gnBaseFeature.h Source File

00001 
00002 // File:            gnBaseFeature.h
00003 // Purpose:         abstract Feature class
00004 // Description:     Provides an interface for Features in memory and on disk.
00005 // Changes:        
00006 // Version:         libGenome 0.1.0 
00007 // Author:          Aaron Darling 
00008 // Last Edited:     April 15, 2001, 10:34:50pm 
00009 // Modified by:     
00010 // Copyright:       (c) Aaron Darling 
00011 // Licenses:        Proprietary 
00013 #ifndef _gnBaseFeature_h_
00014 #define _gnBaseFeature_h_
00015 
00016 #include "gn/gnDefs.h"
00017 #include <string>
00018 #include <vector>
00019 #include "gn/gnClone.h"
00020 #include "gn/gnLocation.h"
00021 #include "gn/gnBaseQualifier.h"
00022 
00023 class gnFragmentSpec;
00024 
00031 class GNDLLEXPORT gnBaseFeature : public gnClone
00032 {
00033 public:
00034         gnBaseFeature();
00035         gnBaseFeature( string& name, uint32 id = 0, gnFragmentSpec* spec = NULL, gnLocation::gnLocationType lt = gnLocation::LT_Nothing, boolean broken = false );
00039         ~gnBaseFeature();
00040 
00041         virtual gnBaseFeature* Clone() const = 0;
00046         virtual string GetName() const;
00051         virtual void SetName( const string& name );
00056         virtual uint32 GetID() const;
00061         virtual void SetID(uint32 id);
00067         virtual gnFragmentSpec* GetSpec() const;
00072         virtual void SetSpec(gnFragmentSpec* spec);
00078         virtual gnLocation::gnLocationType GetLocationType() const;
00085         virtual void SetLocationType( gnLocation::gnLocationType lType );
00090         virtual uint32 GetLocationListLength() const;
00098         virtual boolean AddLocation( const gnLocation& l, uint32 listI = 0);
00104         virtual gnLocation GetLocation( uint32 listI ) const;
00110         virtual boolean RemoveLocation( uint32 listI );
00117         virtual boolean SetLocation( const gnLocation& l, uint32 listI );
00123         virtual boolean MovePositive( const gnSeqI i );
00129         virtual boolean MoveNegative( const gnSeqI i );
00135         virtual boolean CropStart( const gnSeqI i );
00141         virtual boolean CropEnd( const gnSeqI i );
00147         virtual boolean Crop( const gnLocation& l );
00152         virtual boolean IsBroken() const;
00157         virtual void SetBroken(boolean broke);
00158 
00164         virtual boolean Contains( gnSeqI i ) const;
00170         virtual boolean Contains( const gnLocation& l ) const;
00176         virtual boolean Contains( gnBaseFeature* feature ) const;
00182         virtual boolean IsContainedBy( const gnLocation& l ) const;
00188         virtual boolean Intersects( const gnLocation& l ) const;
00194         virtual boolean Intersects( gnBaseFeature* feature ) const;
00195 
00200         virtual uint32 GetQualifierListLength() const;
00206         virtual boolean AddQualifier( gnBaseQualifier* qualifier );
00212         virtual boolean HasQualifier( const string& name ) const;
00219         virtual uint32 FirstIndexOfQualifier( const string& name, uint32 listI ) const;
00226         virtual uint32 LastIndexOfQualifier( const string& name, uint32 listI ) const;
00232         virtual string GetQualifierName( uint32 listI ) const;
00238         virtual string GetQualifierValue( uint32 listI ) const;
00244         virtual gnBaseQualifier* GetQualifier( uint32 listI );
00250         virtual boolean RemoveQualifier( uint32 listI );
00258         virtual boolean SetQualifier( string& name, string& value, uint32 listI );
00265         virtual boolean SetQualifierName( string& name, uint32 listI );
00272         virtual boolean SetQualifierValue( string& value, uint32 listI );
00273 protected:
00274         uint32 m_id;
00275         string m_name;
00276         boolean m_broken;
00277         gnLocation::gnLocationType m_locationType;
00278         vector< gnLocation > m_locationList;
00279         vector< gnBaseQualifier* > m_qualifierList;
00280         gnFragmentSpec* m_spec;
00281 };// class gnBaseFeature
00282 
00283 inline
00284 string gnBaseFeature::GetName() const{
00285         return m_name;
00286 }
00287 inline
00288 void gnBaseFeature::SetName( const string& name ){
00289         m_name = name;
00290 }
00291 inline
00292 uint32 gnBaseFeature::GetID() const{
00293         return m_id;
00294 }
00295 inline
00296 void gnBaseFeature::SetID(uint32 id){
00297         m_id = id;
00298 }
00299 inline
00300 gnFragmentSpec* gnBaseFeature::GetSpec() const{
00301         return m_spec;
00302 }
00303 inline
00304 void gnBaseFeature::SetSpec(gnFragmentSpec* spec){
00305         m_spec = spec;
00306 }
00307 inline
00308 boolean gnBaseFeature::IsBroken() const{
00309         return m_broken;
00310 }
00311 inline
00312 void gnBaseFeature::SetBroken(boolean broke){
00313         m_broken = broke;
00314 }
00315 
00316 inline
00317 gnLocation::gnLocationType gnBaseFeature::GetLocationType() const{
00318         return m_locationType;
00319 }
00320 inline
00321 void gnBaseFeature::SetLocationType( gnLocation::gnLocationType lType ){
00322         m_locationType = lType;
00323 }
00324 inline
00325 uint32 gnBaseFeature::GetLocationListLength() const{
00326         return m_locationList.size();
00327 }
00328 inline
00329 boolean gnBaseFeature::Crop( const gnLocation& l ){
00330         return CropStart(l.GetStart()) && CropEnd(l.GetEnd());
00331 }
00332 inline
00333 uint32 gnBaseFeature::GetQualifierListLength() const{
00334         return m_qualifierList.size();
00335 }
00336 
00337 #endif
00338         // _gnBaseFeature_h_