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gnBaseFeature.cpp Go to the documentation of this file. // File: gnBaseFeature.cpp // Purpose: implements the gnBaseFeature // Description: // Changes: // Version: libGenome 0.1.0 // Author: Aaron Darling // Last Edited: April 15, 2001, 11:13:00pm // Modified by: // Copyright: (c) Aaron Darling // Licenses: Proprietary #include "gn/gnBaseFeature.h" #include "gn/gnLocation.h" #include "gn/gnStringQualifier.h" #include "gn/gnDebug.h" #include <list> gnBaseFeature::gnBaseFeature( ) { m_id = 0; m_name = ""; m_locationType = gnLocation::LT_Nothing; m_broken = false; m_spec = NULL; } gnBaseFeature::gnBaseFeature( string& name, uint32 id, gnFragmentSpec* spec, gnLocation::gnLocationType lt, boolean broken ) { m_id = id; m_name = name; m_locationType = lt; m_broken = broken; m_spec = NULL; } gnBaseFeature::~gnBaseFeature() { for( uint32 i=0; i < m_qualifierList.size(); i++) delete m_qualifierList[i]; } // Clone // Location Modification methods boolean gnBaseFeature::MovePositive( const gnSeqI i ) { boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].MovePositive(i); } return still_valid; } boolean gnBaseFeature::MoveNegative( const gnSeqI i ) { boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].MoveNegative(i); } return still_valid; } //delete everything bigger than i boolean gnBaseFeature::CropEnd( const gnSeqI i ) { boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].CropEnd(i); } return still_valid; } //delete everything less than i boolean gnBaseFeature::CropStart( const gnSeqI i ){ boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].CropStart(i); } return still_valid; } uint32 gnBaseFeature::FirstIndexOfQualifier( const string& name, uint32 listI ) const{ if(listI >= m_qualifierList.size()) return GNSEQI_END; uint32 i=listI; for(; i < m_qualifierList.size(); i++){ string qname = m_qualifierList[i]->GetName(); if(qname == name) break; } return i; } uint32 gnBaseFeature::LastIndexOfQualifier( const string& name, uint32 listI ) const{ if(listI >= m_qualifierList.size()) return GNSEQI_END; uint32 i=m_qualifierList.size()-1; for(; i >= listI; i--) if(m_qualifierList[i]->GetName() == name) break; return i; } boolean gnBaseFeature::RemoveQualifier( uint32 listI ){ if(listI < m_qualifierList.size()){ m_qualifierList.erase(m_qualifierList.begin() + listI); return true; } return false; } boolean gnBaseFeature::SetQualifier( string& name, string& value, uint32 listI ){ if(listI < m_qualifierList.size()){ m_qualifierList[listI] = new gnStringQualifier(name, value); return true; } return false; } boolean gnBaseFeature::SetQualifierName( string& name, uint32 listI ){ if(listI < m_qualifierList.size()){ gnStringQualifier* new_qual = new gnStringQualifier(name, m_qualifierList[listI]->GetValue()); delete m_qualifierList[listI]; m_qualifierList[listI] = new_qual; return true; } return false; } boolean gnBaseFeature::SetQualifierValue( string& value, uint32 listI ){ if(listI < m_qualifierList.size()){ gnStringQualifier* new_qual = new gnStringQualifier(m_qualifierList[listI]->GetName(), value); delete m_qualifierList[listI]; m_qualifierList[listI] = new_qual; return true; } return false; } // Compare methods boolean gnBaseFeature::Contains( gnSeqI i ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if((m_locationList[locationI].GetStart() <= i) && (m_locationList[locationI].GetEnd() >= i)) return true; } return false; } boolean gnBaseFeature::Contains( const gnLocation& l ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if(m_locationList[locationI].Contains(l)) return true; } return false; } boolean gnBaseFeature::Contains( gnBaseFeature* feature ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ uint32 i=0; for(; i < feature->GetLocationListLength(); i++){ if(m_locationList[locationI].Contains(feature->GetLocation(i))) break; //it's contained so we'll break the loop early } if(i == feature->GetLocationListLength()) return false; //the loop went full cycle. we found an uncontained location } return true; } boolean gnBaseFeature::IsContainedBy( const gnLocation& l ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if(!l.Contains(m_locationList[locationI])) return false; } return true; } boolean gnBaseFeature::Intersects( const gnLocation& l ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if(!l.Intersects(m_locationList[locationI])) return false; } return true; } boolean gnBaseFeature::Intersects( gnBaseFeature* feature ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ uint32 i=0; for(; i < feature->GetLocationListLength(); i++){ if(m_locationList[locationI].Intersects(feature->GetLocation(i))) break; //it's contained so we'll break the loop early } if(i == feature->GetLocationListLength()) return false; //the loop went full cycle. we found an uncontained location } return true; } inline boolean gnBaseFeature::AddLocation( const gnLocation& l, uint32 listI ){ if(listI <= m_locationList.size()){ m_locationList.insert(m_locationList.begin() + listI, l); return true; } return false; } gnLocation gnBaseFeature::GetLocation( uint32 listI ) const{ if(listI < m_locationList.size()) return m_locationList[listI]; return gnLocation(); } boolean gnBaseFeature::RemoveLocation( uint32 listI ){ if(listI < m_locationList.size()){ m_locationList.erase(m_locationList.begin() + listI); return true; } return false; } boolean gnBaseFeature::SetLocation( const gnLocation& l, uint32 listI ){ if(listI < m_locationList.size()){ m_locationList[listI] = l; return true; } return false; } boolean gnBaseFeature::AddQualifier( gnBaseQualifier* qualifier ){ if(qualifier != NULL){ m_qualifierList.push_back(qualifier); return true; } return false; } boolean gnBaseFeature::HasQualifier( const string& name ) const{ for(uint32 i=0; i < m_qualifierList.size(); i++) if(m_qualifierList[i]->GetName() == name) return true; return false; } string gnBaseFeature::GetQualifierName( uint32 listI ) const{ if(listI < m_qualifierList.size()) return m_qualifierList[listI]->GetName(); return string(); } string gnBaseFeature::GetQualifierValue( uint32 listI ) const{ if(listI < m_qualifierList.size()) return m_qualifierList[listI]->GetValue(); return string(); } gnBaseQualifier* gnBaseFeature::GetQualifier( uint32 listI ){ if(listI < m_qualifierList.size()) return m_qualifierList[listI]; return NULL; }