#include "sequence.hpp"
#include "listvector.hpp"
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ListSeqsCommand::ListSeqsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ListSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ListSeqsCommand::ListSeqsCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["accnos"] = 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 = ""; }
it = parameters.find("alignreport");
//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["alignreport"] = inputDir + it->second; }
}
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("list");
//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["list"] = inputDir + it->second; }
}
it = parameters.find("name");
//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["name"] = inputDir + it->second; }
}
it = parameters.find("group");
//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["group"] = inputDir + it->second; }
}
it = parameters.find("taxonomy");
//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["taxonomy"] = inputDir + it->second; }
}
else if (listfile != "") { inputFileName = listfile; readList(); }
else if (taxfile != "") { inputFileName = taxfile; readTax(); }
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
//sort in alphabetical order
sort(names.begin(), names.end());
- if (outputDir == "") { outputDir += hasPath(inputFileName); }
+ if (outputDir == "") { outputDir += m->hasPath(inputFileName); }
- string outputFileName = outputDir + getRootName(getSimpleName(inputFileName)) + "accnos";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "accnos";
ofstream out;
- openOutputFile(outputFileName, out);
+ m->openOutputFile(outputFileName, out);
//output to .accnos file
for (int i = 0; i < names.size(); i++) {
- if (m->control_pressed) { out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
out << names[i] << endl;
}
out.close();
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
m->mothurOutEndLine();
return 0;
try {
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
string name;
-
+
while(!in.eof()){
if (m->control_pressed) { in.close(); return 0; }
if (name != "") { names.push_back(name); }
- gobble(in);
+ m->gobble(in);
}
in.close();
int ListSeqsCommand::readList(){
try {
ifstream in;
- openInputFile(listfile, in);
+ m->openInputFile(listfile, in);
if(!in.eof()){
//read in list vector
try {
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
string name, firstCol, secondCol;
while(!in.eof()){
//get name after last ,
names.push_back(secondCol);
- gobble(in);
+ m->gobble(in);
}
in.close();
return 0;
try {
ifstream in;
- openInputFile(groupfile, in);
+ m->openInputFile(groupfile, in);
string name, group;
while(!in.eof()){
if (m->control_pressed) { in.close(); return 0; }
- in >> name; //read from first column
+ in >> name; m->gobble(in); //read from first column
in >> group; //read from second column
names.push_back(name);
- gobble(in);
+ m->gobble(in);
}
in.close();
return 0;
try {
ifstream in;
- openInputFile(alignfile, in);
+ m->openInputFile(alignfile, in);
string name, junk;
//read column headers
names.push_back(name);
- gobble(in);
+ m->gobble(in);
}
in.close();
try {
ifstream in;
- openInputFile(taxfile, in);
+ m->openInputFile(taxfile, in);
string name, firstCol, secondCol;
while(!in.eof()){
names.push_back(firstCol);
- gobble(in);
+ m->gobble(in);
}
in.close();