fixed catchall "clunky" names

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 66fbf9afd2b368d678d5fc99bb55bcc71d2c1f68..ace1b00dc0b45e9500d6ba9aa8657fc44b854042 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -182,6 +182,7 @@ int CatchAllCommand::execute() {
                path = path.substr(0, (path.find_last_of("othur")-5));
                path = m->getFullPathName(path);
                
+               savedOutputDir = outputDir;
                string catchAllCommandExe = ""; 
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
@@ -246,6 +247,7 @@ int CatchAllCommand::execute() {
                                                remove(filename.c_str());
                                        
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+                                               if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
                                        
                                                outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
                                                outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -289,6 +291,7 @@ int CatchAllCommand::execute() {
                                                remove(filename.c_str());
                                        
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+                                               if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
                                        
                                                outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
                                                outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -353,6 +356,7 @@ int CatchAllCommand::execute() {
                                remove(filename.c_str());
                                
                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+                               if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
                                
                                outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
                                outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -372,7 +376,7 @@ int CatchAllCommand::execute() {
                }
                
                if (sharedfile == "") {  
-                       string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+                       string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
                        summaryfilename = m->getFullPathName(summaryfilename);
                        outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
                }else { //combine summaries
@@ -430,7 +434,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
        try {
                
                ofstream out;
-               string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+               string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
                
                //open combined file
                m->openOutputFile(combineFileName, out);