fixed bug with trim.flows that was adding flow files names to the .flow.files file...

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 359b68c9c97f144f0914f4ff309c973ca2ec5d60..6e1f809ce55a332020240bdc0b5e30398b5d5b49 100644 (file)
--- 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;
@@ -178,10 +179,23 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                        
                        vector<char*> cPara;
                        
+                       string path = pDataArray->m->argv;
+                       string tempPath = path;
+                       for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                       path = path.substr(0, (tempPath.find_last_of('m')));
+                       
+                       string uchimeCommand = path;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       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]; 
@@ -396,6 +410,10 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
                        
                        //uchime_main(numArgs, uchimeParameters); 
                        //cout << "commandString = " << commandString << endl;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+                       commandString = "\"" + commandString + "\"";
+#endif
                        system(commandString.c_str());
                        
                        //free memory