#include <gnContigSpec.h>
Inheritance diagram for gnContigSpec:
Public Member Functions | |
virtual void | Clear () |
Clears all data from this spec. | |
virtual gnContigSpec * | Clone () const =0 |
virtual gnContigSpec * | CloneRange (const gnSeqI startI, const gnSeqI len) const =0 |
virtual void | CropEnd (gnSeqI cropLen) |
Crop the last cropLen bases from the sequence. | |
virtual void | CropStart (gnSeqI cropLen) |
Crop the first cropLen bases from the sequence. | |
virtual gnSeqI | GetLength () const |
Get the length of this contig inside of the sequence data. | |
virtual uint32 | GetSourceContigIndex () const |
Returns this contig's index in its source sequence. | |
virtual gnSeqI | GetSourceLength () const =0 |
Get the length of the source for this spec. | |
virtual string | GetSourceName () const |
Get the name of the source associated with this spec. | |
virtual gnSeqI | GetStart () const |
Get the base pair index where this contig starts inside of the sequence data. | |
gnContigSpec () | |
virtual boolean | SeqRead (const gnSeqI start, gnSeqC *buf, gnSeqI &bufLen, const uint32 contigI) const |
Reads sequence data from this spec. | |
virtual void | SetLength (const gnSeqI len) |
Sets the length of reads into this sequence. | |
virtual void | SetReverseComplement (const boolean value) |
Sets the reverse complement bit for this contig. | |
virtual void | SetSourceContigIndex (const uint32 contigI) |
Sets this contig's index in its source sequence. | |
virtual void | SetSourceName (const string &sourceName) |
Sets the name of the source associated with this contig. | |
virtual void | SetStart (const gnSeqI start) |
Sets the starting base pair to read from in the contig's sequence. | |
virtual | ~gnContigSpec () |
Destructor, frees memory. | |
Protected Member Functions | |
virtual boolean | Read (const gnSeqI start, gnSeqC *buf, gnSeqI &bufLen) const =0 |
all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement. | |
Protected Attributes | |
gnSeqI | m_length |
uint32 | m_SourceContigIndex |
gnSeqI | m_start |
Definition at line 27 of file gnContigSpec.h.
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Definition at line 30 of file gnContigSpec.h. |
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Destructor, frees memory. Definition at line 34 of file gnContigSpec.h. |
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Clears all data from this spec.
Reimplemented from gnBaseSpec.
Reimplemented in gnSourceSpec, and gnStringSpec. Definition at line 60 of file gnContigSpec.cpp. References gnBaseSpec::Clear(), m_length, m_SourceContigIndex, and m_start. Referenced by gnStringSpec::Clear(), gnSourceSpec::Clear(), and gnStringSpec::gnStringSpec(). |
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Implements gnBaseSpec.
Implemented in gnSourceSpec, and gnStringSpec.
Referenced by gnSequence::gnSequence(). |
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Implements gnBaseSpec.
Implemented in gnSourceSpec, and gnStringSpec.
Referenced by gnFragmentSpec::CloneRange(). |
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Crop the last cropLen bases from the sequence. CropEnd will delete features and headers associated with the cropped bases.
Implements gnBaseSpec. Definition at line 22 of file gnContigSpec.cpp. |
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Crop the first cropLen bases from the sequence. CropStart will delete features and headers associated with the cropped bases.
Implements gnBaseSpec. Definition at line 16 of file gnContigSpec.cpp. References GetSourceLength(), gnSeqI, m_length, and m_start. |
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Get the length of this contig inside of the sequence data.
Implements gnBaseSpec. Definition at line 133 of file gnContigSpec.h. References gnSeqI, and m_length. Referenced by gnFragmentSpec::CloneRange(), gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). |
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Returns this contig's index in its source sequence.
References m_SourceContigIndex, and uint32. Referenced by gnSequence::globalToSource(). |
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Get the length of the source for this spec.
Implemented in gnSourceSpec, and gnStringSpec.
Referenced by CropStart(), gnSequence::globalToSource(), SeqRead(), and SetReverseComplement(). |
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Get the name of the source associated with this spec.
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Get the base pair index where this contig starts inside of the sequence data.
References gnSeqI, and m_start. Referenced by gnSequence::globalToSource(). |
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all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement.
Implemented in gnSourceSpec, and gnStringSpec.
Referenced by SeqRead(). |
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Reads sequence data from this spec. SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence. Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with a valid contig index. SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen". SeqRead will return false if a serious error occurs.
Implements gnBaseSpec. Definition at line 34 of file gnContigSpec.cpp. References gnFilter::DNAComplementFilter(), GetSourceLength(), gnSeqC, gnSeqI, m_length, m_start, Read(), gnFilter::ReverseFilter(), and uint32. |
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Sets the length of reads into this sequence. This does not affect the actual sequence data but only how much of it is used in this contig.
References gnSeqI, and m_length. Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). |
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Sets the reverse complement bit for this contig. This routine will translate the start index to the reverse base pair.
Implements gnBaseSpec. Definition at line 26 of file gnContigSpec.cpp. References GetSourceLength(), m_length, and m_start. Referenced by gnFragmentSpec::SetReverseComplement(). |
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Sets this contig's index in its source sequence.
References m_SourceContigIndex, and uint32. |
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Sets the name of the source associated with this contig.
Referenced by gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnDNXSource::ParseStream(). |
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Sets the starting base pair to read from in the contig's sequence. This does not affect the actual sequence data but only where to begin using it in this contig.
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Definition at line 104 of file gnContigSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), CropEnd(), CropStart(), GetLength(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), SeqRead(), SetLength(), and SetReverseComplement(). |
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Definition at line 105 of file gnContigSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), GetSourceContigIndex(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), and SetSourceContigIndex(). |
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Definition at line 103 of file gnContigSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), CropStart(), GetStart(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), SeqRead(), SetReverseComplement(), and SetStart(). |