebd 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -10,7 +10,7 @@
  *
  */
 
-#include "mothur.h"
+
 #include "command.hpp"
 #include "classify.h"
 #include "referencedb.h"
@@ -75,7 +75,6 @@ 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 +129,7 @@ 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 +162,7 @@ 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();