dunno

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 0846bbd9d1755f73e690e4bf11f72f0282fdfe25..f238094c9563587be29064a8f3fdbce54314c0f9 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                                
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        abskew = validParameter.validFile(parameters, "abskew", false); if (abskew == "not found"){     useAbskew = false;  abskew = "1.9";     }else{  useAbskew = true;  }
                        if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
@@ -461,7 +461,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        path = path.substr(0, (tempPath.find_last_of('m')));
                        
                        string uchimeCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        uchimeCommand = path + "uchime";        //      format the database, -o option gives us the ability
 #else
                        uchimeCommand = path + "uchime.exe";
@@ -927,14 +927,15 @@ string ChimeraUchimeCommand::getNamesFile(string& inputFile){
                string inputString = "fasta=" + inputFile;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-               
+               m->mothurCalling = true;
+        
                Command* uniqueCommand = new DeconvoluteCommand(inputString);
                uniqueCommand->execute();
                
                map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
                
                delete uniqueCommand;
-               
+               m->mothurCalling = false;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                
                nameFile = filenames["name"][0];
@@ -987,6 +988,11 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
        try {
+               
+               outputFName = m->getFullPathName(outputFName);
+               filename = m->getFullPathName(filename);
+               alns = m->getFullPathName(alns);
+               
                //to allow for spaces in the path
                outputFName = "\"" + outputFName + "\"";
                filename = "\"" + filename + "\"";
@@ -1000,7 +1006,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                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";
@@ -1238,7 +1244,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                
                //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
@@ -1304,7 +1310,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
                int num = 0;
                vector<string> files;
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                //break up file into multiple files
                m->divideFile(filename, processors, files);
                
@@ -1487,7 +1493,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                                
                //loop through and create all the processes you want
                while (process != processors) {