Merge remote-tracking branch 'origin/master'

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 062779335148afcc61fb1fd51236467776b9d19b..c5c678e78a344eed06ea0308c0df6178e7f22a51 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -69,6 +69,27 @@ string ChimeraPintailCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraPintailCommand::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 =  "pintail.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "pintail.accnos"; }
+            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, "ChimeraPintailCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraPintailCommand::ChimeraPintailCommand(){        
        try {
                abort = true; calledHelp = true;
@@ -225,13 +246,13 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                        
                        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, "window", false);                   if (temp == "not found") { temp = "0"; }
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "25"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -397,11 +418,11 @@ int ChimeraPintailCommand::execute(){
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
                        string outputFileName, accnosFileName;
                        if (maskfile != "") {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("accnos");
                        }else {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
                        }
                        
                        if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;    }
@@ -488,7 +509,7 @@ int ChimeraPintailCommand::execute(){
                #else
                                                
                        //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[s], processors);
                        
                                for (int i = 0; i < (positions.size()-1); i++) {
@@ -611,7 +632,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
                        }
                        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
@@ -697,7 +718,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
 
 int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 0;
                int num = 0;