X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=31b6bb7137579796c3a6652b283858bff435731a;hp=ed71559fba582e8d5a696621ab943a4851579704;hb=0470f6d037aacb3563c3f7010708120a4a67d4e6;hpb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index ed71559..31b6bb7 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -12,10 +12,74 @@
 
 //***************************************************************************************************************
 
-ScreenSeqsCommand::ScreenSeqsCommand(){
+ScreenSeqsCommand::ScreenSeqsCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
-		if(globaldata->getFastaFile() == "")		{	cout << "you must provide a fasta formatted file" << endl;	}
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string AlignArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
+			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+			
+			parser = new OptionParser();
+			parser->parse(option, parameters);   	delete parser; 
+			
+			ValidParameters* validParameter = new ValidParameters();
+		
+			//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;  }
+			}
+			
+			//check for required parameters
+			fastafile = validParameter->validFile(parameters, "fasta", true);
+			if (fastafile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
+			else if (fastafile == "not open") { abort = true; }	
+			else { globaldata->setFastaFile(fastafile); }
+		
+			groupfile = validParameter->validFile(parameters, "group", true);
+			if (groupfile == "not open") { abort = true; }	
+			else if (groupfile == "not found") { groupfile = ""; }
+			else { 
+				globaldata->setGroupFile(groupfile);
+			}
+			
+			namefile = validParameter->validFile(parameters, "name", true);
+			if (namefile == "not open") { abort = true; }
+			else if (namefile == "not found") { namefile = ""; }	
+			else { 
+				globaldata->setNameFile(namefile);
+			}
+
+		
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			string temp;
+			temp = validParameter->validFile(parameters, "start", false);			if (temp == "not found") { temp = "-1"; }
+			convert(temp, startPos); 
+		
+			temp = validParameter->validFile(parameters, "end", false);				if (temp == "not found") { temp = "-1"; }
+			convert(temp, endPos);  
+
+			temp = validParameter->validFile(parameters, "maxambig", false);		if (temp == "not found") { temp = "-1"; }
+			convert(temp, maxAmbig);  
+
+			temp = validParameter->validFile(parameters, "maxhomop", false);		if (temp == "not found") { temp = "-1"; }
+			convert(temp, maxHomoP);  
+
+			temp = validParameter->validFile(parameters, "minlength", false);		if (temp == "not found") { temp = "-1"; }
+			convert(temp, minLength); 
+			
+			temp = validParameter->validFile(parameters, "maxlength", false);		if (temp == "not found") { temp = "-1"; }
+			convert(temp, maxLength); 
+		
+			delete validParameter;
+		}
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function ScreenSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -26,6 +90,36 @@ ScreenSeqsCommand::ScreenSeqsCommand(){
 		exit(1);
 	}	
 }
+//**********************************************************************************************************************
+
+void ScreenSeqsCommand::help(){
+	try {
+		cout << "The screen.seqs command reads a fastafile and creates ....." << "\n";
+		cout << "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group." << "\n";
+		cout << "The fasta parameter is required." << "\n";
+		cout << "The start parameter .... The default is -1." << "\n";
+		cout << "The end parameter .... The default is -1." << "\n";
+		cout << "The maxambig parameter .... The default is -1." << "\n";
+		cout << "The maxhomop parameter .... The default is -1." << "\n";
+		cout << "The minlength parameter .... The default is -1." << "\n";
+		cout << "The maxlength parameter .... The default is -1." << "\n";
+		cout << "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile." << "\n";
+		cout << "The screen.seqs command should be in the following format: " << "\n";
+		cout << "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  " << "\n";
+		cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  " << "\n";	
+		cout << "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...)." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ScreenSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
 
 //***************************************************************************************************************
 
@@ -35,21 +129,16 @@ ScreenSeqsCommand::~ScreenSeqsCommand(){	/*	do nothing	*/	}
 
 int ScreenSeqsCommand::execute(){
 	try{
-		int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
-		convert(globaldata->getStartPos(), startPos);
-		convert(globaldata->getEndPos(), endPos);
-		convert(globaldata->getMaxAmbig(), maxAmbig);
-		convert(globaldata->getMaxHomoPolymer(), maxHomoP);
-		convert(globaldata->getMinLength(), minLength);
-		convert(globaldata->getMaxLength(), maxLength);
 		
+		if (abort == true) { return 0; }
+				
 		ifstream inFASTA;
-		openInputFile(globaldata->getFastaFile(), inFASTA);
+		openInputFile(fastafile, inFASTA);
 		
 		set<string> badSeqNames;
 		
-		string goodSeqFile = getRootName(globaldata->getFastaFile()) + "good" + getExtension(globaldata->getFastaFile());
-		string badSeqFile = getRootName(globaldata->getFastaFile()) + "bad" + getExtension(globaldata->getFastaFile());
+		string goodSeqFile = getRootName(fastafile) + "good" + getExtension(fastafile);
+		string badSeqFile = getRootName(fastafile) + "bad" + getExtension(fastafile);
 		
 		ofstream goodSeqOut;	openOutputFile(goodSeqFile, goodSeqOut);
 		ofstream badSeqOut;		openOutputFile(badSeqFile, badSeqOut);		
@@ -73,10 +162,10 @@ int ScreenSeqsCommand::execute(){
 			}
 			gobble(inFASTA);
 		}	
-		if(globaldata->getNameFile() != ""){
+		if(namefile != ""){
 			screenNameGroupFile(badSeqNames);
 		}
-		else if(globaldata->getGroupFile() != ""){
+		else if(groupfile != ""){
 			screenGroupFile(badSeqNames);
 		}