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CPhrap_Seq Class Reference

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+ Inheritance diagram for CPhrap_Seq:
+ Collaboration diagram for CPhrap_Seq:

List of all members.

Public Types

typedef map< TSeqPos, TSeqPosTPadMap

Public Member Functions

 CPhrap_Seq (TPhrapReaderFlags flags)
 CPhrap_Seq (const string &name, TPhrapReaderFlags flags)
virtual ~CPhrap_Seq (void)
void Read (CNcbiIstream &in)
void ReadData (CNcbiIstream &in)
virtual void ReadTag (CNcbiIstream &in, char tag)=0
void SetComplemented (bool value)
bool IsComplemented (void) const
TPhrapReaderFlags GetFlags (void) const
bool FlagSet (EPhrapReaderFlags value) const
const stringGetName (void) const
TSeqPos GetPaddedLength (void) const
TSeqPos GetUnpaddedLength (void) const
const stringGetData (void) const
CRef< CSeq_idGetId (void) const
TSeqPos GetPaddedPos (TSeqPos unpadded) const
TSeqPos GetUnpaddedPos (TSeqPos padded, TSeqPos *link=0) const
CRef< CBioseqCreateBioseq (void) const
const TPadMapGetPadMap (void) const
TSeqPos GetAlignedFrom (void) const
TSeqPos GetAlignedTo (void) const

Protected Member Functions

void CreateComplementedDescr (CRef< CSeq_descr > &descr) const
void CreatePadsFeat (CRef< CSeq_annot > &annot) const
void SetAligned (TSeqPos from, TSeqPos to)

Private Member Functions

void x_FillSeqData (CSeq_data &data) const
void CopyFrom (CPhrap_Seq &seq)

Private Attributes

TPhrapReaderFlags m_Flags
string m_Name
TSeqPos m_PaddedLength
TSeqPos m_UnpaddedLength
string m_Data
TPadMap m_PadMap
bool m_Complemented
TSeqPos m_AlignedFrom
TSeqPos m_AlignedTo
CRef< CSeq_idm_Id

Friends

class CPhrap_Sequence

Detailed Description

Definition at line 105 of file phrap.cpp.


Member Typedef Documentation

Definition at line 145 of file phrap.cpp.


Constructor & Destructor Documentation

Definition at line 182 of file phrap.cpp.

Definition at line 193 of file phrap.cpp.

virtual CPhrap_Seq::~CPhrap_Seq ( void  ) [inline, virtual]

Definition at line 110 of file phrap.cpp.


Member Function Documentation

void CPhrap_Seq::CopyFrom ( CPhrap_Seq seq) [private]
CRef< CBioseq > CPhrap_Seq::CreateBioseq ( void  ) const
void CPhrap_Seq::CreateComplementedDescr ( CRef< CSeq_descr > &  descr) const [protected]
void CPhrap_Seq::CreatePadsFeat ( CRef< CSeq_annot > &  annot) const [protected]
bool CPhrap_Seq::FlagSet ( EPhrapReaderFlags  value) const [inline]
TSeqPos CPhrap_Seq::GetAlignedFrom ( void  ) const [inline]
TSeqPos CPhrap_Seq::GetAlignedTo ( void  ) const [inline]
const string& CPhrap_Seq::GetData ( void  ) const [inline]

Definition at line 136 of file phrap.cpp.

References m_Data.

TPhrapReaderFlags CPhrap_Seq::GetFlags ( void  ) const [inline]
CRef< CSeq_id > CPhrap_Seq::GetId ( void  ) const [inline]
const string& CPhrap_Seq::GetName ( void  ) const [inline]
TSeqPos CPhrap_Seq::GetPaddedLength ( void  ) const [inline]
TSeqPos CPhrap_Seq::GetPaddedPos ( TSeqPos  unpadded) const [inline]
const TPadMap& CPhrap_Seq::GetPadMap ( void  ) const [inline]

Definition at line 146 of file phrap.cpp.

References m_PadMap.

Referenced by CPhrap_Contig::x_AddAlignRanges().

TSeqPos CPhrap_Seq::GetUnpaddedLength ( void  ) const [inline]
TSeqPos CPhrap_Seq::GetUnpaddedPos ( TSeqPos  padded,
TSeqPos link = 0 
) const [inline]
bool CPhrap_Seq::IsComplemented ( void  ) const [inline]

Reimplemented in CPhrap_Contig, and CPhrap_Read.

Definition at line 222 of file phrap.cpp.

References CheckStreamState(), m_Name, and m_PaddedLength.

virtual void CPhrap_Seq::ReadTag ( CNcbiIstream in,
char  tag 
) [pure virtual]
void CPhrap_Seq::SetAligned ( TSeqPos  from,
TSeqPos  to 
) [inline, protected]

Definition at line 154 of file phrap.cpp.

References m_AlignedFrom, and m_AlignedTo.

Referenced by CPhrap_Read::ReadQuality().

void CPhrap_Seq::SetComplemented ( bool  value) [inline]
void CPhrap_Seq::x_FillSeqData ( CSeq_data data) const [private]

Friends And Related Function Documentation

friend class CPhrap_Sequence [friend]

Definition at line 163 of file phrap.cpp.


Member Data Documentation

Definition at line 174 of file phrap.cpp.

Referenced by CopyFrom(), GetAlignedFrom(), and SetAligned().

Definition at line 175 of file phrap.cpp.

Referenced by CopyFrom(), GetAlignedTo(), ReadData(), and SetAligned().

Definition at line 173 of file phrap.cpp.

Referenced by CopyFrom(), CreateComplementedDescr(), IsComplemented(), and SetComplemented().

Definition at line 171 of file phrap.cpp.

Referenced by CopyFrom(), GetData(), ReadData(), and x_FillSeqData().

Definition at line 166 of file phrap.cpp.

Referenced by CopyFrom(), FlagSet(), GetFlags(), and ReadData().

CRef<CSeq_id> CPhrap_Seq::m_Id [mutable, private]

Definition at line 176 of file phrap.cpp.

Referenced by CopyFrom(), and GetId().

Definition at line 168 of file phrap.cpp.

Referenced by CopyFrom(), CreatePadsFeat(), GetId(), GetName(), Read(), and ReadData().

Definition at line 169 of file phrap.cpp.

Referenced by CopyFrom(), GetPaddedLength(), Read(), and ReadData().

Definition at line 172 of file phrap.cpp.

Referenced by CopyFrom(), CreatePadsFeat(), GetPaddedPos(), GetPadMap(), GetUnpaddedPos(), and ReadData().

Definition at line 170 of file phrap.cpp.

Referenced by CopyFrom(), CreateBioseq(), GetUnpaddedLength(), ReadData(), and x_FillSeqData().


The documentation for this class was generated from the following file:
Modified on Tue May 05 11:10:37 2015 by modify_doxy.py rev. 426318