fixed bug with windows version of trim.seqs when run with 1 processor. fixed file...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0c9504d09a109a39168af9b9d582ef20732e6647..d81045e500d71b138efe15ba4b178395d17f7ba4 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -304,7 +304,49 @@ CommandFactory::~CommandFactory(){
        delete shellcommand;
        delete pipecommand;
 }
+/***********************************************************/
 
+/***********************************************************/
+int CommandFactory::checkForRedirects(string optionString) {
+    try {
+        
+        int pos = optionString.find("outputdir");
+        if (pos != string::npos) { //user has set outputdir in command option string
+            string outputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }              
+                else if(optionString[i] == '=')  { foundEquals = true; }
+                if (foundEquals)       {   outputOption += optionString[i]; }
+            }
+            if(m->dirCheck(outputOption)){ 
+                setOutputDirectory(outputOption); 
+                m->mothurOut("Setting output directory to: " + outputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        pos = optionString.find("inputdir");
+        if (pos != string::npos) { //user has set inputdir in command option string
+            string intputOption = "";
+            bool foundEquals = false;
+            for(int i=pos;i<optionString.length();i++){
+                if(optionString[i] == ',')       { break;               }              
+                else if(optionString[i] == '=')  { foundEquals = true; }
+                if (foundEquals)       {   intputOption += optionString[i]; }
+            }
+            if(m->dirCheck(intputOption)){ 
+                setInputDirectory(intputOption); 
+                m->mothurOut("Setting input directory to: " + intputOption); m->mothurOutEndLine();
+            }
+        }
+        
+        return 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "CommandFactory", "getCommand");
+               exit(1);
+       }
+}
 /***********************************************************/
 
 /***********************************************************/
@@ -313,7 +355,9 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
        try {
         
                delete command;   //delete the old command
-               
+        
+        checkForRedirects(optionString);
+                       
                //user has opted to redirect output from dir where input files are located to some other place
                if (outputDir != "") { 
                        if (optionString != "") { optionString += ", outputdir=" + outputDir; }
@@ -463,6 +507,8 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
        try {
                delete pipecommand;   //delete the old command
                
+        checkForRedirects(optionString);
+        
                //user has opted to redirect output from dir where input files are located to some other place
                if (outputDir != "") { 
                        if (optionString != "") { optionString += ", outputdir=" + outputDir; }