#include <SSAHAMain.h>
Inheritance diagram for CommandLineArg:
Public Member Functions | |
| CommandLineArg (const string &nameLong, const string &nameShort) | |
| virtual bool | isThisMe (const string &argName) |
| virtual void | addValue (const string &value)=0 |
Static Public Member Functions | |
| static void | parseCommandLine (int numArgs, char *args[], QueryParameterStruct &queryParams) |
Protected Attributes | |
| string | nameLong_ |
| string | nameShort_ |
Definition at line 161 of file SSAHAMain.h.
| CommandLineArg::CommandLineArg | ( | const string & | nameLong, | |
| const string & | nameShort | |||
| ) | [inline] |
Definition at line 175 of file SSAHAMain.h.
00175 : 00176 nameLong_( nameLong ), nameShort_( nameShort ) {} // Is the current argument equal to 'my' argument name?
| void CommandLineArg::parseCommandLine | ( | int | numArgs, | |
| char * | args[], | |||
| QueryParameterStruct & | queryParams | |||
| ) | [static] |
Definition at line 158 of file SSAHAMain.cpp.
References QueryParameterStruct::bandExtension, QueryParameterStruct::doAlignment, QueryParameterStruct::logMode, QueryParameterStruct::maxGap, QueryParameterStruct::maxInsert, QueryParameterStruct::maxStore, QueryParameterStruct::minPrint, QueryParameterStruct::numRepeats, QueryParameterStruct::packHits, QueryParameterStruct::parserFriendly, QueryParameterStruct::printHashStats, QueryParameterStruct::queryEnd, QueryParameterStruct::queryFormat, QueryParameterStruct::queryName, QueryParameterStruct::queryReplace, QueryParameterStruct::queryStart, QueryParameterStruct::queryType, QueryParameterStruct::reverseQuery, QueryParameterStruct::runQuery, QueryParameterStruct::saveName, QueryParameterStruct::sortMatches, QueryParameterStruct::stepLength, QueryParameterStruct::subjectFormat, QueryParameterStruct::subjectName, QueryParameterStruct::subjectReplace, QueryParameterStruct::subjectType, QueryParameterStruct::substituteThreshold, and QueryParameterStruct::wordLength.
Referenced by main().
00159 { 00160 00161 int firstArg; 00162 00163 // Add mandatory parameters 00164 if ( (args[2])[0] == '-' ) 00165 { 00166 // then only one file name given: assume this is a subject file 00167 // to be hashed 00168 firstArg = 2; 00169 queryParams.subjectName = (string) args[1]; 00170 queryParams.runQuery = false; 00171 } 00172 else 00173 { 00174 // two file names given: assume first is query, second is subject 00175 firstArg = 3; 00176 queryParams.queryName = (string) args[1]; 00177 queryParams.subjectName = (string) args[2]; 00178 } 00179 00180 // Parse options 00181 vector<CommandLineArg*> validArgs; 00182 validArgs.push_back 00183 ( new CommandLineArgInt( "-wordLength", "-wl", queryParams.wordLength ) ); 00184 validArgs.push_back 00185 ( new CommandLineArgInt( "-stepLength", "-sl", queryParams.stepLength ) ); 00186 validArgs.push_back 00187 ( new CommandLineArgInt( "-maxStore", "-ms", queryParams.maxStore ) ); 00188 validArgs.push_back 00189 ( new CommandLineArgInt( "-minPrint", "-mp", queryParams.minPrint ) ); 00190 validArgs.push_back 00191 ( new CommandLineArgInt( "-maxGap", "-mg", queryParams.maxGap ) ); 00192 validArgs.push_back 00193 ( new CommandLineArgInt( "-maxInsert", "-mi", queryParams.maxInsert ) ); 00194 validArgs.push_back 00195 ( new CommandLineArgInt( "-numRepeats", "-nr", queryParams.numRepeats ) ); 00196 validArgs.push_back 00197 ( new CommandLineArgInt( "-substituteWords", "-sw", 00198 queryParams.substituteThreshold ) ); 00199 validArgs.push_back 00200 ( new CommandLineArgInt( "-bandExtension", "-be", 00201 queryParams.bandExtension ) ); 00202 validArgs.push_back 00203 ( new CommandLineArgInt( "-sortMatches", "-sm", queryParams.sortMatches ) ); 00204 validArgs.push_back 00205 ( new CommandLineArgInt 00206 ( "-doAlignment", "-da", queryParams.doAlignment )); 00207 validArgs.push_back 00208 ( new