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#ifndef COMMAND_HPP
#define COMMAND_HPP
//test2
/*
* command.h
* nast
*
* Created by Pat Schloss on 10/23/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
/*This class is a parent to all the command classes. */
#include "mothur.h"
#include "optionparser.h"
#include "validparameter.h"
#include "mothurout.h"
#include "commandparameter.h"
#include "currentfile.h"
#include "utils.hpp"
class Command {
public:
Command() {
m = MothurOut::getInstance(); current = CurrentFile::getInstance();
inputdirs = current->getInputDir();
outputdir = current->getOutputDir();
}
//needed by gui
virtual string getCommandName() = 0;
virtual string getCommandCategory() = 0;
virtual string getHelpString() = 0;
virtual string getCitation() = 0;
virtual string getDescription() = 0;
virtual string getCommonQuestions() { return "Common Questions for commands."; }
virtual string getCommandParameters() {
vector<string> parameterNames = setParameters();
sort(parameterNames.begin(), parameterNames.end());
string results = util.getStringFromVector(parameterNames, ", ");
return results;
}
virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
string getOutputFileName(string type, map<string, string> variableParts) { //uses the pattern to create an output filename for a given type and input file name.
try {
string filename = "";
map<string, vector<string> >::iterator it;
//is this a type this command creates
it = outputTypes.find(type);
if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
else {
string patternTemp = getOutputPattern(type);
vector<string> patterns;
util.splitAtDash(patternTemp, patterns);
//find pattern to use based on number of variables passed in
string pattern = "";
bool foundPattern = false;
vector<int> numVariablesPerPattern;
for (int i = 0; i < patterns.size(); i++) {
int numVariables = 0;
for (int j = 0; j < patterns[i].length(); j++) { if (patterns[i][j] == '[') { numVariables++; } }
numVariablesPerPattern.push_back(numVariables);
if (numVariables == variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
}
//if you didn't find an exact match do we have something that might work
if (!foundPattern) {
for (int i = 0; i < numVariablesPerPattern.size(); i++) {
if (numVariablesPerPattern[i] < variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
}
if (!foundPattern) { m->mothurOut("[ERROR]: Not enough variable pieces for " + type + ".\n"); m->setControl_pressed(true); }
}
if (pattern != "") {
int numVariables = 0;
for (int i = 0; i < pattern.length(); i++) { if (pattern[i] == '[') { numVariables++; } }
vector<string> pieces;
util.splitAtComma(pattern, pieces);
for (int i = 0; i < pieces.size(); i++) {
if (pieces[i][0] == '[') {
map<string, string>::iterator it = variableParts.find(pieces[i]);
if (it == variableParts.end()) {
m->mothurOut("[ERROR]: Did not provide variable for " + pieces[i] + ".\n"); m->setControl_pressed(true);
}else {
if (it->second != "") {
if (it->first == "[filename]") { filename += it->second; }
else if (it->first == "[extension]") {
if (filename.length() > 0) { //rip off last "."
filename = filename.substr(0, filename.length()-1);
}
filename += it->second + ".";
}else if ((it->first == "[group]") || (it->first == "[tag]")) {
string group = it->second;
for (int j = 0; j < group.length(); j++) {
if (group[j] == '-') { group[j] = '_'; }
}
filename += group + ".";
}else { filename += it->second + "."; }
}
}
}else {
filename += pieces[i] + ".";
}
}
if (filename.length() > 0) { //rip off last "."
filename = filename.substr(0, filename.length()-1);
}
}
}
return filename;
}
catch(exception& e) {
m->errorOut(e, "command", "getOutputFileName");
exit(1);
}
}
virtual string getOutputPattern(string) = 0; //pass in type, returns something like: [filename],align or [filename],[distance],subsample.shared strings in [] means its a variable. This is used by the gui to predict output file names. use variable keywords: [filename], [distance], [group], [extension], [tag]
virtual vector<string> setParameters() = 0; //to fill parameters
virtual vector<CommandParameter> getParameters() { return parameters; }
virtual int execute() = 0;
virtual void help() = 0;
void citation() { m->mothurOut("\n"+getCitation()+"\n"); }
void commonQuestions() { m->mothurOut("\n"+getCommonQuestions()+"\n"); }
virtual ~Command() { }
protected:
MothurOut* m;
Utils util;
CurrentFile* current;
bool calledHelp;
string outputdir;
vector<string> inputdirs;
map<string, vector<string> > outputTypes;
vector<CommandParameter> parameters;
map<string, vector<string> >::iterator itTypes;
};
#endif
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