fixes while testing 1.33.0

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index a6dc5b72e0b403df37dd77b7ee593ca5ff19de73..b1db1921a3a074ae059f8341570aa28477ef0cc0 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -12,6 +12,7 @@
 \r
 #include "mothur.h"\r
 #include "mothurout.h"\r
+#include "currentfile.h"\r
 \r
 class Command;\r
 \r
@@ -25,24 +26,32 @@ public:
        bool isValidCommand(string);\r
        bool isValidCommand(string, string);\r
        void printCommands(ostream&);\r
-       void setOutputDirectory(string o)               {       outputDir = o;  m->setOutputDir(o);     }\r
-       void setInputDirectory(string i)                {       inputDir = i;           }\r
+    void printCommandsCategories(ostream&);\r
+       void setOutputDirectory(string o)               {       if(m->dirCheck(o) || (o == "")) {  outputDir = o; m->setOutputDir(o); } }\r
+       void setInputDirectory(string i)                {       if(m->dirCheck(i) || (i == "")) {  inputDir = i;        }       }\r
        void setLogfileName(string n, bool a)   {       logFileName = n;  append = a;           }\r
        string getLogfileName()                                 {       return logFileName;     }\r
        bool getAppend()                                                {       return append;                  }\r
        string getOutputDir()                                   {       return outputDir;               }\r
+    string getInputDir()                                       {       return inputDir;                }\r
        bool MPIEnabled(string);\r
-\r
+       map<string, string> getListCommands()   {       return commands;                }\r
+       \r
 private:\r
        Command* command;\r
        Command* shellcommand;\r
        Command* pipecommand;\r
+       \r
        MothurOut* m;\r
+       CurrentFile* currentFile;\r
+       \r
        map<string, string> commands;\r
        map<string, string>::iterator it;\r
        string outputDir, inputDir, logFileName;\r
        bool append;\r
        \r
+    int checkForRedirects(string);\r
+    \r
        static CommandFactory* _uniqueInstance;\r
        CommandFactory( const CommandFactory& ); // Disable copy constructor\r
        void operator=( const CommandFactory& ); // Disable assignment operator\r