chimeracheck method added

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index e8fa34df2e8f681bf158ef80b384a93e9ef49b4c..2efed601c74832305eeb39e8c1dcbc8afd80d0d2 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -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", "ksize" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -54,7 +54,11 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        quanfile = validParameter.validFile(parameters, "quantile", true);
                        if (quanfile == "not open") { abort = true; }
                        else if (quanfile == "not found") { quanfile = "";  }
-                               
+                       
+                       namefile = validParameter.validFile(parameters, "name", true);
+                       if (namefile == "not open") { abort = true; }
+                       else if (namefile == "not found") { namefile = "";  }
+
                        maskfile = validParameter.validFile(parameters, "mask", false);
                        if (maskfile == "not found") { maskfile = "";  }        
                        else if (maskfile != "default")  { 
@@ -79,6 +83,9 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
                        convert(temp, ksize);
                        
+                       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"; }
                        convert(temp, window);
                                        
@@ -153,12 +160,10 @@ int ChimeraSeqsCommand::execute(){
                if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine();  }
                
                //saves time to avoid generating it
-               if (consfile != "")                     {               chimera->setCons(consfile);                                             }
-               else                                            {               chimera->setCons("");                                                   }
+               chimera->setCons(consfile);     
                
                //saves time to avoid generating it
-               if (quanfile != "")                     {               chimera->setQuantiles(quanfile);                                }
-               else                                            {               chimera->setQuantiles("");                                              }
+               chimera->setQuantiles(quanfile);                                
                
                chimera->setMask(maskfile);
                chimera->setFilter(filter);
@@ -168,6 +173,8 @@ int ChimeraSeqsCommand::execute(){
                chimera->setIncrement(increment);
                chimera->setNumWanted(numwanted);
                chimera->setKmerSize(ksize);
+               chimera->setSVG(svg);
+               chimera->setName(namefile);
                                
                //find chimeras
                chimera->getChimeras();