gnFileContig.h Source File

00001 
00002 // File:            gnFileContig.h
00003 // Purpose:         File Position holder.
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 _gnFileContig_h_
00014 #define _gnFileContig_h_
00015 
00016 #include "gn/gnDefs.h"
00017 
00018 #include <string>
00019 #include "gn/gnClone.h"
00020 #ifdef __GNUG__
00021 #include "pair.h"
00022 #endif
00023 
00031 class GNDLLEXPORT gnFileContig : public gnClone
00032 {
00033 public:
00034         gnFileContig();
00035         gnFileContig( string nameStr, const uint64 pos, const uint64 len );
00036         gnFileContig( const gnFileContig& fc );
00037         ~gnFileContig();
00038 
00039         gnFileContig* Clone() const;
00040         void Clear();
00041 
00042         string GetName() const;
00043         gnSeqI GetSeqLength() const;
00044         pair<uint64,uint64> GetFileStartEnd() const;
00045         uint64 GetFileLength() const;
00046         pair<uint64,uint64> GetSectStartEnd( const gnContigSection i ) const;
00047         uint64 GetSectLength( gnContigSection i ) const;
00048         boolean HasRepeatSeqGap() const;
00049         pair<uint32,uint32> GetRepeatSeqGapSize() const;
00050 
00051         boolean SetName( string nameStr );
00052         boolean SetSeqLength( const gnSeqI len );
00053         boolean AddToSeqLength( const gnSeqI len );
00054         boolean SetFileStart( const uint64 s );
00055         boolean SetFileEnd( const uint64 e );
00056         boolean SetFileStartEnd( const pair<uint64,uint64> se );
00057         boolean SetSectStart( const gnContigSection i, const uint64 s );
00058         boolean SetSectEnd( const gnContigSection i, const uint64 e );
00059         boolean SetSectStartEnd( const gnContigSection i, const pair<uint64,uint64> se);
00060         boolean SetRepeatSeqGap( const boolean rsg );
00061         boolean SetRepeatSeqGapSize( const pair<uint64,uint64> rsgSize );
00062         boolean SetRepeatSeqSize( const uint64 seqSize );
00063         boolean SetRepeatGapSize( const uint64 gapSize );
00064 private:
00065         string m_name;
00066         gnSeqI m_seqLength;
00067         pair<uint64,uint64> m_fileStartEnd;
00068         
00069         pair<uint64,uint64> m_startEndArray[CONTIG_SECTION_SIZE];
00070         // sequence access
00071         boolean m_repeatSeqGap;  // if true, use m_repeatSeqGapSize
00072         pair< uint64, uint64 > m_repeatSeqGapSize;
00073 };// class gnFileContig
00074 
00075   // Clone
00076 inline
00077 gnFileContig* gnFileContig::Clone() const
00078 {
00079         return new gnFileContig( *this );
00080 }
00081   // GET
00082 inline
00083 string gnFileContig::GetName() const
00084 {
00085         return m_name;
00086 }
00087 inline
00088 gnSeqI gnFileContig::GetSeqLength() const
00089 {
00090         return m_seqLength;
00091 }
00092 inline
00093 pair<uint64,uint64> gnFileContig::GetFileStartEnd() const
00094 {
00095         return m_fileStartEnd;
00096 }
00097 inline
00098 uint64 gnFileContig::GetFileLength() const
00099 {
00100         return m_fileStartEnd.second - m_fileStartEnd.first + 1;
00101 }
00102 inline
00103 pair<uint64,uint64> gnFileContig::GetSectStartEnd( const gnContigSection i ) const
00104 {
00105         if( (uint32)i < CONTIG_SECTION_SIZE )
00106                 return m_startEndArray[(uint32)i];
00107         return pair<uint64,uint64>(0,0);
00108 }
00109 inline
00110 uint64 gnFileContig::GetSectLength( gnContigSection i ) const
00111 {
00112         if( (uint32)i < CONTIG_SECTION_SIZE )
00113                 return m_startEndArray[(uint32)i].second - m_startEndArray[(uint32)i].first + 1;
00114         return 0;
00115 }
00116 inline
00117 boolean gnFileContig::HasRepeatSeqGap() const
00118 {
00119         return m_repeatSeqGap;
00120 }
00121 inline
00122 pair<uint32,uint32> gnFileContig::GetRepeatSeqGapSize() const
00123 {
00124         return m_repeatSeqGapSize;
00125 }
00126   // SET
00127 inline
00128 boolean gnFileContig::SetName( string nameStr )
00129 {
00130         m_name = nameStr;
00131         return true;
00132 }
00133 inline
00134 boolean gnFileContig::SetSeqLength( const gnSeqI len )
00135 {
00136         m_seqLength = len;
00137         return true;
00138 }
00139 inline
00140 boolean gnFileContig::AddToSeqLength( const gnSeqI len )
00141 {
00142         m_seqLength += len;
00143         return true;
00144 }
00145 inline
00146 boolean gnFileContig::SetFileStart( const uint64 s )
00147 {
00148         m_fileStartEnd.first = s;
00149         return true;
00150 }
00151 inline
00152 boolean gnFileContig::SetFileEnd( const uint64 e )
00153 {
00154         m_fileStartEnd.second = e;
00155         return true;
00156 }
00157 inline
00158 boolean gnFileContig::SetFileStartEnd( const pair<uint64,uint64> se )
00159 {
00160         m_fileStartEnd = se;
00161         return true;    
00162 }
00163 inline
00164 boolean gnFileContig::SetSectStart( const gnContigSection i, const uint64 s )
00165 {
00166         if( (uint32)i < CONTIG_SECTION_SIZE )
00167         {
00168                 m_startEndArray[(uint32)i].first = s;
00169                 return true;
00170         }
00171         return false;
00172 }
00173 inline
00174 boolean gnFileContig::SetSectEnd( const gnContigSection i, const uint64 e )
00175 {
00176         if( (uint32)i < CONTIG_SECTION_SIZE )
00177         {
00178                 m_startEndArray[(uint32)i].second = e;
00179                 return true;
00180         }
00181         return false;
00182 }
00183 inline
00184 boolean gnFileContig::SetSectStartEnd( const gnContigSection i, const pair<uint64,uint64> se )
00185 {
00186         if( (uint32)i < CONTIG_SECTION_SIZE )
00187         {
00188                 m_startEndArray[(uint32)i] = se;
00189                 return true;
00190         }
00191         return false;
00192 }
00193 inline
00194 boolean gnFileContig::SetRepeatSeqGap( const boolean rsg )
00195 {
00196         m_repeatSeqGap = rsg;
00197         return true;
00198 }
00199 inline
00200 boolean gnFileContig::SetRepeatSeqGapSize( const pair<uint64,uint64> rsgSize )
00201 {
00202         return  SetRepeatSeqSize( rsgSize.first ) && 
00203                 SetRepeatGapSize( rsgSize.second );
00204 }
00205 
00206 
00207 #endif
00208         // _gnFileContig_h_