started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstr...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index bd0ad956aababd99e7e926cfd7a305c20890f428..925de63c17bf44011e9bb29e1e4b9a7a980fd3ff 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -12,6 +12,7 @@
 #include "pintail.h"
 #include "ccode.h"
 #include "chimeracheckrdp.h"
+#include "chimeraslayer.h"
 
 
 //***************************************************************************************************************
@@ -25,7 +26,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -86,15 +87,34 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
                        svg = isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
+                       temp = validParameter.validFile(parameters, "window", false);   
+                       if ((temp == "not found") && (method == "chimeraslayer")) { temp = "100"; }                     
+                       else if (temp == "not found") { temp = "0"; }
                        convert(temp, window);
-                                       
+                       
+                       temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
+                       convert(temp, match);
+                       
+                       temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
+                       convert(temp, mismatch);
+                       
+                       temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.0"; }
+                       convert(temp, divR);
+                       
+                       temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
+                       convert(temp, minSimilarity);
+                       
+                       temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "5"; }
+                       convert(temp, parents); 
+                        
                        temp = validParameter.validFile(parameters, "increment", false);                
-                       if ((temp == "not found") && (method == "chimeracheck")) { temp = "10"; }
+                       if ((temp == "not found") && ((method == "chimeracheck") || (method == "chimeraslayer"))) { 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") && (method == "chimeraslayer")) { temp = "10"; }              
+                       else if (temp == "not found") { temp = "20"; }
                        convert(temp, numwanted);
 
                        
@@ -170,6 +190,7 @@ int ChimeraSeqsCommand::execute(){
                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 if (method == "chimeraslayer")             {               chimera = new ChimeraSlayer(fastafile, templatefile);           }
                else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0;          }
                
                //set user options
@@ -191,6 +212,12 @@ int ChimeraSeqsCommand::execute(){
                chimera->setKmerSize(ksize);
                chimera->setSVG(svg);
                chimera->setName(namefile);
+               chimera->setMatch(match);
+               chimera->setMisMatch(mismatch);
+               chimera->setDivR(divR);
+               chimera->setParents(parents);
+               chimera->setMinSim(minSimilarity);
+               
                                
                //find chimeras
                chimera->getChimeras();