continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 6af8aa3f3d4f1ae3085743eb90b4472edfbfe301..e8fa34df2e8f681bf158ef80b384a93e9ef49b4c 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -10,8 +10,8 @@
 #include "chimeraseqscommand.h"
 #include "bellerophon.h"
 #include "pintail.h"
-#include "alignedsimilarity.h"
 #include "ccode.h"
+#include "chimeracheckrdp.h"
 
 
 //***************************************************************************************************************
@@ -25,7 +25,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -63,7 +63,9 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                                if (ableToOpen == 1) { abort = true; }
                                in.close();
                        }
-
+                       
+                       method = validParameter.validFile(parameters, "method", false);                 if (method == "not found") { method = "pintail"; }
+                       
                        string temp;
                        temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
                        filter = isTrue(temp);
@@ -74,16 +76,21 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
                        convert(temp, processors);
                        
+                       temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
+                       convert(temp, ksize);
+                       
                        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 = "25"; }
+                       temp = validParameter.validFile(parameters, "increment", false);                
+                       if ((temp == "not found") && (method == "chimeracheck")) { temp = "10"; }
+                       else if (temp == "not found") { temp = "25"; }
                        convert(temp, increment);
                        
-                       temp = validParameter.validFile(parameters, "numwanted", false);                        if (temp == "not found") { temp = "20"; }
+                       temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "20"; }
                        convert(temp, numwanted);
 
-                       method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "pintail"; }
+                       
                        
                        if (((method == "pintail") || (method == "alignsim")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail and alignsim methods."); mothurOutEndLine(); abort = true;  }
                        
@@ -136,10 +143,10 @@ int ChimeraSeqsCommand::execute(){
                
                if (abort == true) { return 0; }
                
-               if (method == "bellerophon")    {               chimera = new Bellerophon(fastafile);                           }
-               else if (method == "pintail")   {               chimera = new Pintail(fastafile, templatefile);         }
-               //else if (method == "alignsim")        {               chimera = new AlignSim(fastafile, templatefile);        }
-               else if (method == "ccode")             {               chimera = new Ccode(fastafile, templatefile);           }
+               if (method == "bellerophon")                    {               chimera = new Bellerophon(fastafile);                                           }
+               else if (method == "pintail")                   {               chimera = new Pintail(fastafile, templatefile);                         }
+               else if (method == "ccode")                             {               chimera = new Ccode(fastafile, templatefile);                           }
+               else if (method == "chimeracheck")              {               chimera = new ChimeraCheckRDP(fastafile, templatefile);         }
                else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
                
                //set user options
@@ -160,6 +167,7 @@ int ChimeraSeqsCommand::execute(){
                chimera->setWindow(window);
                chimera->setIncrement(increment);
                chimera->setNumWanted(numwanted);
+               chimera->setKmerSize(ksize);
                                
                //find chimeras
                chimera->getChimeras();