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gnBaseFeature Class Reference Features of DNA sequences can be accessed and manipulated using classes derived from gnBaseFeature. More... #include <gnBaseFeature.h> Inheritance diagram for gnBaseFeature:: List of all members. Public Methods   gnBaseFeature ()   gnBaseFeature (string &name, uint32 id=0, gnFragmentSpec *spec=NULL, gnLocation::gnLocationType lt=gnLocation::LT_Nothing, boolean broken=false)   ~gnBaseFeature ()   Destructor, frees memory. More... virtual gnBaseFeature*  Clone () const=0 virtual string  GetName () const   Gets the feature name (e.g. More... virtual void  SetName (const string &name)   Sets the feature name. More... virtual uint32  GetID () const   Gets this feature's ID. More... virtual void  SetID (uint32 id)   Sets this feature's ID. More... virtual gnFragmentSpec*  GetSpec () const   Gets the gnFragmentSpec to which this feature refers. More... virtual void  SetSpec (gnFragmentSpec *spec)   Sets the gnFragmentSpec to which this feature refers. More... virtual gnLocation::gnLocationType  GetLocationType () const   Gets this feature's location type. More... virtual void  SetLocationType (gnLocation::gnLocationType lType)   Sets this feature's location type. More... virtual uint32  GetLocationListLength () const   Returns the number of locations this feature describes. More... virtual boolean  AddLocation (const gnLocation &l, uint32 listI=0)   Adds a new location before the location at listI. More... virtual gnLocation  GetLocation (uint32 listI) const   Gets the location at listI. More... virtual boolean  RemoveLocation (uint32 listI)   Deletes the location at listI. More... virtual boolean  SetLocation (const gnLocation &l, uint32 listI)   Sets the location at listI to a new location. More... virtual boolean  MovePositive (const gnSeqI i)   Increases this feature's coordinates by a specific number of bases. More... virtual boolean  MoveNegative (const gnSeqI i)   Decreases this feature's coordinates by a specific number of bases. More... virtual boolean  CropStart (const gnSeqI i)   Crops the start locations of this feature by the specified amount. More... virtual boolean  CropEnd (const gnSeqI i)   Crops the end locations of this feature by the specified amount. More... virtual boolean  Crop (const gnLocation &l)   Crops the locations of this feature to fit within the given location. More... virtual boolean  IsBroken () const   Returns true if the feature is broken. More... virtual void  SetBroken (boolean broke)   Sets whether the feature is broken or not. More... virtual boolean  Contains (gnSeqI i) const   Checks if the given coordinate is contained by this feature. More... virtual boolean  Contains (const gnLocation &l) const   Checks if the given location is contained by this feature. More... virtual boolean  Contains (gnBaseFeature *feature) const   Checks if the given feature is entirely contained by this feature. More... virtual boolean  IsContainedBy (const gnLocation &l) const   Checks if this feature is entirely contained by the given location. More... virtual boolean  Intersects (const gnLocation &l) const   Checks if the given location intersects this feature. More... virtual boolean  Intersects (gnBaseFeature *feature) const   Checks if the given feature intersects this feature. More... virtual uint32  GetQualifierListLength () const   Returns the number of qualifiers in this feature. More... virtual boolean  AddQualifier (gnBaseQualifier *qualifier)   Adds a new qualifier. More... virtual boolean  HasQualifier (const string &name) const   Looks for a qualifier by name. More... virtual uint32  FirstIndexOfQualifier (const string &name, uint32 listI) const   Searches for a qualifier by name, starting at the index listI. More... virtual uint32  LastIndexOfQualifier (const string &name, uint32 listI) const   Searches for a qualifier by name, ending at the index listI. More... virtual string  GetQualifierName (uint32 listI) const   Gets the name of the qualifier at the list index listI. More... virtual string  GetQualifierValue (uint32 listI) const   Gets the value of the qualifier at the list index listI. More... virtual gnBaseQualifier*  GetQualifier (uint32 listI)   Gets the qualifier at the list index listI. More... virtual boolean  RemoveQualifier (uint32 listI)   Deletes the qualifier at the list index listI. More... virtual boolean  SetQualifier (string &name, string &value, uint32 listI)   Set the name and value of the qualifier at the list index listI. More... virtual