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GB2 Namespace Reference


Detailed Description

A Grigoriev It is used to predict origin and terminus locations in bacterial and archaeal genomes

entropy = sum (p * log(2) p) where p - frequency of dif codons entropy is a measure of randomness, it mean that coding sequences have entropy lower than random sequence


Classes

class  ABIFormat
class  AboutDialogController
class  ActorCfgModel
class  AddDocumentTask
class  AddExistingDocumentDialogImpl
class  AddExistingDocumentDialogModel
class  AddNewDocumentDialogImpl
class  AddNewDocumentDialogModel
class  AddPluginTask
class  AddToViewContext
class  ADVAlignmentSupport
class  ADVAnnotationCreation
class  ADVClipboard
class  ADVCreateAnnotationsTask
class  ADVSequenceObjectContext
class  ADVSequenceWidget
class  ADVSequenceWidgetAction
class  ADVSingleSequenceHeaderWidget
class  ADVSingleSequenceWidget
class  ADVSplitWidget
class  AlignedSeq
class  AnnotatedDNAView
class  AnnotatedDNAViewFactory
class  AnnotatedDNAViewState
class  Annotation
class  AnnotationData
class  AnnotationDataPrototype
class  AnnotationGroup
class  AnnotationGroupModification
class  AnnotationGroupSelection
class  AnnotationModification
class  AnnotationSelection
class  AnnotationSelectionData
class  AnnotationSettings
class  AnnotationSettingsDialogController
class  AnnotationSettingsRegistry
class  AnnotationsTreeView
class  AnnotationTableObject
class  AnnotationTableObjectConstraints
class  AnnotationTableObjectTest
class  AnnotatorPlugin
class  AnnotatorTests
class  AnnotatorViewContext
class  AppContext
class  AppContextImpl
class  AppSettings
class  AppSettingsDialogController
class  AppSettingsGUI
class  AppSettingsGUIImpl
class  AppSettingsGUIPageController
class  AppSettingsGUIPageState
class  AppSettingsGUIPageWidget
class  AppSettingsImpl
class  AppSettingsTreeItem
class  ASTreeItem
class  AtomData
class  Attribute
class  AVAnnotationItem
class  AVGroupItem
class  AVItem
class  AVQualifierItem
class  AWidget
class  BallAndStickGLRenderer
struct  Base
class  BaseContentGraphAlgorithm
class  BaseContentGraphFactory
class  BaseDNAAlphabetIds
class  BaseDocumentFormatConfigurators
class  BaseDocumentFormats
class  BaseIOAdapters
class  BioDataTypes
class  BioStruct3D
class  BioStruct3DColorScheme
 Abstract BioStruct3DColorScheme. More...
class  BioStruct3DColorSchemeFactory
 Abstract factory for BioStruct3DColorScheme. More...
class  BioStruct3DGLRenderer
 Abstract biological 3D structure OpenGL renderer. More...
class  BioStruct3DGLRendererFactory
 BioStruct3DGLRenderer abstract factory. More...
class  BioStruct3DGLWidget
class  BioStruct3DObject
class  BioStruct3DObjectTests
class  BioStruct3DSplitter
class  BioStruct3DViewContext
class  BioStruct3DViewPlugin
class  Bond
class  BusPortEditor
class  CDCResultItem
class  CfgTreeItem
class  CfgTreeModel
class  ChainsColorScheme
class  CheckUpdatesTask
class  ChemicalElemColorScheme
class  ChooseItemDialog
class  ChromatogramView
class  ChromatogramViewRenderArea
class  ChromaViewAction
class  ChromaViewContext
class  ChromaViewPlugin
class  CloseDesignerTask
class  CloseProjectTask
 CloseProjectTask schema:. More...
class  ClustalWAlnFormat
class  CollocationsAlgorithm
class  CollocationsAlgorithmItem
class  CollocationsAlgorithmListener
class  CollocationsAlgorithmSettings
class  CollocationsDialogController
class  CollocationSearchTask
class  Color4f
 Color. More...
class  ComboBoxDelegate
class  Configuration
class  ConfigurationEditor
class  ConfigurationValidator
struct  ContextIdContainer
class  CopyDataTask
class  CoreDataTypes
class  CorePlugin
class  CreateAnnotationDialog
class  CreateAnnotationModel
class  CreateAnnotationsTask
class  CreateAnnotationWidgetController
class  CreateObjectRelationDialogController
class  CumulativeSkewGraphAlgorithm
class  CumulativeSkewGraphFactory
class  DataType
class  DataTypeConvertion
class  DataTypeRegistry
class  DataTypeSet
class  DBXRefInfo
class  DBXRefRegistry
class  DefaultModePreset
