working on current change

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 04c3bd325edf89638503cdcb49c2842c75ed1d17..71a2db9723c32a39ea8e158074fbfac8a29de1ca 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -25,7 +25,8 @@ vector<string> GetSeqsCommand::setParameters(){
                CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-               
+               CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
+
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
@@ -81,6 +82,7 @@ GetSeqsCommand::GetSeqsCommand(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();
@@ -199,21 +201,24 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                        m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); 
                                        abort = true;
                                } 
-                       }       
+                       }else { m->setAccnosFile(accnosfile); } 
                        
                        if (accnosfile2 == "not found") { accnosfile2 = ""; }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -222,14 +227,22 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; }
                        else if (qualfile == "not found") {  qualfile = "";  }
+                       else { m->setQualFile(qualfile); }
+                       
+                       accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
+                       if (accnosfile2 == "not open") { abort = true; }
+                       else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
+                       
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
@@ -823,7 +836,15 @@ int GetSeqsCommand::compareAccnos(){
                        in >> name;
                        
                        if (namesAccnos.count(name) == 0){ //name unique to accnos2
-                               namesAccnos2.insert(name);
+                               int pos = name.find_last_of('_');
+                               string tempName = name;
+                               if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
+                               if (namesAccnos.count(tempName) == 0){
+                                       namesAccnos2.insert(name);
+                               }else { //you are in both so erase
+                                       namesAccnos.erase(name);
+                                       namesDups.insert(name);
+                               }
                        }else { //you are in both so erase
                                namesAccnos.erase(name);
                                namesDups.insert(name);