gnCompare.h Source File

00001 
00002 // File:            gnCompare.h
00003 // Purpose:         Compares all sequences
00004 // Description:     Compares 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 _gnCompare_h_
00014 #define _gnCompare_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <string>
00019 #include "gn/gnClone.h"
00020 
00021 class GNDLLEXPORT gnCompare : public gnClone
00022 {
00023 public:
00024         
00029         static const gnCompare *ProteinSeqCompare();
00035         static const gnCompare *DNASeqCompare();
00041         static const gnCompare *RNASeqCompare();
00042         
00043         enum gnCompareType{
00044                 ProteinSeqCompareType,
00045                 DNASeqCompareType,
00046                 RNASeqCompareType,
00047         };
00048 
00049         gnCompare();
00058         gnCompare( const gnCompareType c_type );
00059         gnCompare( const gnCompare& sf );
00060         ~gnCompare();
00061         
00062         gnCompare* Clone() const;
00063 
00064         string GetName() const;
00065         void SetName( string name );
00066 
00067         // Use less than comparisons since all other operators can be derived
00068         // gnSeqC less than operations
00069         boolean LessThan( gnSeqC ch, gnSeqC ch2, boolean case_sensitive = false) const;
00073         boolean Contains( gnSeqC ch, gnSeqC ch2, boolean case_sensitive = false ) const;
00074         // True if ch2 is general enough to equal ch
00075         // gnSeqC[] less than operations
00076         boolean LessThan( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive = false ) const;
00077         boolean Contains( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive = false ) const;
00078         // string
00079         boolean LessThan( const string &seq, const string &seq2, boolean case_sensitive = false) const;
00080         boolean Contains( const string &seq, const string &seq2, boolean case_sensitive = false) const;
00081         
00082         // fill map
00083 
00084         //adds a character which is equivalent to itself
00085         void SetSingle( const gnSeqC ch );
00086         //adds a pair of equivalent characters
00087         void SetPair( const gnSeqC ch, const gnSeqC ch2 );
00088         //adds ch as being wholly contained by ch2
00089         void SetContained( const gnSeqC ch, const gnSeqC ch2 );
00090 
00091         void RemoveSingle( const gnSeqC ch );
00092         void RemovePair( const gnSeqC ch, const gnSeqC ch2 );
00093         void RemoveContained( const gnSeqC ch, const gnSeqC ch2 );
00094         
00095 private:
00096         void CreateProteinComparator();
00097         void CreateDNAComparator();
00098         void CreateRNAComparator();
00099 
00100         void AddArrayEntry( gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2);
00101         void DelArrayEntry( gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2);
00102 
00103         string m_name;
00104         boolean m_ignoreCase;
00105         
00106         gnSeqC* m_pairArray[GNSEQC_MAX];
00107         gnSeqC* m_containArray[GNSEQC_MAX];
00108         
00109 };//class gnCompare
00110 
00111 inline
00112 gnCompare* gnCompare::Clone() const{
00113         return new gnCompare(*this);
00114 }
00115 
00116 inline
00117 string gnCompare::GetName() const{
00118         return m_name;
00119 }
00120 inline
00121 void gnCompare::SetName( string name ){
00122         m_name = name;
00123 }
00124 
00125 // gnSeqC
00126 inline
00127 boolean gnCompare::LessThan( gnSeqC ch, gnSeqC ch2, boolean case_sensitive) const
00128 {
00129         if(!case_sensitive){
00130                 ch = toupper(ch);
00131                 ch2 = toupper(ch2);
00132         }
00133                 
00134         if(strchr(m_pairArray[ch], ch2) == 0)
00135                 return ch < ch2 ? true : false;
00136         return false;
00137 }
00138 
00139 
00140 // gnSeqC[]
00141 inline
00142 boolean gnCompare::LessThan( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive ) const{
00143         for( uint32 i=0; i < len ; ++i )
00144                 if(LessThan(seq[i], seq2[i], case_sensitive))
00145                         return true;
00146         return false;
00147 }
00148 
00149 // string
00150 inline
00151 boolean gnCompare::LessThan( const string &seq, const string &seq2, boolean case_sensitive) const
00152 {
00153         gnSeqI shorter_len = seq.length() < seq2.length() ? seq.length() : seq2.length();
00154         return LessThan( (gnSeqC*)seq.data(), (gnSeqC*)seq2.data(), shorter_len, case_sensitive );
00155 }
00156 
00157 // fill map
00158 inline
00159 void gnCompare::SetSingle( const gnSeqC ch ){
00160         AddArrayEntry(m_pairArray, ch, ch);
00161         AddArrayEntry(m_containArray, ch, ch);
00162 }
00163 inline
00164 void gnCompare::SetPair( const gnSeqC ch, const gnSeqC ch2 ){
00165         AddArrayEntry(m_pairArray, ch, ch2);
00166         AddArrayEntry(m_pairArray, ch2, ch);
00167 }
00168 inline
00169 void gnCompare::SetContained( const gnSeqC ch, const gnSeqC ch2 ){
00170         AddArrayEntry(m_containArray, ch2, ch);
00171 }
00172 
00173 inline
00174 void gnCompare::RemoveSingle( const gnSeqC ch )
00175 {
00176         DelArrayEntry(m_pairArray, ch, ch);
00177         DelArrayEntry(m_containArray, ch, ch);
00178 }
00179 inline
00180 void gnCompare::RemovePair( const gnSeqC ch, const gnSeqC ch2 )
00181 {
00182         DelArrayEntry(m_pairArray, ch, ch2);
00183         DelArrayEntry(m_pairArray, ch2, ch);
00184 }
00185 inline
00186 void gnCompare::RemoveContained( const gnSeqC ch, const gnSeqC ch2 )
00187 {
00188         DelArrayEntry(m_containArray, ch2, ch);
00189 }
00190 
00191 #endif
00192         // _gnSeqCompare_h_