X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.cpp;h=9013e7d33f66f38b7ce1283ee92a45be3d4ab76c;hb=6d12ed0ba66fb35e9e2781fe3ca361e2293f2476;hp=105fd11b90afd8ce700bb3b20b66bcc9b39bdbb2;hpb=348a7bac1d3c5d17ae0e4a93b78f69f4e200a190;p=mothur.git

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 105fd11..9013e7d 100644
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -8,91 +8,46 @@
  */
 
 #include "chimeraseqscommand.h"
-#include "bellerophon.h"
-#include "pintail.h"
 
-//***************************************************************************************************************
-
-ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
+//**********************************************************************************************************************
+vector<string> ChimeraSeqsCommand::getValidParameters(){	
 	try {
-		abort = false;
-		
-		//allow user to run help
-		if(option == "help") { help(); abort = true; }
-		
-		else {
-			//valid paramters for this command
-			string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template" };
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-			
-			OptionParser parser(option);
-			map<string,string> parameters = parser.getParameters();
-			
-			ValidParameters validParameter;
-			
-			//check to make sure all parameters are valid for command
-			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
-				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
-			}
-			
-			//check for required parameters
-			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { abort = true; }
-			else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true;  }	
-			
-			templatefile = validParameter.validFile(parameters, "template", true);
-			if (templatefile == "not open") { abort = true; }
-			else if (templatefile == "not found") { templatefile = "";  }	
-			
-
-			string temp;
-			temp = validParameter.validFile(parameters, "filter", false);			if (temp == "not found") { temp = "T"; }
-			filter = isTrue(temp);
-			
-			temp = validParameter.validFile(parameters, "correction", false);		if (temp == "not found") { temp = "T"; }
-			correction = isTrue(temp);
-			
-			temp = validParameter.validFile(parameters, "processors", false);		if (temp == "not found") { temp = "1"; }
-			convert(temp, processors);
-			
-			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"; }
-			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;  }
-			
-
-		}
+		vector<string> myArray; 
+		return myArray;
 	}
 	catch(exception& e) {
-		errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
+		m->errorOut(e, "ChimeraSeqsCommand", "getValidParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-
-void ChimeraSeqsCommand::help(){
+vector<string> ChimeraSeqsCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray; 
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChimeraSeqsCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ChimeraSeqsCommand::getRequiredFiles(){	
 	try {
-		mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n");
-		mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method.  fasta is required.\n");
-		mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter.  The default is false. \n");
-		mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.   The default is true. \n");
-		mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
-		mothurOut("The method parameter allows you to specify the method for finding chimeric sequences.  The default is pintail. \n");
-		mothurOut("The chimera.seqs command should be in the following format: \n");
-		mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
-		mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
-		mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");	
+		vector<string> myArray;
+		return myArray;
 	}
 	catch(exception& e) {
-		errorOut(e, "ChimeraSeqsCommand", "help");
+		m->errorOut(e, "ChimeraSeqsCommand", "getRequiredFiles");
 		exit(1);
 	}
 }
+//***************************************************************************************************************
+
+ChimeraSeqsCommand::ChimeraSeqsCommand(string option)  {}
+//**********************************************************************************************************************
+
+void ChimeraSeqsCommand::help(){}
 
 //***************************************************************************************************************
 
@@ -101,44 +56,12 @@ ChimeraSeqsCommand::~ChimeraSeqsCommand(){	/*	do nothing	*/	}
 //***************************************************************************************************************
 
 int ChimeraSeqsCommand::execute(){
-	try{
-		
-		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;		}
-		
-		//set user options
-		chimera->setFilter(filter);
-		chimera->setCorrection(correction);
-		chimera->setProcessors(processors);
-		chimera->setWindow(window);
-		chimera->setIncrement(increment);
-		chimera->setTemplate(templatefile); 
-		
-		//find chimeras
-		chimera->getChimeras();
-		
-		string outputFileName = getRootName(fastafile) + method + ".chimeras";
-		ofstream out;
-		openOutputFile(outputFileName, out);
-		
-		//print results
-		chimera->print(out);
-		
-		out.close();
-		
-		delete chimera;
-		
-		return 0;
-		
-	}
-	catch(exception& e) {
-		errorOut(e, "ChimeraSeqsCommand", "execute");
-		exit(1);
-	}
+	
+		m->mothurOut("The chimera.seqs command has been broken up into 5 separate commands.\n");
+		m->mothurOut("The chimera.bellerophon, chimera.ccode, chimera.check, chimera.pintail and chimera.slayer commands.\n");
+	
+	return 0;
 }
+//**********************************************************************************************************************
 
-/**************************************************************************************************/