X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.h;h=b7da889701f3ac2bc7883cf5c39356550eb2e25d;hb=8338fe821bc5e3f3cf15a5bf165eabe103b1ebce;hp=45dd8a8ef332f634564c3911b18b96ae641a49dc;hpb=d0051dc9939d3477bd92b42c86bcd3eda743b955;p=mothur.git

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 45dd8a8..b7da889 100644
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -59,7 +59,7 @@ private:
 	int printFile(vector<seqPriorityNode>&, string);
 	int deconvoluteResults(SequenceParser&, string, string, string);
 	int driverGroups(SequenceParser&, string, string, string, string, int, int, vector<string>);
-	int createProcessesGroups(SequenceParser&, string, string, string, string, vector<string>);
+	int createProcessesGroups(SequenceParser&, string, string, string, string, vector<string>, string, string, string);
 
 
 };
@@ -141,7 +141,7 @@ struct uchimeData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){ 
 	uchimeData* pDataArray;
@@ -149,9 +149,9 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 	
 	try {
 		
-		pDataArray->outputFName = pDataArray->m->getFullPathName(outputFName);
-		pDataArray->filename = pDataArray->m->getFullPathName(filename);
-		pDataArray->alns = pDataArray->m->getFullPathName(alns);
+		pDataArray->outputFName = pDataArray->m->getFullPathName(pDataArray->outputFName);
+		pDataArray->filename = pDataArray->m->getFullPathName(pDataArray->filename);
+		pDataArray->alns = pDataArray->m->getFullPathName(pDataArray->alns);
 		
 		//clears files
 		ofstream out, out1, out2;
@@ -189,7 +189,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			path = path.substr(0, (tempPath.find_last_of('m')));
 			
 			string uchimeCommand = path;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			uchimeCommand += "uchime ";
 #else
 			uchimeCommand += "uchime";
@@ -330,17 +330,6 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 				cPara.push_back(tempIdsmoothwindow);
 			}
 			
-			/*if (useMinsmoothid) {
-			 char* tempminsmoothid = new char[14]; 
-			 //strcpy(tempminsmoothid, "--minsmoothid"); 
-			 *tempminsmoothid = '\0'; strncat(tempminsmoothid, "--minsmoothid", 13);
-			 cPara.push_back(tempminsmoothid);
-			 char* tempMinsmoothid = new char[minsmoothid.length()+1];
-			 *tempMinsmoothid = '\0'; strncat(tempMinsmoothid, minsmoothid.c_str(), minsmoothid.length());
-			 //strcpy(tempMinsmoothid, minsmoothid.c_str());
-			 cPara.push_back(tempMinsmoothid);
-			 }*/
-			
 			if (pDataArray->useMaxp) {
 				char* tempmaxp = new char[7]; 
 				//strcpy(tempmaxp, "--maxp"); 
@@ -414,7 +403,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			
 			//uchime_main(numArgs, uchimeParameters); 
 			//cout << "commandString = " << commandString << endl;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 			commandString = "\"" + commandString + "\"";
 #endif
@@ -498,9 +487,9 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
 	
 	try {
 		
-		pDataArray->outputFName = pDataArray->m->getFullPathName(outputFName);
-		pDataArray->filename = pDataArray->m->getFullPathName(filename);
-		pDataArray->alns = pDataArray->m->getFullPathName(alns);
+		pDataArray->outputFName = pDataArray->m->getFullPathName(pDataArray->outputFName);
+		pDataArray->filename = pDataArray->m->getFullPathName(pDataArray->filename);
+		pDataArray->alns = pDataArray->m->getFullPathName(pDataArray->alns);
 		
 		int totalSeqs = 0;
 		int numChimeras = 0;