X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.h;h=b7da889701f3ac2bc7883cf5c39356550eb2e25d;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=359b68c9c97f144f0914f4ff309c973ca2ec5d60;hpb=4c5e7a20a03ddc6feb49ff9d21fcb4c79bc5508d;p=mothur.git

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 359b68c..b7da889 100644
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -48,6 +48,7 @@ private:
 	string fastafile, groupfile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
 	int processors;
 	
+	
 	vector<string> outputNames;
 	vector<string> fastaFileNames;
 	vector<string> nameFileNames;
@@ -58,7 +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);
 
 
 };
@@ -140,7 +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;
@@ -148,6 +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(); 
@@ -178,10 +183,23 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			
 			vector<char*> cPara;
 			
+			string path = pDataArray->m->argv;
+			string tempPath = path;
+			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) || (__linux__) || (__unix__) || (__unix)
+			uchimeCommand += "uchime ";
+#else
+			uchimeCommand += "uchime";
+			uchimeCommand = "\"" + uchimeCommand + "\"";
+#endif			
+			
 			char* tempUchime;
-			tempUchime= new char[8]; 
+			tempUchime= new char[uchimeCommand.length()+1]; 
 			*tempUchime = '\0';
-			strncat(tempUchime, "uchime ", 7); 
+			strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
 			cPara.push_back(tempUchime);
 			
 			char* tempIn = new char[8]; 
@@ -312,17 +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"); 
@@ -396,6 +403,10 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			
 			//uchime_main(numArgs, uchimeParameters); 
 			//cout << "commandString = " << commandString << endl;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+			commandString = "\"" + commandString + "\"";
+#endif
 			system(commandString.c_str());
 			
 			//free memory
@@ -476,6 +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;