CommandLineArgInt( "-queryStart", "-qs", queryParams.queryStart ) ); 00209 validArgs.push_back 00210 ( new CommandLineArgInt( "-queryEnd", "-qe", queryParams.queryEnd ) ); 00211 validArgs.push_back 00212 ( new CommandLineArgBool( "-hashStats", "-hs", queryParams.printHashStats )); 00213 validArgs.push_back 00214 ( new CommandLineArgBool( "-packHits", "-ph", queryParams.packHits )); 00215 validArgs.push_back 00216 ( new CommandLineArgBool 00217 ( "-reverseQuery", "-rq", queryParams.reverseQuery )); 00218 validArgs.push_back 00219 ( new CommandLineArgBool 00220 ( "-parserFriendly", "-pf", queryParams.parserFriendly ) ); 00221 validArgs.push_back 00222 ( new CommandLineArgString( "-queryType", "-qt", queryParams.queryType ) ); 00223 validArgs.push_back 00224 ( new CommandLineArgString( "-subjectType", "-st", queryParams.subjectType)); 00225 validArgs.push_back 00226 ( new CommandLineArgString( "-queryFormat", "-qf", queryParams.queryFormat)); 00227 validArgs.push_back 00228 ( new CommandLineArgString 00229 ( "-subjectFormat", "-sf", queryParams.subjectFormat) ); 00230 // validArgs.push_back 00231 // ( new CommandLineArgString( "-reportMode", "-rm", queryParams.reportMode ) ); 00232 validArgs.push_back 00233 ( new CommandLineArgString( "-queryReplace", "-qr", queryParams.queryReplace ) ); 00234 validArgs.push_back 00235 ( new CommandLineArgString( "-subjectReplace", "-sr", queryParams.subjectReplace ) ); 00236 validArgs.push_back 00237 ( new CommandLineArgString( "-logMode", "-lm", queryParams.logMode ) ); 00238 validArgs.push_back 00239 ( new CommandLineArgString( "-saveName", "-sn", queryParams.saveName ) ); 00240 00241 string thisArg; 00242 vector<CommandLineArg*>::iterator pArg = validArgs.end(); 00243 for ( int i(firstArg); i < numArgs ; i++ ) 00244 { 00245 thisArg = (string) args[i]; 00246 if (pArg != validArgs.end()) 00247 // ... then an instance of CommandLineArg is waiting to parse the current 00248 // command line arg 00249 { 00250 (*pArg)->addValue( thisArg ); 00251 pArg = validArgs.end(); 00252 } // ~if 00253 else 00254 // ... trawl through the list of command line args and see if any of 'em 00255 // recognize the current command line arg 00256 { 00257 for (pArg = validArgs.begin() ; pArg != validArgs.end(); ++pArg ) 00258 { 00259 if ( (*pArg)->isThisMe(thisArg) ) break; // *pArg recognizes the arg 00260 } // ~for 00261 if ( pArg == validArgs.end() ) 00262 // ... then the argument has not been recognized - complain! 00263 { 00264 cerr << "Error: command line argument " << thisArg << " not found.\n"; 00265 exit(1); 00266 } // ~if 00267 00268 // if pArg is an instance of type CommandLineArgBool, then there is 00269 // no associated value, so don't try to read one 00270 if ( dynamic_cast<CommandLineArgBool*>(*pArg)) pArg=validArgs.end(); 00271 } // ~else 00272 } // ~for 00273 00274 // Deallocate memory 00275 for ( vector<CommandLineArg*>::iterator i = validArgs.begin(); 00276 i != validArgs.end(); ++i ) delete *i; 00277 00278 00279 } // ~parseCommandLine
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| virtual bool CommandLineArg::isThisMe | ( | const string & | argName | ) | [inline, virtual] |
Reimplemented in CommandLineArgBool.
Definition at line 178 of file SSAHAMain.h.
References nameLong_, and nameShort_.
00179 { 00180 return ( ( argName == nameLong_ ) || ( argName == nameShort_ ) ); 00181 }
| virtual void CommandLineArg::addValue | ( | const string & | value | ) | [pure virtual] |
Implemented in CommandLineArgString, CommandLineArgInt, and CommandLineArgBool.
string CommandLineArg::nameLong_ [protected] |
Definition at line 184 of file SSAHAMain.h.
Referenced by CommandLineArgBool::isThisMe(), and isThisMe().
string CommandLineArg::nameShort_ [protected] |
Definition at line 185 of file SSAHAMain.h.
Referenced by CommandLineArgBool::isThisMe(), and isThisMe().
1.5.2