X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.cpp;h=d60470cdebcc70114afcb79cc08edbb333816292;hb=4160a27002f4a3ca436fcd62eca0366b09f8e901;hp=360e1955bab31055c4ad06f71c933a4228058386;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;p=mothur.git

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 360e195..d60470c 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -11,50 +11,55 @@
 #include "sequence.hpp"
 #include "listvector.hpp"
 
+
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getValidParameters(){	
+vector<string> ListSeqsCommand::setParameters(){	
 	try {
-		string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+		CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+		CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
+		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+		CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ListSeqsCommand", "getValidParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-ListSeqsCommand::ListSeqsCommand(){	
-	try {
-		abort = true; calledHelp = true; 
-		vector<string> tempOutNames;
-		outputTypes["accnos"] = tempOutNames;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+		m->errorOut(e, "ListSeqsCommand", "setParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredParameters(){	
+string ListSeqsCommand::getHelpString(){	
 	try {
-		string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","or"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-		return myArray;
+		string helpString = "";
+		helpString += "The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+		helpString += "The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n";
+		helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
+		helpString += "Example list.seqs(fasta=amazon.fasta).\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ListSeqsCommand", "getRequiredParameters");
+		m->errorOut(e, "ListSeqsCommand", "getHelpString");
 		exit(1);
 	}
 }
+
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredFiles(){	
+ListSeqsCommand::ListSeqsCommand(){	
 	try {
-		vector<string> myArray;
-		return myArray;
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["accnos"] = tempOutNames;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ListSeqsCommand", "getRequiredFiles");
+		m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
 		exit(1);
 	}
 }
@@ -68,9 +73,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -186,22 +189,6 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void ListSeqsCommand::help(){
-	try {
-		m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
-		m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n");
-		m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
-		m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ListSeqsCommand", "help");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-
 int ListSeqsCommand::execute(){
 	try {
 		
@@ -226,6 +213,7 @@ int ListSeqsCommand::execute(){
 
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
+		outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
 		
 		//output to .accnos file
 		for (int i = 0; i < names.size(); i++) {
@@ -237,12 +225,21 @@ int ListSeqsCommand::execute(){
 		out.close();
 		
 		if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
-
+		
+		m->setAccnosFile(outputFileName);
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
+		m->mothurOut(outputFileName); m->mothurOutEndLine();	
 		m->mothurOutEndLine();
 		
+		//set accnos file as new current accnosfile
+		string current = "";
+		itTypes = outputTypes.find("accnos");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+		}
+		
 		return 0;		
 	}
 
@@ -259,19 +256,33 @@ int ListSeqsCommand::readFasta(){
 		ifstream in;
 		m->openInputFile(fastafile, in);
 		string name;
-	
+		
+		//ofstream out;
+		//string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+		//m->openOutputFile(newFastaName, out);
+		//int count = 1;
+		//string lastName = "";
+		
 		while(!in.eof()){
 			
 			if (m->control_pressed) { in.close(); return 0; }
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
+			//if (lastName == "") { lastName = name; }
+			//if (name != lastName) { count = 1; }
+		//	lastName = name;
+			
+			//Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+			//newSeq.printSequence(out);
 			
 			if (name != "") {  names.push_back(name);  }
 			
 			m->gobble(in);
+			//count++;
 		}
 		in.close();	
+		//out.close();
 		
 		return 0;
 
@@ -444,6 +455,7 @@ int ListSeqsCommand::readTax(){
 			names.push_back(firstCol);
 			
 			m->gobble(in);
+			
 		}
 		in.close();