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