X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=f1804ed8b826d00b4993a708804733335bb1b194;hb=134a9c1275862a6b3ea10a2c0f11965c0a535854;hp=b77e69f665b078c0bf52956099f455833eb81749;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index b77e69f..f1804ed 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -12,7 +12,59 @@
 #include "listvector.hpp"
 
 //**********************************************************************************************************************
-
+vector<string> RemoveSeqsCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir", "dups" };
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RemoveSeqsCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+RemoveSeqsCommand::RemoveSeqsCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["fasta"] = tempOutNames;
+		outputTypes["taxonomy"] = tempOutNames;
+		outputTypes["name"] = tempOutNames;
+		outputTypes["group"] = tempOutNames;
+		outputTypes["alignreport"] = tempOutNames;
+		outputTypes["list"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> RemoveSeqsCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"accnos"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RemoveSeqsCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> RemoveSeqsCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RemoveSeqsCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 	try {
 		abort = false;
@@ -36,6 +88,15 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["fasta"] = tempOutNames;
+			outputTypes["taxonomy"] = tempOutNames;
+			outputTypes["name"] = tempOutNames;
+			outputTypes["group"] = tempOutNames;
+			outputTypes["alignreport"] = tempOutNames;
+			outputTypes["list"] = tempOutNames;
+			
 			//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 = "";		}
 			
@@ -210,8 +271,10 @@ int RemoveSeqsCommand::execute(){
 //**********************************************************************************************************************
 int RemoveSeqsCommand::readFasta(){
 	try {
-		if (outputDir == "") {  outputDir += m->hasPath(fastafile);  }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -241,7 +304,7 @@ int RemoveSeqsCommand::readFasta(){
 		out.close();
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); 
+		outputTypes["fasta"].push_back(outputFileName); 
 		
 		return 0;
 		
@@ -254,8 +317,10 @@ int RemoveSeqsCommand::readFasta(){
 //**********************************************************************************************************************
 int RemoveSeqsCommand::readList(){
 	try {
-		if (outputDir == "") {  outputDir += m->hasPath(listfile);  }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
+		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		
@@ -310,7 +375,7 @@ int RemoveSeqsCommand::readList(){
 		out.close();
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); 
+		outputTypes["list"].push_back(outputFileName); 
 				
 		return 0;
 
@@ -323,8 +388,9 @@ int RemoveSeqsCommand::readList(){
 //**********************************************************************************************************************
 int RemoveSeqsCommand::readName(){
 	try {
-		if (outputDir == "") {  outputDir += m->hasPath(namefile);  }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
 
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
@@ -338,7 +404,7 @@ int RemoveSeqsCommand::readName(){
 		while(!in.eof()){
 			if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 
-			in >> firstCol;				
+			in >> firstCol;		m->gobble(in);		
 			in >> secondCol;			
 
 			vector<string> parsedNames;
@@ -395,7 +461,7 @@ int RemoveSeqsCommand::readName(){
 		out.close();
 
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); 
+		outputTypes["name"].push_back(outputFileName);
 				
 		return 0;
 	}
@@ -408,8 +474,10 @@ int RemoveSeqsCommand::readName(){
 //**********************************************************************************************************************
 int RemoveSeqsCommand::readGroup(){
 	try {
-		if (outputDir == "") {  outputDir += m->hasPath(groupfile);  }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 
@@ -437,7 +505,7 @@ int RemoveSeqsCommand::readGroup(){
 		out.close();
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); 
+		outputTypes["group"].push_back(outputFileName); 
 		
 		return 0;
 	}
@@ -449,8 +517,9 @@ int RemoveSeqsCommand::readGroup(){
 //**********************************************************************************************************************
 int RemoveSeqsCommand::readTax(){
 	try {
-		if (outputDir == "") {  outputDir += m->hasPath(taxfile);  }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 
@@ -478,7 +547,7 @@ int RemoveSeqsCommand::readTax(){
 		out.close();
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); 
+		outputTypes["taxonomy"].push_back(outputFileName);
 		
 		return 0;
 	}
@@ -491,8 +560,10 @@ int RemoveSeqsCommand::readTax(){
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 int RemoveSeqsCommand::readAlign(){
 	try {
-		if (outputDir == "") {  outputDir += m->hasPath(alignfile);  }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
+		
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 
@@ -542,7 +613,7 @@ int RemoveSeqsCommand::readAlign(){
 		out.close();
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputNames.push_back(outputFileName); 
+		outputTypes["alignreport"].push_back(outputFileName);
 		
 		return 0;