Sleipnir: tools/OntoShell/parserconsole.h Source File

00001 /*****************************************************************************
00002 * This file is provided under the Creative Commons Attribution 3.0 license.
00003 *
00004 * You are free to share, copy, distribute, transmit, or adapt this work
00005 * PROVIDED THAT you attribute the work to the authors listed below.
00006 * For more information, please see the following web page:
00007 * http://creativecommons.org/licenses/by/3.0/
00008 *
00009 * This file is a component of the Sleipnir library for functional genomics,
00010 * authored by:
00011 * Curtis Huttenhower (chuttenh@princeton.edu)
00012 * Mark Schroeder
00013 * Maria D. Chikina
00014 * Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
00015 *
00016 * If you use this library, the included executable tools, or any related
00017 * code in your work, please cite the following publication:
00018 * Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
00019 * Olga G. Troyanskaya.
00020 * "The Sleipnir library for computational functional genomics"
00021 *****************************************************************************/
00022 #ifndef PARSERCONSOLE_H
00023 #define PARSERCONSOLE_H
00024 
00025 #include "parser.h"
00026 
00027 class CParserConsole : public CParser {
00028 public:
00029     CParserConsole( const Sleipnir::IOntology**, const Sleipnir::CGenome& );
00030 
00031     bool ProcessLine( const char* );
00032     SLocation GetLocation( const string& = c_szDot, bool = true ) const;
00033 
00034 protected:
00035     typedef bool (CParserConsole::*TPFnParser)( const vector<string>& );
00036 
00037     struct SArgs {
00038         static const char*  c_aszFlags[];
00039 
00040         bool    m_afFlags[ 7 ];
00041         bool&   m_fGenes;
00042         bool&   m_fLong;
00043         bool&   m_fSibs;
00044         bool&   m_fZeroes;
00045         bool&   m_fBonferroni;
00046         bool&   m_fRecursive;
00047         bool&   m_fBackground;
00048 
00049         SArgs( );
00050 
00051         bool Parse( const string& );
00052     };
00053 
00054     static const size_t     c_iWidthGenes       = 5;
00055     static const size_t     c_iWidthID          = 19;
00056     static const size_t     c_iWidthGloss       = 43;
00057     static const size_t     c_iWidthOnto        = 32;
00058     static const size_t     c_iWidthP           = 14;
00059     static const size_t     c_iWidthScreen      = 80;
00060     static const size_t     c_iSizeCutoff       = 40;
00061     static const char       c_cSemicolon        = ';';
00062     static const char       c_cShell            = '!';
00063     static const char       c_szDotDotDot[];
00064     static const char       c_szBackground[];
00065     static const char       c_szBonferroni[];
00066     static const char       c_szGenes[];
00067     static const char       c_szLong[];
00068     static const char       c_szRecursive[];
00069     static const char       c_szSibs[];
00070     static const char       c_szStar[];
00071     static const char       c_szZeroes[];
00072     static const char       c_szHelpHelp[];
00073     static const TPFnParser c_apfnParsers[];
00074     static const char*      c_aszHelps[];
00075 
00076     static void PrintLink( const Sleipnir::IOntology*, size_t, char, const SArgs& );
00077     static void PrintNumber( size_t, size_t );
00078     static void PrintSpaces( size_t );
00079     static void PrintAnnotation( const Sleipnir::IOntology*, size_t, const SArgs&,
00080         const Sleipnir::STermFound* = NULL );
00081     static void PrintGloss( string, size_t, bool );
00082     static void PrintGene( const Sleipnir::CGene&, const SArgs& );
00083     static void PrintGenes( const std::vector<const Sleipnir::CGene*>&, size_t = 0,
00084         const Sleipnir::CGenes* = NULL );
00085     static size_t FormatGenes( const std::vector<const Sleipnir::CGene*>&, std::vector<string>&,
00086         const Sleipnir::CGenes* = NULL );
00087 
00088     bool ParseCat( const std::vector<string>& );
00089     bool ParseCd( const std::vector<string>& );
00090     bool ParseHelp( const std::vector<string>& );
00091     bool ParseLs( const std::vector<string>& );
00092     bool ParseFind( const std::vector<string>& );
00093     bool ParseParentage( const std::vector<string>& );
00094     bool ParseShell( const string& ) const;
00095     void PrintOntology( const Sleipnir::IOntology*, char ) const;
00096     void PrintLocations( const std::vector<SLocation>&, const SArgs& ) const;
00097     void PrintGenes( const std::vector<SLocation>&, const SArgs& ) const;
00098 
00099     SLocation   m_sLocation;
00100 };
00101 
00102 #endif // PARSERCONSOLE_H