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

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index bc96e0530993e63cf099381a1ccd8829f9cc7714..fd80ec965b4040f78dce01579e1974760fbb2a89 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -9,6 +9,7 @@
 
 #include "chimeraccodecommand.h"
 #include "ccode.h"
+#include "referencedb.h"
 //**********************************************************************************************************************
 vector<string> ChimeraCcodeCommand::setParameters(){   
        try {
@@ -21,6 +22,7 @@ vector<string> ChimeraCcodeCommand::setParameters(){
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -49,6 +51,7 @@ string ChimeraCcodeCommand::getHelpString(){
                helpString += "The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n";
                helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n";
                helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n";
+               helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
                helpString += "The chimera.ccode command should be in the following format: \n";
                helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n";
                helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n";
@@ -79,6 +82,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(){
 ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
        try {
                abort = false; calledHelp = false;   
+               ReferenceDB* rdb = ReferenceDB::getInstance();
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
@@ -197,10 +201,6 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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 = ""; }
-
-                       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.ccode command."); m->mothurOutEndLine(); abort = true;  }            
                        
                        maskfile = validParameter.validFile(parameters, "mask", false);
                        if (maskfile == "not found") { maskfile = "";  }        
@@ -230,6 +230,28 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "20"; }
                        convert(temp, numwanted);
+                       
+                       temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
+                       save = m->isTrue(temp); 
+                       rdb->save = save; 
+                       if (save) { //clear out old references
+                               rdb->clearMemory();     
+                       }
+                       
+                       //this has to go after save so that if the user sets save=t and provides no reference we abort
+                       templatefile = validParameter.validFile(parameters, "reference", true);
+                       if (templatefile == "not found") { 
+                               //check for saved reference sequences
+                               if (rdb->referenceSeqs.size() != 0) {
+                                       templatefile = "saved";
+                               }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 (templatefile == "not open") { abort = true; } 
+                       else {  if (save) {     rdb->setSavedReference(templatefile);   }       }
+                       
 
                }
        }