Merge remote-tracking branch 'origin/master'

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 400a715aeedf604efb80e580f6c345677f74a430..87f51e7c95c136403024c593e681a844ca18d006 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -65,6 +65,26 @@ string ChimeraCheckCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){    
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "chimera") {  outputFileName =  "chimeracheck.chimeras"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){    
        try {
                abort = true; calledHelp = true;
@@ -281,7 +301,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(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);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -306,14 +326,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                        
                        temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
                        svg = m->isTrue(temp);
                        if (nameFileNames.size() != 0) { svg = true; }
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
-                       convert(temp, increment);                       
+                       m->mothurConvert(temp, increment);                      
                }
        }
        catch(exception& e) {
@@ -342,7 +362,7 @@ int ChimeraCheckCommand::execute(){
                        if (m->control_pressed) { delete chimera;       return 0;       }
                        
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
-                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
+                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
                        outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
                        
                #ifdef USE_MPI
@@ -427,7 +447,7 @@ int ChimeraCheckCommand::execute(){
                        
                        
                        //break up file
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
                        
                                for (int s = 0; s < (positions.size()-1); s++) {
@@ -522,7 +542,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
                        }
                        delete candidateSeq;
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                unsigned long long pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
@@ -599,7 +619,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 0;
                int num = 0;