gnDNXSource.h Source File

00001 
00002 // File:            gnDNXSource.h
00003 // Purpose:         Implements gnBaseSource for .DNX files
00004 // Description:     
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 _gnDNXSource_h_
00014 #define _gnDNXSource_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 
00019 #include <string>
00020 #include <vector>
00021 #include <fstream>
00022 #include <time.h>
00023 
00024 #include "gn/gnSetup.h"
00025 #include "gn/gnFileSource.h"
00026 #include "gn/gnSourceSpec.h"
00027 #include "gn/gnSequence.h"
00028 
00035 
00036 class GNDLLEXPORT gnDNXSource : public gnFileSource
00037 {
00038 public:
00042         gnDNXSource();  
00047         gnDNXSource( const gnDNXSource& s );
00051         ~gnDNXSource();
00052 
00053         gnDNXSource* Clone() const;
00054 
00055         uint32 GetContigListLength() const;
00056         boolean HasContig( const string& name ) const;
00057         uint32 GetContigID( const string& name ) const;
00058         string GetContigName( const uint32 i ) const;
00059         gnSeqI GetContigSeqLength( const uint32 i ) const;
00060 
00061         boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) ;
00062 
00071         static boolean Write(gnSequence& sequence, const string& filename);
00081         static boolean Write(gnBaseSource *source, const string& filename);
00090         static boolean Write(gnGenomeSpec *spec, const string& filename);
00091 
00092         gnGenomeSpec* GetSpec() const;
00093         gnFileContig* GetFileContig( const uint32 contigI ) const;
00094 private:
00095         boolean ParseStream( istream& fin );
00096         static void ValidateName(string& name);
00097 
00098         gnGenomeSpec *m_DNXSpec;
00099 };// class gnDNXSource
00100 
00101 inline
00102 gnDNXSource* gnDNXSource::Clone() const
00103 {
00104         return new gnDNXSource( *this );
00105 }
00106 
00107 inline
00108 uint32 gnDNXSource::GetContigListLength() const
00109 {
00110         return m_DNXSpec->GetSpecListLength();
00111 }
00112 //read sequence data from the file
00113 inline
00114 boolean gnDNXSource::SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI ) 
00115 {
00116         return m_DNXSpec->SeqRead(start, buf, bufLen, contigI);
00117 }
00118 
00119 inline
00120 boolean gnDNXSource::Write(gnSequence& sequence, const string& filename){
00121         return Write(sequence.GetSpec(), filename);
00122 }
00123 inline
00124 boolean gnDNXSource::Write(gnBaseSource *source, const string& filename){
00125         return Write(source->GetSpec(), filename);
00126 }
00127 inline
00128 gnGenomeSpec *gnDNXSource::GetSpec() const{
00129         return m_DNXSpec->Clone();
00130 }
00131 
00132 #endif
00133         // _gnDNXSource_h_
00134