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sffinfo bug with flow grams right index when clipQualRight=0
[mothur.git] / removegroupscommand.cpp
diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index a29906c5f41769c93b3675b88eb1267fa2eb7127..4f4b1580582b953c3b8318acc68345cc8d45ae48 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -16,17 +16,18 @@
 //**********************************************************************************************************************
 vector<string> RemoveGroupsCommand::setParameters(){   
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
-        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
-               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);         CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
-               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               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 pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);            
+        CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               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);          }
@@ -58,31 +59,26 @@ string RemoveGroupsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string RemoveGroupsCommand::getOutputFileNameTag(string type, string inputName=""){    
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string RemoveGroupsCommand::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 == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "count")       {   outputFileName =  "pick.count_table";   }
-            else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "shared")      {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "design")      {   outputFileName =  "pick" + 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, "RemoveGroupsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "fasta")            {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "taxonomy")    {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "shared")      {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "design")      {   pattern = "[filename],pick,[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, "RemoveGroupsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 RemoveGroupsCommand::RemoveGroupsCommand(){    
@@ -468,7 +464,10 @@ int RemoveGroupsCommand::readFasta(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+        variables["[extension]"] = m->getExtension(fastafile);
+               string outputFileName = getOutputFileName("fasta", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -529,6 +528,10 @@ int RemoveGroupsCommand::readShared(){
                //that way we can take advantage of the reads in inputdata and sharedRabundVector
                InputData* tempInput = new InputData(sharedfile, "sharedfile");
                vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
+        
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+        variables["[extension]"] = m->getExtension(sharedfile);
        
                //save m->Groups
                vector<string> allGroupsNames = m->getAllGroups();
@@ -560,7 +563,8 @@ int RemoveGroupsCommand::readShared(){
                
                while(lookup[0] != NULL) {
                        
-                       string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile);
+                       variables["[tag]"] = lookup[0]->getLabel();
+            string outputFileName = getOutputFileName("shared", variables);
                        ofstream out;
                        m->openOutputFile(outputFileName, out);
                        outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
@@ -608,7 +612,11 @@ int RemoveGroupsCommand::readList(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+               map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[extension]"] = m->getExtension(listfile);
+               string outputFileName = getOutputFileName("list", variables);
+
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -698,7 +706,10 @@ int RemoveGroupsCommand::readName(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);            
+               map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+        variables["[extension]"] = m->getExtension(namefile);
+               string outputFileName = getOutputFileName("name", variables);   
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -778,7 +789,10 @@ int RemoveGroupsCommand::readGroup(){
        try {
                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);  
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -824,7 +838,10 @@ int RemoveGroupsCommand::readCount(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+               map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+        variables["[extension]"] = m->getExtension(countfile);
+               string outputFileName = getOutputFileName("count", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -905,7 +922,10 @@ int RemoveGroupsCommand::readDesign(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(designfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile);
+        map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
+        variables["[extension]"] = m->getExtension(designfile);
+               string outputFileName = getOutputFileName("design", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -953,7 +973,10 @@ int RemoveGroupsCommand::readTax(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+               map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+        variables["[extension]"] = m->getExtension(taxfile);
+               string outputFileName = getOutputFileName("taxonomy", variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
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