boolean  SetQualifierName (string &name, uint32 listI)   Set the name of the qualifier at the list index listI. More... virtual boolean  SetQualifierValue (string &value, uint32 listI)   Set the value of the qualifier at the list index listI. More... Protected Attributes uint32  m_id string  m_name boolean  m_broken gnLocation::gnLocationType  m_locationType vector< gnLocation >  m_locationList vector< gnBaseQualifier* >  m_qualifierList gnFragmentSpec*  m_spec Detailed Description Features of DNA sequences can be accessed and manipulated using classes derived from gnBaseFeature. gnBaseFeature outlines a basic interface and gives functionality its derived sequence classes, such as gnCDSFeature. Definition at line 31 of file gnBaseFeature.h. Constructor & Destructor Documentation gnBaseFeature::gnBaseFeature ( )   Definition at line 19 of file gnBaseFeature.cpp. gnBaseFeature::gnBaseFeature ( string & name, uint32 id = 0, gnFragmentSpec * spec = NULL, gnLocation::gnLocationType lt = gnLocation::LT_Nothing, boolean broken = false )   Definition at line 27 of file gnBaseFeature.cpp. gnBaseFeature::~gnBaseFeature ( )   Destructor, frees memory. Definition at line 35 of file gnBaseFeature.cpp. Member Function Documentation boolean gnBaseFeature::AddLocation ( const gnLocation & l, uint32 listI = 0 ) [inline, virtual]   Adds a new location before the location at listI. Parameters: l   The gnLocation to add. listI   The index into the location list to insert before. Returns: True if successful, false otherwise. See also: gnLocation Definition at line 185 of file gnBaseFeature.cpp. Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). boolean gnBaseFeature::AddQualifier ( gnBaseQualifier * qualifier ) [virtual]   Adds a new qualifier. Parameters: l   The qualifier to add. Returns: True if successful, false otherwise. Definition at line 215 of file gnBaseFeature.cpp. Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). gnBaseFeature * gnBaseFeature::Clone ( ) const [pure virtual]   Reimplemented from gnClone. Reimplemented in gnFeature. Referenced by gnFragmentSpec::GetFeature(). boolean gnBaseFeature::Contains ( gnBaseFeature * feature ) const [virtual]   Checks if the given feature is entirely contained by this feature. Parameters: feature   The feature to check Returns: True if "feature" is contained by this feature. False otherwise Definition at line 145 of file gnBaseFeature.cpp. boolean gnBaseFeature::Contains ( const gnLocation & l ) const [virtual]   Checks if the given location is contained by this feature. Parameters: l   The location to check Returns: True if "l" is contained by this feature. False otherwise Definition at line 138 of file gnBaseFeature.cpp. boolean gnBaseFeature::Contains ( gnSeqI i ) const [virtual]   Checks if the given coordinate is contained by this feature. Parameters: i   The coordinate to check Returns: True if "i" is contained by this feature. False otherwise Definition at line 130 of file gnBaseFeature.cpp. boolean gnBaseFeature::Crop ( const gnLocation & l ) [inline, virtual]   Crops the locations of this feature to fit within the given location. Parameters: l   The location to crop reduce to. Returns: True if successful, false if the feature was broken by the change. Definition at line 329 of file gnBaseFeature.h. boolean gnBaseFeature::CropEnd ( const gnSeqI i ) [virtual]   Crops the end locations of this feature by the specified amount. Parameters: end   The amount to crop. Returns: True if successful, false if the feature was broken by the change. Definition at line 59 of file gnBaseFeature.cpp. Referenced by Crop(), and gnFragmentSpec::CropEnd(). boolean gnBaseFeature::CropStart ( const gnSeqI i ) [virtual]   Crops the start locations of this feature by the specified amount. Parameters: i   The amount to crop. Returns: True if successful, false if the feature was broken by the change. Definition at line 68 of file gnBaseFeature.cpp. Referenced by Crop(), and gnFragmentSpec::CropStart(). uint32 gnBaseFeature::FirstIndexOfQualifier ( const string & name, uint32 listI ) const [virtual]   Searches for a qualifier by name, starting at the index listI. Parameters: name   The name of the qualifier to look for. listI   The index into the qualifier list to start the search at. Returns: The index of the qualifier. Definition at line 75 of file gnBaseFeature.cpp. uint32 gnBaseFeature::GetID ( ) const [inline, virtual]   Gets this feature's ID. Returns: The feature's ID. Definition at line 292 of file gnBaseFeature.h. gnLocation gnBaseFeature::GetLocation ( uint32 listI ) const [virtual]   Gets the location at listI. Parameters: listI   The index into the location list to get. Returns: The location. Definition at line 193 of file gnBaseFeature.cpp. Referenced by Contains(), Intersects(), gnGBKSource::Write(), and main(). uint32 gnBaseFeature::GetLocationListLength ( ) const [inline, virtual]   Returns the number of locations this feature describes. Returns: The number of locations this feature describes. Definition at line 325 of file gnBaseFeature.h. Referenced by Contains(), Intersects(), gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), gnGBKSource::Write(), and main(). gnLocation::gnLocationType gnBaseFeature::GetLocationType ( ) const [inline, virtual]   Gets this feature's location type. Returns: The feature's location type. See also: gnLocationType Definition at line 317 of file gnBaseFeature.h. Referenced by gnGBKSource::Write(). string gnBaseFeature::GetName ( ) const [inline, virtual]   Gets the feature name (e.g. CDS, trna...). Returns: The feature name. Definition at line 284 of file gnBaseFeature.h. Referenced by SetQualifierValue(), gnGBKSource::Write(), and main(). gnBaseQualifier * gnBaseFeature::GetQualifier ( uint32 listI ) [virtual]   Gets the qualifier at the list index listI. Parameters: listI   The index into the qualifier list. Returns: The qualifier. Definition at line 242 of file gnBaseFeature.cpp. Referenced by gnGBKSource::Write(). uint32 gnBaseFeature::GetQualifierListLength ( ) const [inline, virtual]   Returns the number of qualifiers in this feature. Returns: The number of qualifiers in this feature. Definition at line 333 of file gnBaseFeature.h. Referenced by gnGBKSource::Write(). string gnBaseFeature::GetQualifierName ( uint32 listI ) const [virtual]   Gets the name of the qualifier at the list index listI. Parameters: listI   The index into the qualifier list. Returns: The name of the qualifier. Definition at line 230 of file gnBaseFeature.cpp. string gnBaseFeature::GetQualifierValue ( uint32 listI ) const [virtual]   Gets the value of the qualifier at the list index listI. Parameters: listI   The index into the qualifier list. Returns: The value of the qualifier. Definition at line 236 of file gnBaseFeature.cpp. Referenced by print_feature(). gnFragmentSpec * gnBaseFeature::GetSpec ( ) const [inline, virtual]   Gets the gnFragmentSpec to which this feature refers. Returns: The feature's ID. See also: gnFragmentSpec Definition at line 300 of file gnBaseFeature.h. boolean gnBaseFeature::HasQualifier ( const string & name ) const [virtual]   Looks for a qualifier by name. Parameters: name   The name of the qualifier to look for. Returns: True if a qualifier was found, false otherwise. Definition at line 223 of file gnBaseFeature.cpp. boolean gnBaseFeature::Intersects ( gnBaseFeature * feature ) const [virtual]   Checks if the given feature intersects this feature. Parameters: feature   The location to check Returns: True if "feature" intersects this feature. False otherwise Definition at line 172 of file gnBaseFeature.cpp. boolean gnBaseFeature::Intersects ( const gnLocation & l ) const [virtual]   Checks if the given location intersects this feature. Parameters: l   The location to check Returns: True if "l" intersects this feature. False otherwise Definition at line 165 of file gnBaseFeature.cpp. Referenced by gnFragmentSpec::GetIntersectingFeatures(). boolean gnBaseFeature::IsBroken ( ) const [inline, virtual]   Returns true if the feature is broken. Returns: True if the feature is broken Definition at line 308 of file gnBaseFeature.h. Referenced by gnFragmentSpec::GetBrokenFeatures(). boolean gnBaseFeature::IsContainedBy ( const gnLocation & l ) const [virtual]   Checks if this feature is entirely contained by the given location. Parameters: l   The location to check Returns: True if "l" contains by this feature. False otherwise Definition at line 157 of file gnBaseFeature.cpp. Referenced by gnGenomeSpec::AddFeature(), gnFragmentSpec::GetBrokenFeatures(), and gnFragmentSpec::GetContainedFeatures(). uint32 gnBaseFeature::LastIndexOfQualifier ( const string & name, uint32 listI ) const [virtual]   Searches for a qualifier by name, ending at the index listI. Parameters: name   The name of the qualifier to look for. listI   The index into the qualifier list to end the search at. Returns: The index of the qualifier. Definition at line 87 of file gnBaseFeature.cpp. boolean gnBaseFeature::MoveNegative ( const gnSeqI i ) [virtual]   Decreases this feature's coordinates by a specific