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

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 5b249d7ff6892a53ce0493c3fa5319468681a8bd..584e9874fd4cea4136d45c184a4c0662973c3b25 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "chimeracheckcommand.h"
+#include "referencedb.h"
 
 //**********************************************************************************************************************
 vector<string> ChimeraCheckCommand::setParameters(){   
@@ -21,7 +22,8 @@ vector<string> ChimeraCheckCommand::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);          }
                return myArray;
@@ -50,6 +52,7 @@ string ChimeraCheckCommand::getHelpString(){
                helpString += "The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n";
                helpString += "The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n";
                helpString += "You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \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.check command should be in the following format: \n";
                helpString += "chimera.check(fasta=yourFastaFile, reference=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n";
                helpString += "Example: chimera.check(fasta=AD.fasta, reference=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n";
@@ -77,7 +80,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(){
 //***************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(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; }
@@ -195,10 +199,6 @@ ChimeraCheckCommand::ChimeraCheckCommand(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.check command."); m->mothurOutEndLine(); abort = true;  }   
                        
                        namefile = validParameter.validFile(parameters, "name", false);
                        if (namefile == "not found") { namefile = ""; }
@@ -283,6 +283,28 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        m->setProcessors(temp);
                        convert(temp, processors);
                        
+                       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);   }       }
+                       
+                       
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
                        convert(temp, ksize);