#include <gnBaseSpec.h>
Inheritance diagram for gnBaseSpec:
Public Member Functions | |
virtual void | Clear () |
Clears all data from this spec. | |
virtual gnBaseSpec * | Clone () const =0 |
virtual gnBaseSpec * | CloneRange (const gnSeqI startI, const gnSeqI len) const =0 |
virtual void | CropEnd (gnSeqI cropLen)=0 |
Crop the last cropLen bases from the sequence. | |
virtual void | CropStart (gnSeqI cropLen)=0 |
Crop the first cropLen bases from the sequence. | |
virtual gnSeqI | GetLength () const =0 |
Get the length of all the sequence data covered by this spec. | |
virtual string | GetName () const |
Get the name of the contig associated with this spec. | |
gnBaseSpec () | |
virtual boolean | IsCircular () const |
Returns true if this spec's sequence is circular. | |
virtual boolean | IsReverseComplement () const |
Returns true if this spec is read reverse complement. | |
virtual boolean | SeqRead (const gnSeqI start, gnSeqC *buf, gnSeqI &bufLen, const uint32 contigI) const =0 |
Reads sequence data from this spec. | |
virtual void | SetCircular (const boolean value) |
Sets whether this spec should be read circular. | |
virtual void | SetName (const string &name) |
Sets the name for this contig. | |
virtual void | SetReverseComplement (const boolean value)=0 |
Sets the reverse complement bit for this spec. | |
virtual | ~gnBaseSpec () |
Destructor, frees memory. | |
Protected Attributes | |
boolean | m_circular |
string | m_name |
boolean | m_reverseComplement |
string | m_sourceName |
Definition at line 27 of file gnBaseSpec.h.
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Definition at line 30 of file gnBaseSpec.h. |
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Destructor, frees memory. Definition at line 34 of file gnBaseSpec.h. |
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Clears all data from this spec.
Reimplemented in gnContigSpec, gnFragmentSpec, gnGenomeSpec, gnMultiSpec< SubSpec >, gnSourceSpec, gnStringSpec, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >. Definition at line 136 of file gnBaseSpec.h. References m_circular, m_name, m_reverseComplement, and m_sourceName. Referenced by gnContigSpec::Clear(), gnMultiSpec< SubSpec >::Clear(), gnFragmentSpec::gnFragmentSpec(), and gnGenomeSpec::gnGenomeSpec(). |
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Implements gnClone.
Implemented in gnContigSpec, gnFragmentSpec, gnGenomeSpec, gnMultiSpec< SubSpec >, gnSourceSpec, gnStringSpec, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >.
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Implemented in gnContigSpec, gnFragmentSpec, gnGenomeSpec, gnSourceSpec, and gnStringSpec.
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Crop the last cropLen bases from the sequence. CropEnd will delete features and headers associated with the cropped bases.
Implemented in gnContigSpec, gnFragmentSpec, gnMultiSpec< SubSpec >, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >.
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Crop the first cropLen bases from the sequence. CropStart will delete features and headers associated with the cropped bases.
Implemented in gnContigSpec, gnFragmentSpec, gnMultiSpec< SubSpec >, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >.
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Get the length of all the sequence data covered by this spec.
Implemented in gnContigSpec, gnMultiSpec< SubSpec >, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >.
Referenced by gnDNXSource::GetContigSeqLength(). |
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Get the name of the contig associated with this spec.
Referenced by gnSequence::contigName(), gnDNXSource::GetContigID(), gnDNXSource::GetContigName(), gnDNXSource::HasContig(), gnGBKSource::Write(), and gnDNXSource::Write(). |
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Returns true if this spec's sequence is circular.
References m_circular. Referenced by gnSequence::isCircular(), and gnGBKSource::Write(). |
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Returns true if this spec is read reverse complement.
References m_reverseComplement. Referenced by gnSequence::globalToSource(), gnSequence::isReverseComplement(), gnGenomeSpec::SetReverseComplement(), and gnFragmentSpec::SetReverseComplement(). |
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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.
Implemented in gnContigSpec, gnMultiSpec< SubSpec >, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >.
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Sets whether this spec should be read circular. If circular is set, reads beyond the end of this spec will pick up at the beginning and read up to the start index.
References m_circular. Referenced by gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnSequence::setCircular(). |
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Sets the name for this contig.
References m_name. Referenced by gnFASSource::GetSpec(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnDNXSource::ParseStream(), and gnSequence::setContigName(). |
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Sets the reverse complement bit for this spec.
Implemented in gnContigSpec, gnFragmentSpec, and gnGenomeSpec.
Referenced by main(). |
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Definition at line 108 of file gnBaseSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec::gnGenomeSpec(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), IsCircular(), and SetCircular(). |
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Definition at line 110 of file gnBaseSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec::gnGenomeSpec(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), and SetName(). |
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Definition at line 107 of file gnBaseSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec::gnGenomeSpec(), gnSourceSpec::gnSourceSpec(), gnStringSpec::gnStringSpec(), and IsReverseComplement(). |
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Reimplemented in gnMultiSpec< SubSpec >, gnMultiSpec< gnContigSpec >, and gnMultiSpec< gnFragmentSpec >. Definition at line 111 of file gnBaseSpec.h. Referenced by Clear(), gnStringSpec::CloneRange(), gnSourceSpec::CloneRange(), gnSourceSpec::gnSourceSpec(), and gnStringSpec::gnStringSpec(). |