#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 {
+ abort = true;
+ //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) {
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 = ""; }
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; }
}
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; }
}
//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
}
}
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());
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;
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();