added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 05ddaf6459959ad39bb83720547a1b458c7ae807..b42a491fb4f8af800cb193eb71af2fa6692afe17 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -11,6 +11,7 @@
 #include "deconvolutecommand.h"
 #include "uc.h"
 #include "sequence.hpp"
+#include "referencedb.h"
 
 
 //**********************************************************************************************************************
@@ -40,7 +41,7 @@ vector<string> ChimeraUchimeCommand::setParameters(){
                CommandParameter pmaxlen("maxlen", "Number", "", "10000", "", "", "",false,false); parameters.push_back(pmaxlen);
                CommandParameter pucl("ucl", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pucl);
                CommandParameter pqueryfract("queryfract", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pqueryfract);
-               
+
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
@@ -112,7 +113,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(){
 //***************************************************************************************************************
 ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
        try {
-               abort = false; calledHelp = false;   
+               abort = false; calledHelp = false; 
+               ReferenceDB* rdb = ReferenceDB::getInstance();
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
@@ -300,7 +302,6 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        
-                       
                        string path;
                        it = parameters.find("reference");
                        //user has given a template file
@@ -313,12 +314,29 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                                        
                                        templatefile = validParameter.validFile(parameters, "reference", true);
                                        if (templatefile == "not open") { abort = true; }
-                                       else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.uchime command."); m->mothurOutEndLine(); abort = true;  }  
+                                       else if (templatefile == "not found") { //check for saved reference sequences
+                                               if (rdb->getSavedReference() != "") {
+                                                       templatefile = rdb->getSavedReference();
+                                                       m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + "."); m->mothurOutEndLine();
+                                               }else {
+                                                       m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); 
+                                                       m->mothurOutEndLine();
+                                                       abort = true; 
+                                               }
+                                       }
                                }
                        }else if (hasName) {  templatefile = "self"; }
-                       else { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.uchime command, unless you have a namefile."); m->mothurOutEndLine(); abort = true;  }       
-
-                       
+                       else { 
+                               if (rdb->getSavedReference() != "") {
+                                       templatefile = rdb->getSavedReference();
+                                       m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + "."); m->mothurOutEndLine();
+                               }else {
+                                       m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); 
+                                       m->mothurOutEndLine();
+                                       templatefile = ""; abort = true; 
+                               } 
+                       }
+                               
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        convert(temp, processors);
@@ -353,7 +371,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 
                        temp = validParameter.validFile(parameters, "skipgaps2", false);                                if (temp == "not found") { temp = "t"; }
                        skipgaps2 = m->isTrue(temp); 
-
+                       
+                       if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
                }
        }
        catch(exception& e) {