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

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index f224b479d610b179511ec3bd2b88ca2afe2b210a..7af1ac67349843c59a282338387dc127239a1bcb 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -25,19 +25,54 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"label","unique","shared","fasta","list","group","output"};
+                       string Array[] =  {"label","unique","shared","fasta","list","group","output","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("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("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("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
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
@@ -65,6 +100,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){
                        groups = validParameter.validFile(parameters, "unique", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
+                               userGroups = "unique." + groups;
                                splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                                
@@ -73,6 +109,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option){
                        groups = validParameter.validFile(parameters, "shared", false);                 
                        if (groups == "not found") { groups = "";  }
                        else { 
+                               userGroups = groups;
                                splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                                unique = false;
@@ -128,11 +165,18 @@ int GetSharedOTUCommand::execute(){
                if (abort == true) { return 0; }
                
                groupMap = new GroupMap(groupfile);
-               groupMap->readMap();
+               int error = groupMap->readMap();
+               if (error == 1) { delete groupMap; return 0; }
+               
                globaldata->gGroupmap = groupMap;
                
                if (Groups.size() == 0) {
                        Groups = groupMap->namesOfGroups;
+                       
+                       //make string for outputfile name
+                       userGroups = "unique.";
+                       for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
+                       userGroups = userGroups.substr(0, userGroups.length()-1);
                }
        
                //put groups in map to find easier
@@ -238,10 +282,12 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                
                ofstream outNames;
                string outputFileNames;
+               
+               if (outputDir == "") { outputDir += hasPath(listfile); }
                if (output != "accnos") {
-                       outputFileNames = getRootName(listfile) + shared->getLabel() + ".shared.seqs";
+                       outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
                }else {
-                       outputFileNames = getRootName(listfile) + shared->getLabel() + ".accnos";
+                       outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
                }
                openOutputFile(outputFileNames, outNames);
                
@@ -340,8 +386,9 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                }else { mothurOut("\t" + toString(num)); mothurOutEndLine(); }
                
                //if fasta file provided output new fasta file
-               if ((fastafile != "") && wroteSomething) {      
-                       string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".shared.fasta";
+               if ((fastafile != "") && wroteSomething) {
+                       if (outputDir == "") { outputDir += hasPath(fastafile); }
+                       string outputFileFasta = outputDir + getRootName(getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
                        ofstream outFasta;
                        openOutputFile(outputFileFasta, outFasta);