X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifyseqscommand.h;h=59d9ee275800195255961639d77fb6c57d97f417;hp=87d4f51cf78230f6ab301e1d72462a461b9f9da9;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=a9dbc22713bfc056a797361dd757b1a5c98e1c01

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 87d4f51..59d9ee2 100644
--- 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();