X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=distancecommand.h;h=2f53232b5943d835e8c27adf7374a5e3a8ce168f;hp=9d5477d7ee1dca3d715189db8d61fab432c87cf3;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=fc1ed1ae1b022719176910ab71993bd6535810ad

diff --git a/distancecommand.h b/distancecommand.h
index 9d5477d..2f53232 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -24,7 +24,7 @@
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct distanceData {
+struct distanceData {
 	int startLine;
 	int endLine;
 	string dFileName;
@@ -33,7 +33,7 @@ typedef struct distanceData {
 	vector<string> Estimators;
 	MothurOut* m;
 	string output;
-	int numNewFasta;
+	int numNewFasta, count;
 	string countends;
 	
 	distanceData(){}
@@ -53,7 +53,7 @@ typedef struct distanceData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){ 
 	distanceData* pDataArray;
@@ -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"; }
 
@@ -213,8 +214,8 @@ private:
 	
 	#ifdef USE_MPI 
 	int driverMPI(int, int, MPI_File&, float);
-	int driverMPI(int, int, string, unsigned long int&);
-	int driverMPI(int, int, string, unsigned long int&, string);
+	int driverMPI(int, int, string, unsigned long long&);
+	int driverMPI(int, int, string, unsigned long long&, string);
 	#endif
 	
 	//int convertMatrix(string);