X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.h;h=b7da889701f3ac2bc7883cf5c39356550eb2e25d;hb=8338fe821bc5e3f3cf15a5bf165eabe103b1ebce;hp=6e1f809ce55a332020240bdc0b5e30398b5d5b49;hpb=e0dc0bcef2a0f7e1f63abb531dbb1ad533da98ca;p=mothur.git

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 6e1f809..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;
@@ -149,6 +149,10 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 	
 	try {
 		
+		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;
 		pDataArray->m->openOutputFile(pDataArray->outputFName, out); out.close(); 
@@ -181,11 +185,11 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			
 			string path = pDataArray->m->argv;
 			string tempPath = path;
-			for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+			for (int j = 0; j < path.length(); j++) { tempPath[j] = tolower(path[j]); }
 			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";
@@ -326,17 +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"); 
@@ -410,7 +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
@@ -494,6 +487,10 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
 	
 	try {
 		
+		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;