number of bases. Parameters: i   The number of bases to decrease by. Returns: True if successful, false if the feature was broken by the change. Definition at line 50 of file gnBaseFeature.cpp. boolean gnBaseFeature::MovePositive ( const gnSeqI i ) [virtual]   Increases this feature's coordinates by a specific number of bases. Parameters: i   The number of bases to increase by. Returns: True if successful, false if the feature was broken by the change. Definition at line 42 of file gnBaseFeature.cpp. Referenced by gnGenomeSpec::GetFeature(). boolean gnBaseFeature::RemoveLocation ( uint32 listI ) [virtual]   Deletes the location at listI. Parameters: listI   The index into the location list to delete. Returns: True if successful, false otherwise. Definition at line 199 of file gnBaseFeature.cpp. boolean gnBaseFeature::RemoveQualifier ( uint32 listI ) [virtual]   Deletes the qualifier at the list index listI. Parameters: listI   The index into the qualifier list. Returns: True if successful, false otherwise. Definition at line 97 of file gnBaseFeature.cpp. void gnBaseFeature::SetBroken ( boolean broke ) [inline, virtual]   Sets whether the feature is broken or not. Parameters: broke   True if the feature should be broken, false otherwise Definition at line 312 of file gnBaseFeature.h. void gnBaseFeature::SetID ( uint32 id ) [inline, virtual]   Sets this feature's ID. Parameters: id   The feature's ID. Definition at line 296 of file gnBaseFeature.h. boolean gnBaseFeature::SetLocation ( const gnLocation & l, uint32 listI ) [virtual]   Sets the location at listI to a new location. Parameters: l   The new location listI   The index into the location list to set. Returns: True if successful, false otherwise. Definition at line 207 of file gnBaseFeature.cpp. void gnBaseFeature::SetLocationType ( gnLocation::gnLocationType lType ) [inline, virtual]   Sets this feature's location type. LT_BetweenBases is not a valid feature location type. Parameters: lType   The feature's location type. See also: gnLocationType Definition at line 321 of file gnBaseFeature.h. Referenced by gnSEQSource::ParseStream(), and gnGBKSource::ParseStream(). void gnBaseFeature::SetName ( const string & name ) [inline, virtual]   Sets the feature name. Parameters: name   The feature name. Definition at line 288 of file gnBaseFeature.h. boolean gnBaseFeature::SetQualifier ( string & name, string & value, uint32 listI ) [virtual]   Set the name and value of the qualifier at the list index listI. Parameters: name   The new name of the qualifier. value   The new value of the qualifier. listI   The index into the qualifier list. Returns: True if successful, false otherwise. Definition at line 104 of file gnBaseFeature.cpp. boolean gnBaseFeature::SetQualifierName ( string & name, uint32 listI ) [virtual]   Set the name of the qualifier at the list index listI. Parameters: name   The new name of the qualifier. listI   The index into the qualifier list. Returns: True if successful, false otherwise. Definition at line 111 of file gnBaseFeature.cpp. boolean gnBaseFeature::SetQualifierValue ( string & value, uint32 listI ) [virtual]   Set the value of the qualifier at the list index listI. Parameters: value   The new value of the qualifier. listI   The index into the qualifier list. Returns: True if successful, false otherwise. Definition at line 120 of file gnBaseFeature.cpp. void gnBaseFeature::SetSpec ( gnFragmentSpec * spec ) [inline, virtual]   Sets the gnFragmentSpec to which this feature refers. Parameters: spec   A pointer to the fragment spec. Definition at line 304 of file gnBaseFeature.h. Referenced by gnFragmentSpec::AddFeature(). Member Data Documentation boolean gnBaseFeature::m_broken [protected]   Definition at line 276 of file gnBaseFeature.h. uint32 gnBaseFeature::m_id [protected]   Definition at line 274 of file gnBaseFeature.h. vector< gnLocation > gnBaseFeature::m_locationList< gnLocation > [protected]   Definition at line 278 of file gnBaseFeature.h. gnLocation::gnLocationType gnBaseFeature::m_locationType [protected]   Definition at line 277 of file gnBaseFeature.h. string gnBaseFeature::m_name [protected]   Definition at line 275 of file gnBaseFeature.h. vector< gnBaseQualifier * > gnBaseFeature::m_qualifierList< gnBaseQualifier* > [protected]   Definition at line 279 of file gnBaseFeature.h. gnFragmentSpec * gnBaseFeature::m_spec [protected]   Definition at line 280 of file gnBaseFeature.h. The documentation for this class was generated from the following files: gnBaseFeature.h gnBaseFeature.cpp