get.oturep ifstream

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 7b298ef87345ea7b9ce497ac6d0b2e6d2d94759d..43fd9538e40cbe7e62adb8468b3408af715a0fb9 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -133,7 +133,7 @@ void CatchAllCommand::help(){
        try {
                m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
                m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
-               m->mothurOut("The catchall executable must be in a folder called catchall in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
+               m->mothurOut("The catchall executable must be in the same folder as your mothur executable. \n");
                m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
                m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
                m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
@@ -164,9 +164,9 @@ int CatchAllCommand::execute() {
 
                string catchAllCommandExe = ""; 
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
+                       catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
                #else
-                       catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
+                       catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
                #endif
                
                read = new ReadOTUFile(sabundfile);     
@@ -200,9 +200,16 @@ int CatchAllCommand::execute() {
                                        string outputPath = m->getPathName(filename);
                                
                                        //create system command
-                                       string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
-                               
-                                       //run catchall
+                                       string catchAllCommand = "";
+                                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                                               catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+                                       #else
+                                               if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+                                               catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
+                                               //wrap entire string in ""
+                                               catchAllCommand = "\"" + catchAllCommand + "\"";
+                                       #endif
+                                                                       //run catchall
                                        system(catchAllCommand.c_str());
                                
                                        remove(filename.c_str());
@@ -236,7 +243,14 @@ int CatchAllCommand::execute() {
                                        string outputPath = m->getPathName(filename);
                                        
                                        //create system command
-                                       string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+                                       string catchAllCommand = "";
+                                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                                               catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+                                       #else
+                                               if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+                                               catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
+                                               catchAllCommand = "\"" + catchAllCommand + "\"";
+                                       #endif
 
                                        //run catchall
                                        system(catchAllCommand.c_str());
@@ -293,7 +307,14 @@ int CatchAllCommand::execute() {
                        string outputPath = m->getPathName(filename);
                        
                        //create system command
-                       string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
+                       string catchAllCommand = "";
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+                       #else
+                               if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+                               catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
+                               catchAllCommand = "\"" + catchAllCommand + "\"";
+                       #endif
                        
                        //run catchall
                        system(catchAllCommand.c_str());
@@ -427,6 +448,3 @@ int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out
        }
 }
 /**************************************************************************************/
-
-
-