Search Toolkit Book for UpdateViewer
#include <update_viewer.hpp>
Inheritance diagram for UpdateViewer:
Collaboration diagram for UpdateViewer:
Classes | |
| struct | StructureAlignmentInfo |
Public Types | |
| typedef std::list < BlockMultipleAlignment * > | AlignmentList |
Public Member Functions | |
| UpdateViewer (AlignmentManager *alnMgr) | |
| ~UpdateViewer (void) | |
| void | CreateUpdateWindow (void) |
| void | AddAlignments (const AlignmentList &alignmentList) |
| void | ReplaceAlignments (const AlignmentList &alignmentList) |
| void | DeleteAlignment (BlockMultipleAlignment *toDelete) |
| void | ImportSequences (void) |
| void | ImportStructure (void) |
| void | SetInitialState (void) |
| void | SaveDialog (bool prompt) |
| void | SaveAlignments (void) |
| void | BlastUpdate (BlockMultipleAlignment *alignment, bool usePSSMFromMultiple) |
| void | BlastNeighbor (BlockMultipleAlignment *update) |
| void | SavePendingStructures (void) |
| void | SortByIdentifier (void) |
| void | SortByPSSM (void) |
Private Types | |
| typedef std::list< const Sequence * > | SequenceList |
| typedef std::list< ncbi::CRef < ncbi::objects::CBiostruc > > | BiostrucList |
| typedef std::list < StructureAlignmentInfo > | PendingStructureAlignments |
Private Member Functions | |
| const Sequence * | GetMasterSequence (void) const |
| void | FetchSequencesViaHTTP (SequenceList *newSequences, StructureSet *sSet) const |
| void | ReadSequencesFromFile (SequenceList *newSequences, StructureSet *sSet) const |
| void | FetchSequences (StructureSet *sSet, SequenceList *newSequences) const |
| void | SortUpdates (void) |
| void | MakeEmptyAlignments (const SequenceList &newSequences, const Sequence *master, AlignmentList *newAlignments) const |
| void | GetVASTAlignments (const SequenceList &newSequences, const Sequence *master, AlignmentList *newAlignments, PendingStructureAlignments *structureAlignments, unsigned int masterFrom=kMax_UInt, unsigned int masterTo=kMax_UInt) const |
Private Attributes | |
| UpdateViewerWindow * | updateWindow |
| BiostrucList | pendingStructures |
| PendingStructureAlignments | pendingStructureAlignments |
Friends | |
| class | UpdateViewerWindow |
| class | SequenceDisplay |
Detailed Description
Definition at line 56 of file update_viewer.hpp.
Member Typedef Documentation
| typedef std::list< BlockMultipleAlignment * > UpdateViewer::AlignmentList |
Reimplemented from ViewerBase.
Definition at line 69 of file update_viewer.hpp.
typedef std::list< ncbi::CRef < ncbi::objects::CBiostruc > > UpdateViewer::BiostrucList [private] |
Definition at line 117 of file update_viewer.hpp.
typedef std::list< StructureAlignmentInfo > UpdateViewer::PendingStructureAlignments [private] |
Definition at line 123 of file update_viewer.hpp.
typedef std::list< const Sequence * > UpdateViewer::SequenceList [private] |
Definition at line 108 of file update_viewer.hpp.
Constructor & Destructor Documentation
| UpdateViewer::UpdateViewer | ( | AlignmentManager * | alnMgr | ) |
Definition at line 98 of file update_viewer.cpp.
| UpdateViewer::~UpdateViewer | ( | void | ) |
Definition at line 110 of file update_viewer.cpp.
Member Function Documentation
| void UpdateViewer::AddAlignments | ( | const AlignmentList & | alignmentList | ) |
Definition at line 143 of file update_viewer.cpp.
References SequenceDisplay::AddBlockBoundaryRow(), SequenceDisplay::AddRowFromAlignment(), SequenceDisplay::AddRowFromString(), ERRORMSG, ViewerWindowBase::GeometryViolationsShown(), ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), SequenceDisplay::NRows(), ViewerBase::Save(), SequenceDisplay::SetStartingColumn(), ViewerWindowBase::UpdateDisplay(), and updateWindow.
Referenced by AlignmentManager::AlignmentManager(), BlastNeighbor(), BlastUpdate(), ImportSequences(), ImportStructure(), AlignmentManager::RealignDependentSequences(), ReplaceAlignments(), and SortUpdates().
| void UpdateViewer::BlastNeighbor | ( | BlockMultipleAlignment * | update | ) |
Definition at line 1032 of file update_viewer.cpp.
