working on pam

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index 5a672204973d252ce0fca2968c97acfdd112c5b5..0ddc3d477336d34340497b82121cb0c032c9067b 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -13,13 +13,13 @@
 //**********************************************************************************************************************
 vector<string> MergeGroupsCommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none","group",false,false,true); parameters.push_back(pgroup);
+               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -52,26 +52,22 @@ string MergeGroupsCommand::getHelpString(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-string MergeGroupsCommand::getOutputFileNameTag(string type, string inputName=""){     
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string MergeGroupsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "shared")        {   outputFileName = "merge" +  m->getExtension(inputName);       }
-            else if (type == "group")    {   outputFileName =   "merge" +  m->getExtension(inputName);     }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MergeGroupsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "shared") {  pattern = "[filename],merge,[extension]"; } 
+        else if (type == "group") {  pattern = "[filename],merge,[extension]"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MergeGroupsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 MergeGroupsCommand::MergeGroupsCommand(){      
@@ -305,7 +301,10 @@ int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+        variables["[extension]"] = m->getExtension(sharedfile);
+               string outputFileName = getOutputFileName("shared", variables);
         outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
                
                ofstream out;
@@ -328,7 +327,7 @@ int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
                                
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+                               if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
                                process(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -342,7 +341,7 @@ int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
                                lookup = input.getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                
-                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+                               if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
                                process(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -384,7 +383,7 @@ int MergeGroupsCommand::processSharedFile(GroupMap*& designMap){
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        
-                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+                       if (!m->printedSharedHeaders) { lookup[0]->printHeaders(out); }
                        process(lookup, out);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -408,7 +407,10 @@ int MergeGroupsCommand::processGroupFile(GroupMap*& designMap){
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+               string outputFileName = getOutputFileName("group", variables);
                outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
                
                ofstream out;