gnRNASequence.h Source File

00001 
00002 // File:            gnRNASequence.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 _gnRNASequence_h_
00015 #define _gnRNASequence_h_
00016 
00017 #include "gn/gnDefs.h"
00018 
00019 #include <string>
00020 #include <list>
00021 #include "gn/gnSequence.h"
00022 #include "gn/gnFilter.h"
00023 
00028 
00029 class GNDLLEXPORT gnRNASequence : public gnSequence
00030 {
00031 public:
00035         gnRNASequence();
00040         gnRNASequence( const gnSeqC* seq );
00045         gnRNASequence( const string& str );
00050         gnRNASequence( const gnGenomeSpec& gngs );
00055         gnRNASequence( const gnFragmentSpec& gnfs );
00060         gnRNASequence( const gnContigSpec& gncs );
00066         gnRNASequence( gnSeqC *bases, const gnSeqI length);
00071         gnRNASequence( const gnRNASequence& seq);
00072 private:
00073         gnGenomeSpec *spec;
00074         list<const gnBaseFilter*> filter_list;
00075         const gnCompare* comparator;
00076 }; // class gnRNASequence
00077 
00078 inline
00079 gnRNASequence::gnRNASequence() : gnSequence(){
00080         filter_list.push_back(gnFilter::fullRNASeqFilter());
00081         comparator = gnCompare::RNASeqCompare();
00082 }
00083 inline
00084 gnRNASequence::gnRNASequence( const gnSeqC* seq ) : gnSequence(seq){
00085         filter_list.push_back(gnFilter::fullRNASeqFilter());
00086         comparator = gnCompare::RNASeqCompare();
00087 }
00088 inline
00089 gnRNASequence::gnRNASequence( const string& str ) : gnSequence(str){
00090         filter_list.push_back(gnFilter::fullRNASeqFilter());
00091         comparator = gnCompare::RNASeqCompare();
00092 }
00093 inline
00094 gnRNASequence::gnRNASequence( const gnGenomeSpec& gngs ) : gnSequence(gngs){
00095         filter_list.push_back(gnFilter::fullRNASeqFilter());
00096         comparator = gnCompare::RNASeqCompare();
00097 }
00098 inline
00099 gnRNASequence::gnRNASequence( const gnFragmentSpec& gnfs ) : gnSequence(gnfs){
00100         filter_list.push_back(gnFilter::fullRNASeqFilter());
00101         comparator = gnCompare::RNASeqCompare();
00102 }
00103 inline
00104 gnRNASequence::gnRNASequence( const gnContigSpec& gncs ) : gnSequence(gncs){
00105         filter_list.push_back(gnFilter::fullRNASeqFilter());
00106         comparator = gnCompare::RNASeqCompare();
00107 }
00108 inline
00109 gnRNASequence::gnRNASequence( gnSeqC *bases, const gnSeqI length) : gnSequence(bases, length){
00110         filter_list.push_back(gnFilter::fullRNASeqFilter());
00111         comparator = gnCompare::RNASeqCompare();
00112 }
00113 inline
00114 gnRNASequence::gnRNASequence( const gnRNASequence& seq) : gnSequence(seq){
00115         filter_list.push_back(gnFilter::fullRNASeqFilter());
00116         comparator = gnCompare::RNASeqCompare();
00117 }
00118 
00119 #endif
00120         // _gnRNASequence_h_