References AddAlignments(), BlockMultipleAlignment::AddUnalignedBlocks(), BlockMultipleAlignment::alignDependentFrom, BlockMultipleAlignment::alignDependentTo, BlockMultipleAlignment::alignMasterFrom, BlockMultipleAlignment::alignMasterTo, ViewerBase::alignmentManager, StructureSet::alignmentManager, AlignmentManager::blaster, copy(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), DELETE_ALL_AND_CLEAR, eDiag_Error, eDiag_Info, SequenceDisplay::Empty(), ERRORMSG, GetAlignmentByBestNeighbor(), ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), AlignmentManager::GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), BlockMultipleAlignment::NRows(), StructureBase::parentSet, REG_ADVANCED_SECTION, REG_FOOTPRINT_RES, RegistryGetInteger(), SetDiagPostLevel(), TRACEMSG, BlockMultipleAlignment::UpdateBlockMapAndColors(), and WARNINGMSG.
Referenced by SequenceDisplay::MouseDown().
| void UpdateViewer::BlastUpdate | ( | BlockMultipleAlignment * | alignment, |
| bool | usePSSMFromMultiple | ||
| ) |
Definition at line 879 of file update_viewer.cpp.
References AddAlignments(), ViewerBase::alignmentManager, AlignmentManager::blaster, copy(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), SequenceDisplay::Empty(), ERRORMSG, ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), AlignmentManager::GetCurrentMultipleAlignment(), TRACEMSG, and WARNINGMSG.
Referenced by SequenceDisplay::MouseDown().
| void UpdateViewer::CreateUpdateWindow | ( | void | ) |
Definition at line 125 of file update_viewer.cpp.
References ViewerBase::GetCurrentDisplay(), SequenceDisplay::GetStartingColumn(), GlobalMessenger(), ViewerWindowBase::NewDisplay(), Messenger::PostRedrawSequenceViewer(), ViewerWindowBase::ScrollToColumn(), Messenger::UnPostRedrawSequenceViewer(), UpdateViewerWindow, and updateWindow.
Referenced by AlignmentManager::RealignDependentSequences(), and AlignmentManager::ShowUpdateWindow().
| void UpdateViewer::DeleteAlignment | ( | BlockMultipleAlignment * | toDelete | ) |
Definition at line 183 of file update_viewer.cpp.
References ViewerBase::GetCurrentAlignments(), and ReplaceAlignments().
Referenced by SequenceDisplay::MouseDown().
| void UpdateViewer::FetchSequences | ( | StructureSet * | sSet, |
| SequenceList * | newSequences | ||
| ) | const [private] |
Definition at line 401 of file update_viewer.cpp.
References FetchSequencesViaHTTP(), ReadSequencesFromFile(), and ViewerBase::viewerWindow.
Referenced by ImportSequences().
| void UpdateViewer::FetchSequencesViaHTTP | ( | SequenceList * | newSequences, |
| StructureSet * | sSet | ||
| ) | const [private] |
Definition at line 310 of file update_viewer.cpp.
References CRef< C, Locker >::Empty(), ERRORMSG, FetchSequenceViaHTTP(), StructureSet::FindOrCreateSequence(), Sequence::isProtein, and ViewerBase::viewerWindow.
Referenced by FetchSequences().
| const Sequence * UpdateViewer::GetMasterSequence | ( | void | ) | const [private] |
Definition at line 272 of file update_viewer.cpp.
References ViewerBase::alignmentManager, ERRORMSG, ViewerBase::GetCurrentAlignments(), AlignmentManager::GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetMaster(), AlignmentManager::GetStructureProteins(), and size.
Referenced by ImportSequences(), and ImportStructure().
| void UpdateViewer::GetVASTAlignments | ( | const SequenceList & | newSequences, |
| const Sequence * | master, | ||
| AlignmentList * | newAlignments, | ||
| PendingStructureAlignments * | structureAlignments, | ||
| unsigned int | masterFrom = kMax_UInt, |
||
| unsigned int | masterTo = kMax_UInt |
||
| ) | const [private] |
Definition at line 444 of file update_viewer.cpp.
