X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=e23a0ac6a431ad14cdab21fb0bfa4276f4afd8c6;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index e23a0ac..36e0f60 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -10,6 +10,53 @@
 #include "secondarystructurecommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"fasta","map", "outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){	
+	try {
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["aligncheck"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"fasta","map"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 AlignCheckCommand::AlignCheckCommand(string option)  {
@@ -36,6 +83,10 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["aligncheck"] = tempOutNames;
+			
 			//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 = "";		}
@@ -44,7 +95,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 				it = parameters.find("fasta");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->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;		}
 				}
@@ -52,7 +103,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 				it = parameters.find("map");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["map"] = inputDir + it->second;		}
 				}
@@ -70,7 +121,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 			//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(fastafile); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it	
 			}
 
 		}
@@ -109,19 +160,20 @@ int AlignCheckCommand::execute(){
 		readMap();
 		
 		ifstream in;
-		openInputFile(fastafile, in);
+		m->openInputFile(fastafile, in);
 		
 		ofstream out;
-		string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
-		openOutputFile(outfile, out);
+		string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+		m->openOutputFile(outfile, out);
 		
 		out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
 		out << "loop" << '\t' << "tilde" << '\t' << "total" << endl;
 
 		
 		while(!in.eof()){
+			if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
 			
-			Sequence seq(in);  gobble(in);
+			Sequence seq(in);  m->gobble(in);
 			if (seq.getName() != "") {
 				statData data = getStats(seq.getAligned());
 				
@@ -135,9 +187,11 @@ int AlignCheckCommand::execute(){
 		in.close();
 		out.close();
 		
+		if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outfile); m->mothurOutEndLine();	
+		m->mothurOut(outfile); m->mothurOutEndLine();	outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
 		m->mothurOutEndLine();
 		
 		return 0;		
@@ -155,13 +209,13 @@ void AlignCheckCommand::readMap(){
 		structMap.resize(1, 0);
 		ifstream in;
 		
-		openInputFile(mapfile, in);
+		m->openInputFile(mapfile, in);
 		
 		while(!in.eof()){
 			int position;
 			in >> position;
 			structMap.push_back(position);	
-			gobble(in);
+			m->gobble(in);
 		}
 		in.close();