gnDNASequence.h Source File

00001 
00002 // File:            gnDNASequence.h
00003 // Purpose:         Sequence class
00004 // Description:     Provides a high level sequence interface to all types of
00005 //                                      sequence data.
00006 // Changes:        
00007 // Version:         libGenome 0.1.0 
00008 // Author:          Aaron Darling 
00009 // Last Edited:     April 15, 2001, 10:34:50pm 
00010 // Modified by:     
00011 // Copyright:       (c) Aaron Darling 
00012 // Licenses:        Proprietary 
00014 #ifndef _gnDNASequence_h_
00015 #define _gnDNASequence_h_
00016 
00017 #include "gn/gnDefs.h"
00018 
00019 #include <string>
00020 #include <list>
00021 #include "gn/gnSequence.h"
00022 #include "gn/gnFilter.h"
00027 
00028 class GNDLLEXPORT gnDNASequence : public gnSequence
00029 {
00030 public:
00034         gnDNASequence();
00039         gnDNASequence( const gnSeqC* seq );
00044         gnDNASequence( const string& str );
00049         gnDNASequence( const gnGenomeSpec& gngs );
00054         gnDNASequence( const gnFragmentSpec& gnfs );
00059         gnDNASequence( const gnContigSpec& gncs );
00065         gnDNASequence( gnSeqC *bases, const gnSeqI length);
00070         gnDNASequence( const gnDNASequence& seq);
00071 private:
00072         gnGenomeSpec *spec;
00073         list<const gnBaseFilter*> filter_list;
00074         const gnCompare* comparator;
00075 }; // class gnDNASequence
00076 
00077 inline
00078 gnDNASequence::gnDNASequence() : gnSequence(){
00079         filter_list.push_back(gnFilter::fullDNASeqFilter());
00080         comparator = gnCompare::DNASeqCompare();
00081 }
00082 inline
00083 gnDNASequence::gnDNASequence( const gnSeqC* seq ) : gnSequence(seq){
00084         filter_list.push_back(gnFilter::fullDNASeqFilter());
00085         comparator = gnCompare::DNASeqCompare();
00086 }
00087 inline
00088 gnDNASequence::gnDNASequence( const string& str ) : gnSequence(str){
00089         filter_list.push_back(gnFilter::fullDNASeqFilter());
00090         comparator = gnCompare::DNASeqCompare();
00091 }
00092 inline
00093 gnDNASequence::gnDNASequence( const gnGenomeSpec& gngs ) : gnSequence(gngs){
00094         filter_list.push_back(gnFilter::fullDNASeqFilter());
00095         comparator = gnCompare::DNASeqCompare();
00096 }
00097 inline
00098 gnDNASequence::gnDNASequence( const gnFragmentSpec& gnfs ) : gnSequence(gnfs){
00099         filter_list.push_back(gnFilter::fullDNASeqFilter());
00100         comparator = gnCompare::DNASeqCompare();
00101 }
00102 inline
00103 gnDNASequence::gnDNASequence( const gnContigSpec& gncs ) : gnSequence(gncs){
00104         filter_list.push_back(gnFilter::fullDNASeqFilter());
00105         comparator = gnCompare::DNASeqCompare();
00106 }
00107 inline
00108 gnDNASequence::gnDNASequence( gnSeqC *bases, const gnSeqI length) : gnSequence(bases, length){
00109         filter_list.push_back(gnFilter::fullDNASeqFilter());
00110         comparator = gnCompare::DNASeqCompare();
00111 }
00112 inline
00113 gnDNASequence::gnDNASequence( const gnDNASequence& seq) : gnSequence(seq){
00114         filter_list.push_back(gnFilter::fullDNASeqFilter());
00115         comparator = gnCompare::DNASeqCompare();
00116 }
00117 
00118 #endif
00119         // _gnDNASequence_h_