fixed bugs in venn and aligner

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 105fd11b90afd8ce700bb3b20b66bcc9b39bdbb2..28e3e6a72d22e787b796fa04b8edda00eca560f8 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -22,7 +22,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -44,6 +44,10 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        if (templatefile == "not open") { abort = true; }
                        else if (templatefile == "not found") { templatefile = "";  }   
                        
+                       consfile = validParameter.validFile(parameters, "conservation", true);
+                       if (consfile == "not open") { abort = true; }
+                       else if (consfile == "not found") { consfile = "";  }   
+                       
 
                        string temp;
                        temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "T"; }
@@ -58,12 +62,12 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
                        convert(temp, window);
                                        
-                       temp = validParameter.validFile(parameters, "increment", false);                        if (temp == "not found") { temp = "10"; }
+                       temp = validParameter.validFile(parameters, "increment", false);                        if (temp == "not found") { temp = "25"; }
                        convert(temp, increment);
                                
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "pintail"; }
                        
-                       if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true;  }
+                       if ((method == "pintail") && (templatefile == "") && (consfile == "")) { mothurOut("You must provide a template or conservation file with the pintail method."); mothurOutEndLine(); abort = true;  }
                        
 
                }
@@ -105,9 +109,11 @@ int ChimeraSeqsCommand::execute(){
                
                if (abort == true) { return 0; }
                
-               if (method == "bellerophon")    {       chimera = new Bellerophon(fastafile);   }
-               else if (method == "pintail")   {       chimera = new Pintail(fastafile);               }
-               else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
+               if (method == "bellerophon")    {               chimera = new Bellerophon(fastafile);                   }
+               else if (method == "pintail")   {               chimera = new Pintail(fastafile, templatefile); 
+                       if (consfile != "")                     {               chimera->setCons(consfile);                                             }
+                       else                                            {               chimera->setCons("");                                                   }
+               }else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;         }
                
                //set user options
                chimera->setFilter(filter);
@@ -115,8 +121,7 @@ int ChimeraSeqsCommand::execute(){
                chimera->setProcessors(processors);
                chimera->setWindow(window);
                chimera->setIncrement(increment);
-               chimera->setTemplate(templatefile); 
-               
+                               
                //find chimeras
                chimera->getChimeras();
                
@@ -139,6 +144,5 @@ int ChimeraSeqsCommand::execute(){
                exit(1);
        }
 }
-
 /**************************************************************************************************/