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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* The class CommandLineParser is used to parse the command line arguments. It then
* sets some parameters, and calls the required functions.
* To get it to parse the command line, and execute the required job, create a
* CommandLineParser object and pass the list of arguments to the constructor.
*/
#ifndef COMMANDLINEPARSER_H
#define COMMANDLINEPARSER_H
#include <vector>
#include <string>
#include "../Clustal.h"
#include "../general/clustalw.h"
#include "../general/userparams.h"
#include "../general/utils.h"
#include "../general/debuglogObject.h"
#include "../general/statsObject.h"
namespace clustalw
{
typedef std::vector<std::string> StringArray;
typedef struct {
const char *str;
int *flag;
int type;
StringArray* arg;
} CmdLineData;
class CommandLineParser
{
public:
/* Functions */
CommandLineParser(StringArray* args, bool xmenus);
~CommandLineParser();
private:
/* Functions */
/** separate argument options and values
*
* put all the parameters and their values in the
* vectors, and also to check that all parameters that require a value
* have it.
*
* @param args contains parameters as value and optional option pairs
* @param parameters used for storing parsed arguments
* @param paramArgs used for storing values of parsed arguments
* @return number of parsed parameters or -1 on error
*/
int checkParam(StringArray* args, StringArray* params, StringArray* paramArg);
/** Parse all parameters
*/
void parseParams(StringArray* args, bool xmenus);
void setOptionalParam();
int findMatch(string probe, StringArray* list, int n);
CmdLineData getCmdLineDataStruct(const char *str, int *flag, int type, StringArray* arg);
void printCmdLineData(const CmdLineData& temp);
string ConvertStringToLower(string strToConvert);
void exitWithErrorMsg(string msg);
void reportBadOptionAndExit(string option, string expectedType);
void reportInvalidOptionAndExit(string option);
/* Attributes */
Clustal *clustalObj;
static const int MAXARGS = 100;
static const int NOARG = 0;
static const int INTARG = 1;
static const int FLTARG = 2;
static const int STRARG = 3;
static const int FILARG = 4;
static const int OPTARG = 5;
int setOptions;
int setHelp;
int setFullHelp;
int setQuiet;
int setInteractive;
int setBatch;
int setGapOpen;
int setGapExtend;
int setPWGapOpen;
int setPWGapExtend;
int setOutOrder;
int setBootLabels;
int setPWMatrix;
int setMatrix;
int setPWDNAMatrix;
int setDNAMatrix;
int setNegative;
int setNoWeights;
int setOutput;
int setOutputTree;
int setQuickTree;
int setType;
int setCase;
int setSeqNo;
int setSeqNoRange;
int setRange;
int setTransWeight;
int setSeed;
int setScore;
int setWindow;
int setKtuple;
int setKimura;
int setTopDiags;
int setPairGap;
int setTossGaps;
int setNoPGap;
int setNoHGap;
int setNoVGap;
int setHGapRes;
int setUseEndGaps;
int setMaxDiv;
int setGapDist;
int setDebug;
int setOutfile;
int setInfile;
int setProfile1;
int setProfile2;
int setAlign;
int setConvert;
int setNewTree;
int setUseTree;
int setNewTree1;
int setUseTree1;
int setNewTree2;
int setUseTree2;
int setBootstrap;
int setTree;
int setProfile;
int setSequences;
int setSecStruct1;
int setSecStruct2;
int setSecStructOutput;
int setHelixGap;
int setStrandGap;
int setLoopGap;
int setTerminalGap;
int setHelixEndIn;
int setHelixEndOut;
int setStrandEndIn;
int setStrandEndOut;
int profileType;
int setDoIteration;
int setNumIterations;
int setTreeAlgorithm;
int setMaxSeqLen;
int setStatsFile;
int setOutputPim;
string userMatrixName;
string pwUserMatrixName;
string DNAUserMatrixName;
string pwDNAUserMatrixName;
CmdLineData cmdLineFile[4];
CmdLineData cmdLineVerb[20];
CmdLineData cmdLinePara[56];
string clustalTreeName;
string distTreeName;
string phylipTreeName;
string nexusTreeName;
string p1TreeName;
string p2TreeName;
string pimName;
StringArray* typeArg;
StringArray* bootLabelsArg;
StringArray* outOrderArg;
StringArray* caseArg;
StringArray* seqNoArg;
StringArray* seqNoRangeArg;
StringArray* scoreArg;
StringArray* outputArg;
StringArray* outputTreeArg;
StringArray* outputSecStrArg;
StringArray* cmdLineType;
StringArray* clusterAlgorithm;
StringArray* iterationArg;
StringArray* params; // parameter names
StringArray* paramArg; // parameter values
};
}
#endif
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