References BlockMultipleAlignment::AddAlignedBlockAtEnd(), BlockMultipleAlignment::AddUnalignedBlocks(), StructureSet::alignmentManager, ERRORMSG, CChem_graph_alignment_Base::GetAlignment(), GetAsnDataViaHTTP(), CChem_graph_alignment_Base::GetBiostruc_ids(), CChem_graph_alignment_Base::GetDimension(), CBiostruc_annot_set_Base::GetFeatures(), CBiostruc_annot_set_Base::GetId(), CChem_graph_alignment_Base::GetTransform(), Sequence::identifier, INFOMSG, CBiostruc_annot_set_Base::IsSetId(), MakeEmptyAlignment(), MoleculeIdentifier::mmdbID, MoleculeIdentifier::moleculeID, StructureBase::parentSet, MoleculeIdentifier::pdbID, CBiostruc_annot_set_Base::SetFeatures(), Block::SetRangeOfRow(), MoleculeIdentifier::ToString(), BlockMultipleAlignment::UpdateBlockMapAndColors(), WARNINGMSG, Block::width, and WriteASNToFile().
Referenced by ImportStructure().
| void UpdateViewer::ImportSequences | ( | void | ) |
Definition at line 419 of file update_viewer.cpp.
References AddAlignments(), ERRORMSG, FetchSequences(), GetMasterSequence(), MakeEmptyAlignments(), StructureBase::parentSet, and WARNINGMSG.
Referenced by UpdateViewerWindow::OnImport().
| void UpdateViewer::ImportStructure | ( | void | ) |
Definition at line 583 of file update_viewer.cpp.
References AddAlignments(), BlockMultipleAlignment::AddUnalignedBlocks(), ViewerBase::alignmentManager, StructureSet::alignmentManager, DELETE_ALL_AND_CLEAR, eDiag_Fatal, eDiag_Info, eModel_type_ncbi_all_atom, eModel_type_ncbi_backbone, CBiomol_descr_Base::eMolecule_type_protein, map_checker< std::map< Key, T, Compare > >::end(), ERRORMSG, ExtractBiostrucAndBioseqs(), map_checker< std::map< Key, T, Compare > >::find(), StructureSet::FindOrCreateSequence(), StructureSet::frameMap, AlignmentManager::GetCurrentMultipleAlignment(), GetMasterSequence(), CRef< C, Locker >::GetPointer(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), GetUserDir(), GetVASTAlignments(), StructureSet::isAlphaOnly, LoadStructureViaCache(), Sequence::molecule, ne(), StructureSet::objects, StructureBase::parentSet, pendingStructureAlignments, pendingStructures, ReadASNFromFile(), CRef< C, Locker >::Reset(), SequenceSet::sequences, StructureSet::sequenceSet, SetDiagPostLevel(), TRACEMSG, BlockMultipleAlignment::UpdateBlockMapAndColors(), MoleculeIdentifier::VALUE_NOT_SET, and ViewerBase::viewerWindow.
Referenced by UpdateViewerWindow::OnImport().
| void UpdateViewer::MakeEmptyAlignments | ( | const SequenceList & | newSequences, |
| const Sequence * | master, | ||
| AlignmentList * | newAlignments | ||
| ) | const [private] |
Definition at line 390 of file update_viewer.cpp.
References MakeEmptyAlignment().
Referenced by ImportSequences().
| void UpdateViewer::ReadSequencesFromFile | ( | SequenceList * | newSequences, |
| StructureSet * | sSet | ||
| ) | const [private] |
Definition at line 333 of file update_viewer.cpp.
References ERRORMSG, CFastaReader::fAssumeProt, StructureSet::FindOrCreateSequence(), in(), CFastaReader::ReadSet(), ViewerBase::viewerWindow, and WARNINGMSG.
Referenced by FetchSequences().
| void UpdateViewer::ReplaceAlignments | ( | const AlignmentList & | alignmentList | ) |
Definition at line 174 of file update_viewer.cpp.
References AddAlignments(), DELETE_ALL_AND_CLEAR, SequenceDisplay::Empty(), ViewerBase::GetCurrentAlignments(), and ViewerBase::GetCurrentDisplay().
Referenced by AlignmentManager::BlockAlignAllUpdates(), AlignmentManager::BlockAlignUpdate(), DeleteAlignment(), AlignmentManager::ExtendAllUpdates(), AlignmentManager::ExtendUpdate(), AlignmentManager::MergeUpdates(), UpdateViewerWindow::OnDelete(), AlignmentManager::PurgeSequence(), AlignmentManager::ThreadAllUpdates(), and AlignmentManager::ThreadUpdate().
| void UpdateViewer::SaveAlignments | ( | void | ) |
Definition at line 194 of file update_viewer.cpp.
