changes while testing

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 87d4f51cf78230f6ab301e1d72462a461b9f9da9..59d9ee275800195255961639d77fb6c57d97f417 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -43,8 +43,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.seqs";               }
        string getCommandCategory()             { return "Phylotype Analysis";  }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        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"; }
        
@@ -162,8 +163,6 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                        inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
                }
                
-               pDataArray->count = pDataArray->end;
-               
                //make classify
                Classify* myclassify;
         string outputMethodTag = pDataArray->method + ".";
@@ -182,7 +181,7 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                
                if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
                
-               int count = 0;
+               pDataArray->count = 0;
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
                        
                        if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
@@ -208,15 +207,15 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                                        
                                if (myclassify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
                                
-                               count++;
+                               pDataArray->count++;
                        }
                        delete candidateSeq;
                        //report progress
-                       if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");       }
                        
                }
                //report progress
-               if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");               }
                
                delete myclassify;
                inFASTA.close();