X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=distancecommand.h;h=2f53232b5943d835e8c27adf7374a5e3a8ce168f;hp=91f0ed50b3003345454690b7aecc049c449854d8;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/distancecommand.h b/distancecommand.h
index 91f0ed5..2f53232 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -33,7 +33,7 @@ struct distanceData {
 	vector<string> Estimators;
 	MothurOut* m;
 	string output;
-	int numNewFasta;
+	int numNewFasta, count;
 	string countends;
 	
 	distanceData(){}
@@ -86,7 +86,7 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
 		ofstream outFile(pDataArray->dFileName.c_str(), ios::trunc);
 		outFile.setf(ios::fixed, ios::showpoint);
 		outFile << setprecision(4);
-		
+		pDataArray->count = 0;
 		
 		if (pDataArray->output != "square") { 
 			if((pDataArray->output == "lt") && (pDataArray->startLine == 0)){	outFile << pDataArray->alignDB.getNumSeqs() << endl;	}
@@ -119,11 +119,10 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
 				if (pDataArray->output == "lt") { outFile << endl; }
 				
 				if(i % 100 == 0){
-					pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
-				}
-				
+					pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 				}
+				pDataArray->count++;
 			}
-			pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+			pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
 		}else{
 			if(pDataArray->startLine == 0){	outFile << pDataArray->alignDB.getNumSeqs() << endl;	}
 			
@@ -148,11 +147,11 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
 				outFile << endl; 
 				
 				if(i % 100 == 0){
-					pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+					pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 				}
-				
+				pDataArray->count++;
 			}
-			pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+			pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n"); 
 		}
 		
 		outFile.close();
@@ -178,7 +177,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "dist.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing";	}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
 	string getDescription()		{ return "calculate the pairwaise distances between aligned sequences"; }