gnRNASequence.h Source File

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# gnRNASequence.h

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    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_