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

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 03ccb82f6ef5c9c437942420163ac286fa35c203..d63dc79974ac007f504f7f1928ed8d0f031dcfe3 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -22,19 +22,78 @@ GetSeqsCommand::GetSeqsCommand(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 @@ GetSeqsCommand::GetSeqsCommand(string option){
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
                        
-                       if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); 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 listfile."); mothurOutEndLine(); abort = true;  }
                }
 
        }
@@ -117,7 +179,8 @@ int GetSeqsCommand::execute(){
 //**********************************************************************************************************************
 void GetSeqsCommand::readFasta(){
        try {
-               string outputFileName = getRootName(fastafile) + "pick" +  getExtension(fastafile);
+               if (outputDir == "") { outputDir += hasPath(fastafile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" +  getExtension(fastafile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -160,7 +223,8 @@ void GetSeqsCommand::readFasta(){
 //**********************************************************************************************************************
 void GetSeqsCommand::readList(){
        try {
-               string outputFileName = getRootName(listfile) + "pick" +  getExtension(listfile);
+               if (outputDir == "") { outputDir += hasPath(listfile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" +  getExtension(listfile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -224,8 +288,8 @@ void GetSeqsCommand::readList(){
 //**********************************************************************************************************************
 void GetSeqsCommand::readName(){
        try {
-       
-               string outputFileName = getRootName(namefile) + "pick" +  getExtension(namefile);
+               if (outputDir == "") { outputDir += hasPath(namefile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" +  getExtension(namefile);
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -307,8 +371,8 @@ void GetSeqsCommand::readName(){
 //**********************************************************************************************************************
 void GetSeqsCommand::readGroup(){
        try {
-       
-               string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+               if (outputDir == "") { outputDir += hasPath(groupfile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -353,7 +417,8 @@ void GetSeqsCommand::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 GetSeqsCommand::readAlign(){
        try {
-               string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+               if (outputDir == "") { outputDir += hasPath(alignfile); }
+               string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);