gnTranslator.h Source File

00001 
00002 // File:            gnTranslator.h
00003 // Purpose:         Translator for all Sequences
00004 // Description:     Translates DNA and protein sequences
00005 // Changes:        
00006 // Version:         libGenome 0.1.0 
00007 // Author:          Aaron Darling 
00008 // Last Edited:     April 15, 2001, 10:34:50pm 
00009 // Modified by:     
00010 // Copyright:       (c) Aaron Darling 
00011 // Licenses:        Proprietary 
00013 #ifndef _gnTranslator_h_
00014 #define _gnTranslator_h_
00015 
00016 
00017 #include "gn/gnDefs.h"
00018 
00019 #include <string>
00020 #include <vector>
00021 #include "gn/gnClone.h"
00022 #include "gn/gnBaseFilter.h"
00023 #include "gn/gnCompare.h"
00024 
00025 
00037 class GNDLLEXPORT gnTranslator : public gnBaseFilter
00038 {
00039 public:
00040 
00041         static const gnTranslator *ProteinDNATranslator();
00042         static const gnTranslator *ProteinRNATranslator();
00043         static const gnTranslator *DNAProteinTranslator();
00044         static const gnTranslator *RNAProteinTranslator();
00045 
00046         enum gnTranslatorType{
00047                 ProteinDNATranslatorType,
00048                 ProteinRNATranslatorType,
00049                 DNAProteinTranslatorType,
00050                 RNAProteinTranslatorType,
00051         };
00052         
00053         gnTranslator();
00054         gnTranslator( gnTranslatorType t_type );
00055         gnTranslator( const gnTranslator& sf );
00056 
00057         gnTranslator* Clone() const;
00058 
00059         // gnSeqC 
00060         virtual gnSeqC Filter( const gnSeqC ch ) const;
00061 
00062         virtual void Filter( gnSeqC** seq, uint32& len ) const;
00063         // string
00064         virtual void Filter( string &seq ) const;
00065 
00066         // Default gnSeqC
00071         void SetDefaultChar( const gnSeqC ch1 );
00077         gnSeqC GetDefaultChar() const;
00082         void UseDefaultChar( const boolean use = true);
00088         void SetDefaultInputWidth( const uint32 defaultInputWidth);
00094         uint32 GetDefaultInputWidth() const;
00095 
00096         // fill map
00104         void SetPair( const string& input, const string& output );
00110         void RemovePair( const string& input );
00116         void SetCompare( const gnCompare* comp );
00117 private:
00118         void CreateProteinDNATranslator();
00119         void CreateProteinRNATranslator();
00120         void CreateDNAProteinTranslator();
00121         void CreateRNAProteinTranslator();
00122 
00123         string m_name;
00124 
00125         //for each entry in the input table there is a corresponding
00126         //entry in the output table.
00127         vector<string> m_inputTable, m_outputTable;
00128 
00129         const gnCompare* compare;
00130         
00131         boolean use_default;
00132         gnSeqC m_defaultChar;
00133         uint32 m_defaultInputWidth;
00134 };//class gnTranslator
00135 
00136 inline
00137 gnTranslator* gnTranslator::Clone() const
00138 {
00139         return new gnTranslator(*this);
00140 }
00141 
00142 inline
00143 void gnTranslator::SetDefaultChar( const gnSeqC ch1 )
00144 {
00145         m_defaultChar = ch1;
00146         use_default = true;
00147 }
00148 inline
00149 gnSeqC gnTranslator::GetDefaultChar() const
00150 {
00151         return m_defaultChar;
00152 }
00153 
00154 inline
00155 void gnTranslator::UseDefaultChar(const boolean use)
00156 {
00157         use_default = use;
00158 }
00159 
00160 inline
00161 void gnTranslator::SetDefaultInputWidth( const uint32 defaultInputWidth){
00162         m_defaultInputWidth = defaultInputWidth;
00163 }
00164 
00165 inline
00166 uint32 gnTranslator::GetDefaultInputWidth() const{
00167         return m_defaultInputWidth;
00168 }
00169 
00170 inline
00171 void gnTranslator::SetCompare( const gnCompare* comp ){
00172         compare = comp;
00173 }
00174 
00175 #endif // _gnTranslator_h_