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gnGenomeSpec Member List

This is the complete list of members for gnGenomeSpec, including all inherited members.

• AddFeature(gnBaseFeature *feat) [virtual]
• AddHeader(gnBaseHeader *head, const uint32 i=UINT32_MAX) [virtual]
• AddSpec(gnBaseSpec *spec, const uint32 i=UINT32_MAX) [inline, virtual]
• Clear() [virtual]
• Clone() const [inline, virtual]
• CloneRange(const gnSeqI startI, const gnSeqI len) const [virtual]
• gnMultiSpec::CloneRange(const uint32 startI, const uint32 len) const=0 [pure virtual]
• CropEnd(gnSeqI cropLen) [virtual]
• CropStart(gnSeqI cropLen) [virtual]
• GetBrokenFeatures(const gnLocation &lt, vector< gnBaseFeature *> &feature_vector) const [virtual]
• GetContainedFeatures(const gnLocation &lt, vector< gnBaseFeature *> &feature_vector, vector< uint32 > &index_vector) const [virtual]
• GetFeature(const uint32 i) const [virtual]
• GetFeatureListLength() const [virtual]
• GetHeader(const uint32 i) const [inline, virtual]
• GetHeader(const string &name, uint32 &i) const [virtual]
• GetHeaderListLength() const [inline, virtual]
• GetIntersectingFeatures(const gnLocation &lt, vector< gnBaseFeature *> &feature_vector, vector< uint32 > &index_vector) const [virtual]
• GetLength() const [virtual]
• GetName() const [inline, virtual]
• GetSourceName() const [inline, virtual]
• GetSpec(const uint32 i) const [inline, virtual]
• GetSpecByBase(const gnSeqI baseI) const [inline, virtual]
• GetSpecEndBase(const uint32 specI) const [virtual]
• GetSpecIndexByBase(const gnSeqI baseI) const [virtual]
• GetSpecIndexByName(const string &name) const [virtual]
• GetSpecListLength() const [inline, virtual]
• GetSpecStartBase(const uint32 specI) const [virtual]
• gnBaseSpec() [inline]
• gnClone() [inline]
• gnGenomeSpec()
• gnGenomeSpec(const gnGenomeSpec &s)
• gnMultiSpec() [inline]
• IsCircular() const [inline, virtual]
• IsReverseComplement() const [inline, virtual]
• m_circular [protected]
• m_headerList [protected]
• m_name [protected]
• m_reverseComplement [protected]
• m_sourceName [protected]
• m_SpecList [protected]
• MergeFragments(const uint32 startC, const uint32 endC) [virtual]
• RemoveFeature(const uint32 i) [virtual]
• RemoveHeader(uint32 i) [virtual]
• RemoveSpec(uint32 i) [inline, virtual]
• SeqRead(const gnSeqI start, gnSeqC *buf, uint32 &bufLen, const uint32 contigI) const [virtual]
• SetCircular(const boolean value) [inline, virtual]
• SetName(const string &name) [inline, virtual]
• SetReverseComplement(const boolean value) [virtual]
• SetSourceName(const string &sourceName) [inline, virtual]
• ~gnBaseSpec() [inline, virtual]
• ~gnClone() [inline, virtual]
• ~gnGenomeSpec() [virtual]
• ~gnMultiSpec() [inline, virtual]

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