+++ /dev/null
-/**
- * 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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