X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=663a6bf81d0fbbda91052e6cc0433df8e2d7fb4a;hb=4d7ffb38e091e9e7425d94e112551a3f90cacb0f;hp=36cc7766f03097235fa274f12330611d616cdacb;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;p=mothur.git

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 36cc776..663a6bf 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -9,40 +9,126 @@
 
 #include "deconvolutecommand.h"
 
+/**************************************************************************************/
+DeconvoluteCommand::DeconvoluteCommand(string option)  {	
+	try {
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"fasta", "name","outputdir","inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+			map<string, string>::iterator it;
+		
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("fasta");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["fasta"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("name");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["name"] = inputDir + it->second;		}
+				}
+			}
+
+			
+			//check for required parameters
+			inFastaName = validParameter.validFile(parameters, "fasta", true);
+			if (inFastaName == "not open") { abort = true; }
+			else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); m->mothurOutEndLine(); abort = true;  }	
+			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
+				outputDir = "";	
+				outputDir += hasPath(inFastaName); //if user entered a file with a path then preserve it	
+			}
+			
+			oldNameMapFName = validParameter.validFile(parameters, "name", true);
+			if (oldNameMapFName == "not open") { abort = true; }
+			else if (oldNameMapFName == "not found"){	oldNameMapFName = "";	}
+		}
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+void DeconvoluteCommand::help(){
+	try {
+		m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+		m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
+		m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
+		m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+		m->mothurOut("The unique.seqs command should be in the following format: \n");
+		m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "DeconvoluteCommand", "help");
+		exit(1);
+	}
+}
+
 /**************************************************************************************/
 int DeconvoluteCommand::execute() {	
 	try {
-		globaldata = GlobalData::getInstance();
-	
+		
+		if (abort == true) { return 0; }
+
 		//prepare filenames and open files
-		filename = globaldata->getFastaFile();
-		outputFileName = (getRootName(filename) + "names");
-		outFastafile = (getRootName(filename) + "unique.fasta");
+		string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
+		string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
 		
-		openInputFile(filename, in);
-		openOutputFile(outputFileName, out);
-		openOutputFile(outFastafile, outFasta);
-	
-		//constructor reads in file and store internally
-		fastamap = new FastaMap();
-	
-		//two columns separated by tabs sequence name and then sequence
-		fastamap->readFastaFile(in);
-		
-		//print out new names file 
-		//file contains 2 columns separated by tabs.  the first column is the groupname(name of first sequence found.
-		//the second column is the list of names of identical sequences separated by ','.
-		fastamap->printNamesFile(out);
-		fastamap->printCondensedFasta(outFasta);
+		FastaMap fastamap;
 	
+		if(oldNameMapFName == "")	{	fastamap.readFastaFile(inFastaName);					}
+		else						{	fastamap.readFastaFile(inFastaName, oldNameMapFName);	}
+		
+		if (m->control_pressed) { return 0; }
+		
+		fastamap.printCondensedFasta(outFastaFile);
+		fastamap.printNamesFile(outNameFile);
+		
+		if (m->control_pressed) { remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+		
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+		m->mothurOut(outFastaFile); m->mothurOutEndLine();	
+		m->mothurOut(outNameFile); m->mothurOutEndLine();
+		m->mothurOutEndLine();
+
+
+		
 		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "DeconvoluteCommand", "execute");
 		exit(1);
 	}
 }