added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index af6e33a1254adc623948604100f8b9109e6c18e6..942635ea183cedee17550fd85df3c3daa68d9979 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -64,6 +64,28 @@ string ChimeraCcodeCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraCcodeCommand::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 =  "ccode.chimeras"; }
+            else if (type == "mapinfo") {  outputFileName =  "mapinfo"; }
+            else if (type == "accnos") {  outputFileName =  "ccode.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, "ChimeraCcodeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraCcodeCommand::ChimeraCcodeCommand(){    
        try {
                abort = true; calledHelp = true;
@@ -284,14 +306,16 @@ int ChimeraCcodeCommand::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])) + maskfile + ".ccode.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("accnos");
                        }else {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "ccode.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "ccode.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + getOutputFileNameTag("accnos");
+
                        }
 
-                       string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
+                       string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("mapinfo");
+
                        
                        if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } outputTypes.clear(); return 0;        }
                        
@@ -393,7 +417,7 @@ int ChimeraCcodeCommand::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[s], processors);
                        
                                for (int i = 0; i < (positions.size()-1); i++) {
@@ -524,7 +548,7 @@ int ChimeraCcodeCommand::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
@@ -611,7 +635,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCcodeCommand::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;