References ViewerBase::alignmentManager, blocks, CreatePairwiseSeqAlignFromMultipleRow(), map_checker< std::map< Key, T, Compare > >::end(), ERRORMSG, CUpdate_align_Base::eType_demoted, CUpdate_align_Base::eType_demoted_3d, map_checker< std::map< Key, T, Compare > >::find(), ViewerBase::GetCurrentAlignments(), CUpdate_align_Base::GetDescription(), CUpdate_align_Base::GetSeqannot(), CUpdate_align_Base::IsSetSeqannot(), AlignmentManager::ReplaceUpdatesInASN(), CUpdate_comment_Base::SetComment(), CUpdate_align_Base::SetDescription(), SetInitialState(), CUpdate_align_Base::SetSeqannot(), and CUpdate_align_Base::SetType().
Referenced by UpdateViewerWindow::SaveDialog().
| void UpdateViewer::SaveDialog | ( | bool | prompt | ) | [virtual] |
Reimplemented from ViewerBase.
Definition at line 120 of file update_viewer.cpp.
References UpdateViewerWindow::SaveDialog(), and updateWindow.
| void UpdateViewer::SavePendingStructures | ( | void | ) |
Definition at line 856 of file update_viewer.cpp.
References StructureSet::AddBiostrucToASN(), StructureSet::AddStructureAlignment(), ViewerBase::alignmentManager, ERRORMSG, AlignmentManager::GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetMaster(), StructureBase::parentSet, pendingStructureAlignments, pendingStructures, and TRACEMSG.
Referenced by AlignmentManager::MergeUpdates().
| void UpdateViewer::SetInitialState | ( | void | ) |
Definition at line 114 of file update_viewer.cpp.
References ViewerBase::EnableStacks(), and ViewerBase::KeepCurrent().
Referenced by AlignmentManager::AlignmentManager(), and SaveAlignments().
| void UpdateViewer::SortByIdentifier | ( | void | ) |
Definition at line 1129 of file update_viewer.cpp.
References CompareUpdatesByIdentifier(), SortUpdates(), TRACEMSG, and updateComparisonFunction.
Referenced by UpdateViewerWindow::OnSortUpdates().
| void UpdateViewer::SortByPSSM | ( | void | ) |
Definition at line 1136 of file update_viewer.cpp.
References ViewerBase::alignmentManager, CompareUpdatesByScore(), ViewerBase::currentAlignments, ERRORMSG, Block::Range::from, ViewerBase::GetCurrentAlignments(), AlignmentManager::GetCurrentMultipleAlignment(), BlockMultipleAlignment::GetPSSM(), NStr::IntToString(), LookupNCBIStdaaNumberFromCharacter(), Sequence::sequenceString, SortUpdates(), TRACEMSG, and updateComparisonFunction.
Referenced by UpdateViewerWindow::OnSortUpdates().
| void UpdateViewer::SortUpdates | ( | void | ) | [private] |
Definition at line 1176 of file update_viewer.cpp.
References AddAlignments(), ViewerBase::currentAlignments, SequenceDisplay::Empty(), ERRORMSG, ViewerBase::GetCurrentAlignments(), ViewerBase::GetCurrentDisplay(), and updateComparisonFunction.
Referenced by SortByIdentifier(), and SortByPSSM().
Friends And Related Function Documentation
friend class SequenceDisplay [friend] |
Reimplemented from ViewerBase.
Definition at line 59 of file update_viewer.hpp.
friend class UpdateViewerWindow [friend] |
Definition at line 58 of file update_viewer.hpp.
Referenced by CreateUpdateWindow().
Member Data Documentation
Definition at line 124 of file update_viewer.hpp.
Referenced by ImportStructure(), and SavePendingStructures().
BiostrucList UpdateViewer::pendingStructures [private] |
Definition at line 118 of file update_viewer.hpp.
Referenced by ImportStructure(), and SavePendingStructures().
UpdateViewerWindow* UpdateViewer::updateWindow [private] |
Definition at line 105 of file update_viewer.hpp.
Referenced by AddAlignments(), CreateUpdateWindow(), and SaveDialog().
The documentation for this class was generated from the following files:
- src/app/cn3d/update_viewer.hpp
- src/app/cn3d/update_viewer.cpp
