added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / removeotuscommand.cpp

diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp
index d1c12c888d8e34f377e4ea6ae661fad997021335..25ed99eacbbd3c6dcbcad18daf5fef44ec13b746 100644 (file)
--- a/removeotuscommand.cpp
+++ b/removeotuscommand.cpp
@@ -44,7 +44,7 @@ string RemoveOtusCommand::getHelpString(){
                helpString += "The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n";
                helpString += "Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n";
                helpString += "or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -75,6 +75,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -133,7 +134,8 @@ 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; }
@@ -141,7 +143,7 @@ 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; }
@@ -149,7 +151,7 @@ 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 = ""; }
@@ -185,7 +187,8 @@ int RemoveOtusCommand::execute(){
                //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; }
@@ -193,7 +196,7 @@ 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();
@@ -256,7 +259,7 @@ 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);
@@ -290,7 +293,7 @@ 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;