changes while testing

[mothur.git] / removeotuscommand.cpp

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 0fbed18b8be943fc4134cc18555c5a25cbd25b74..16fd8dce8bab96b030a57effd81d218e122628a5 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -14,13 +14,13 @@
 //**********************************************************************************************************************
 vector<string> RemoveOtusCommand::setParameters(){     
        try {
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               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);          }
@@ -52,7 +52,22 @@ string RemoveOtusCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string RemoveOtusCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "group")       {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],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, "RemoveOtusCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 ///**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(){        
        try {
@@ -182,12 +197,13 @@ int RemoveOtusCommand::execute(){
                groupMap->readMap();
                
                //get groups you want to remove
-               if (accnosfile != "") { readAccnos(); }
+               if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups);  }
                
                //make sure groups are valid
                //takes care of user setting groupNames that are invalid or setting groups=all
                SharedUtil* util = new SharedUtil();
-               util->setGroups(Groups, groupMap->namesOfGroups);
+               vector<string> allGroups = groupMap->getNamesOfGroups();
+               util->setGroups(Groups, allGroups);
                delete util;
                
                if (m->control_pressed) { delete groupMap; return 0; }
@@ -195,7 +211,7 @@ int RemoveOtusCommand::execute(){
                //read through the list file keeping any otus that contain any sequence from the groups selected
                readListGroup();
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -229,14 +245,20 @@ int RemoveOtusCommand::readListGroup(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label +  m->getExtension(listfile);
+               map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+        variables["[extension]"] = m->getExtension(listfile);
+               string outputFileName = getOutputFileName("list", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
                string GroupOutputDir = outputDir;
                if (outputDir == "") {  GroupOutputDir += m->hasPath(groupfile);  }
-               string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label  + m->getExtension(groupfile);
+               variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+               string outputGroupFileName = getOutputFileName("group", variables);
                
                ofstream outGroup;
                m->openOutputFile(outputGroupFileName, outGroup);
@@ -258,7 +280,7 @@ int RemoveOtusCommand::readListGroup(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((list != NULL) && (userLabels.size() != 0)) {
                        
-                       if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str());return 0;  }
+                       if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName);return 0;  }
                        
                        if(labels.count(list->getLabel()) == 1){
                                processList(list, groupMap, out, outGroup, wroteSomething);
@@ -292,7 +314,7 @@ int RemoveOtusCommand::readListGroup(){
                }
                
                
-               if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str()); return 0;  }
+               if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName); return 0;  }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -406,30 +428,6 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr
        }
 }
 //**********************************************************************************************************************
-void RemoveOtusCommand::readAccnos(){
-       try {
-               Groups.clear();
-               
-               ifstream in;
-               m->openInputFile(accnosfile, in);
-               string name;
-               
-               while(!in.eof()){
-                       in >> name;
-                       
-                       Groups.push_back(name);
-                       
-                       m->gobble(in);
-               }
-               in.close();             
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "RemoveOtusCommand", "readAccnos");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************