changes while testing 1.26

[mothur.git] / removeotuscommand.cpp

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index 30f337bf7fffc90bcdf7d9ebb8cc97611c6ebd29..54adeb244693bb13e22884248e71deadeb5e2144 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -52,7 +52,27 @@ string RemoveOtusCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string RemoveOtusCommand::getOutputFileNameTag(string type, string inputName=""){      
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //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 == "group")            {   outputFileName = "pick" + m->getExtension(inputName);  }
+            else if (type == "list")        {   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, "RemoveOtusCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 ///**********************************************************************************************************************
 RemoveOtusCommand::RemoveOtusCommand(){        
        try {
@@ -134,7 +154,8 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
-                       else if (accnosfile == "not found") {  accnosfile = ""; }       
+                       else if (accnosfile == "not found") {  accnosfile = ""; }
+                       else { m->setAccnosFile(accnosfile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
@@ -142,7 +163,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                                groupfile = m->getGroupFile(); 
                                if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setGroupFile(groupfile); }   
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
@@ -150,7 +171,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                                listfile = m->getListFile(); 
                                if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setListFile(listfile); }     
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
@@ -181,12 +202,13 @@ 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; }
@@ -194,7 +216,7 @@ 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();
@@ -228,14 +250,14 @@ 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);
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
                
                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);
+               string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
                
                ofstream outGroup;
                m->openOutputFile(outputGroupFileName, outGroup);
@@ -257,7 +279,7 @@ 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);
@@ -291,7 +313,7 @@ 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;
@@ -405,30 +427,6 @@ 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);
-       }
-}
-//**********************************************************************************************************************