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

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 32426f3092d17468aa2f2599528f915423954376..48bf17119c98d832b0176dcab78675a94ecf80e8 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -22,19 +22,58 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
                else {
                        //valid paramters for this command
                        string AlignArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
-                                                                       "name", "group", "alignreport"};
+                                                                       "name", "group", "alignreport","outputdir","inputdir"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/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 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("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("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;            }
+                               }
+                               
+                               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("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;              }
+                               }
+                       }
+
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
@@ -52,6 +91,12 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
                        if (alignreport == "not open") { abort = true; }
                        else if (alignreport == "not found") { alignreport = ""; }      
                        
+                       //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 = ""; 
+                               outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it  
+                       }
+
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;
@@ -123,8 +168,8 @@ int ScreenSeqsCommand::execute(){
                
                set<string> badSeqNames;
                
-               string goodSeqFile = getRootName(fastafile) + "good" + getExtension(fastafile);
-               string badSeqFile = getRootName(fastafile) + "bad" + getExtension(fastafile);
+               string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
+               string badSeqFile =  outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
                
                ofstream goodSeqOut;    openOutputFile(goodSeqFile, goodSeqOut);
                ofstream badSeqOut;             openOutputFile(badSeqFile, badSeqOut);          
@@ -176,8 +221,8 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
        string seqName, seqList, group;
        set<string>::iterator it;
 
-       string goodNameFile = getRootName(namefile) + "good" + getExtension(namefile);
-       string badNameFile = getRootName(namefile) + "bad" + getExtension(namefile);
+       string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
+       string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
        
        ofstream goodNameOut;   openOutputFile(goodNameFile, goodNameOut);
        ofstream badNameOut;    openOutputFile(badNameFile, badNameOut);                
@@ -222,8 +267,8 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                ifstream inputGroups;
                openInputFile(groupfile, inputGroups);
 
-               string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
-               string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
+               string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
+               string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
                
                ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
                ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);              
@@ -265,8 +310,8 @@ void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
        string seqName, group;
        set<string>::iterator it;
        
-       string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
-       string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
+       string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
+       string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
        
        ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
        ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);              
@@ -308,8 +353,8 @@ void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
        string seqName, group;
        set<string>::iterator it;
        
-       string goodAlignReportFile = getRootName(alignreport) + "good" + getExtension(alignreport);
-       string badAlignReportFile = getRootName(alignreport) + "bad" + getExtension(alignreport);
+       string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
+       string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
        
        ofstream goodAlignReportOut;    openOutputFile(goodAlignReportFile, goodAlignReportOut);
        ofstream badAlignReportOut;             openOutputFile(badAlignReportFile, badAlignReportOut);