added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 790cf79f43505ac56e52681ff86a572ab3453e79..a8f03e06b29c505d219a8a4f5770999586e182ae 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -22,19 +22,78 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list" };
+                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
                        ValidParameters validParameter;
+                       map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
-                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
+                       
+                       //if the user changes the input directory command factory will send this info to us in the output parameter 
+                       string inputDir = validParameter.validFile(parameters, "inputdir", false);              
+                       if (inputDir == "not found"){   inputDir = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("alignreport");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
+                               }
+                               
+                               it = parameters.find("fasta");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
+                               }
+                               
+                               it = parameters.find("accnos");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
+                               }
+                               
+                               it = parameters.find("list");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["list"] = inputDir + it->second;             }
+                               }
+                               
+                               it = parameters.find("name");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["name"] = inputDir + it->second;             }
+                               }
+                               
+                               it = parameters.find("group");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["group"] = inputDir + it->second;            }
+                               }
+                       }
+
+                       
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
@@ -62,7 +121,10 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); mothurOutEndLine(); abort = true; }
                        
-                       if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); mothurOutEndLine(); abort = true;  }
+                       int okay = 2;
+                       if (outputDir != "") { okay++; }
+                       
+                       if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); mothurOutEndLine(); abort = true;  }
                }
 
        }
@@ -117,6 +179,7 @@ int RemoveSeqsCommand::execute(){
 //**********************************************************************************************************************
 void RemoveSeqsCommand::readFasta(){
        try {
+               if (outputDir == "") {  outputDir += hasPath(fastafile);  }
                string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
                ofstream out;
                openOutputFile(outputFileName, out);
@@ -158,6 +221,7 @@ void RemoveSeqsCommand::readFasta(){
 //**********************************************************************************************************************
 void RemoveSeqsCommand::readList(){
        try {
+               if (outputDir == "") {  outputDir += hasPath(listfile);  }
                string outputFileName = getRootName(listfile) + "pick" +  getExtension(listfile);
                ofstream out;
                openOutputFile(outputFileName, out);
@@ -222,7 +286,7 @@ void RemoveSeqsCommand::readList(){
 //**********************************************************************************************************************
 void RemoveSeqsCommand::readName(){
        try {
-       
+               if (outputDir == "") {  outputDir += hasPath(namefile);  }
                string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
 
                ofstream out;
@@ -305,7 +369,7 @@ void RemoveSeqsCommand::readName(){
 //**********************************************************************************************************************
 void RemoveSeqsCommand::readGroup(){
        try {
-       
+               if (outputDir == "") {  outputDir += hasPath(groupfile);  }
                string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
                ofstream out;
                openOutputFile(outputFileName, out);
@@ -348,6 +412,7 @@ void RemoveSeqsCommand::readGroup(){
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 void RemoveSeqsCommand::readAlign(){
        try {
+               if (outputDir == "") {  outputDir += hasPath(alignfile);  }
                string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);