class  DelegateEditor
class  Descriptor
class  DescriptorListDelegate
class  DesignerUtils
class  DetView
class  DetViewRenderArea
class  DeviationGraphAlgorithm
class  DeviationGraphFactory
class  DialogUtils
class  DinucleotitePropertyRegistry
class  DiProperty
class  DisablePluginViewerTask
class  DisableProjectViewTask
class  DisableServiceTask
class  DisplayLists
class  DiStat
class  DNAAlphabet
class  DNAAlphabetRegistry
class  DNAAlphabetRegistryImpl
class  DNAChromatogram
class  DNAChromatogramObject
class  DNAExportAlignmentTask
class  DNAExportPlugin
class  DNAExportSequenceTask
class  DNAExportService
class  DNAExportTaskSettings
class  DNAExportViewContext
class  DNAGraphPackPlugin
class  DNAGraphPackViewContext
class  DNASequence
class  DNASequenceObject
class  DNASequenceObjectConstraints
class  DNASequenceObjectTests
class  DNASequenceSelection
class  DNATranslation
class  DNATranslation1to1Impl
class  DNATranslation3to1Impl
class  DNATranslationImplTests
class  DNATranslationRegistry
class  DockData
class  DockWrapWidget
class  DocManagedGObjectHints
class  Document
class  DocumentConstraintsFilter
class  DocumentFilter
class  DocumentFormat
class  DocumentFormatComboboxController
class  DocumentFormatConfigurator
class  DocumentFormatConfigurators
class  DocumentFormatConstraints
class  DocumentFormatRegistry
class  DocumentFormatRegistryImpl
class  DocumentFormatUtils
class  DocumentMimeData
class  DocumentModelTests
class  DocumentSelection
class  DocumentSerialState
class  DotPlotCalcResultsListener
class  DoubleSpinBoxDelegate
class  DynTable
class  EMBLGenbankAbstractDocument
class  EMBLGenbankAbstractHeader
class  EMBLGenbankAbstractIDLine
class  EMBLPlainTextFormat
class  EnablePluginViewerTask
class  EnableProjectViewTask
class  EnableServiceTask
class  EntropyGraphAlgorithm
class  EntropyGraphFactory
class  ExportDialogController
class  ExportImageDialog
class  ExportWorkflowSchemaTask
class  ExtendedProcStyle
class  FastaFormat
struct  FILEStub
class  FindAlgorithm
class  FindAlgorithmResult
class  FindAlgorithmResultsListener
class  FindAlgorithmSettings
class  FindAlgorithmTask
class  FindAlgorithmTaskSettings
class  FindAlgorithmTestFormat
class  FindDialog
class  FormatUtils
class  FRListItem
class  gauto_array
class  GAutoDeleteList
class  GenbankPlainTextFormat
class  GHints
class  GHintsDefaultImpl
class  GObject
class  GObjectComboBoxController
class  GObjectComboBoxControllerConstraints
class  GObjectConstraints
class  GObjectMimeData
class  GObjectReference
class  GObjectRelation
class  GObjectRelationRole
class  GObjectSelection
class  GObjectTypes
class  GObjectUtils
class  GObjectView
class  GObjectViewAction
class  GObjectViewCloseInterface
class  GObjectViewFactory
class  GObjectViewFactoryRegistry
class  GObjectViewObjectHandler
class  GObjectViewState
class  GObjectViewUtils
class  GObjectViewWindow
class  GObjectViewWindowContext
class  GraphAction
class  GraphMenuAction
class  GraphUtils
class  GScrollBar
class  GSelection
class  GSelectionTypes
class  GSequenceGraphAlgorithm
class  GSequenceGraphData
class  GSequenceGraphDrawer
class  GSequenceGraphFactory
class  GSequenceGraphMinMaxCutOffData
class  GSequenceGraphUtils
class  GSequenceGraphView
class  GSequenceGraphViewRA
class  GSequenceGraphViewWithFactory
class  GSequenceGraphWindowData
class  GSequenceLineView
class  GSequenceLineViewAnnotated
class  GSequenceLineViewAnnotatedRenderArea
class  GSequenceLineViewRenderArea
class  GTest
class  GTest_AnnotatorSearch
class  GTest_BioStruct3DAtomCoordinates
class  GTest_BioStruct3DAtomSequenceId
class  GTest_BioStruct3DNumberOfAtoms
class  GTest_BioStruct3DNumberOfChains
class  GTest_BioStruct3DNumberOfResidues
class  GTest_CalculateACGTContent
class  GTest_CalculateDispersionAndAverage
class  GTest_CalculateFirstTypeError
class  GTest_CalculateSecondTypeError
class  GTest_CheckAnnotationLocation
class  GTest_CheckAnnotationQualifier
class  GTest_CheckAnnotationsLocationsInTwoObjects
class  GTest_CheckAnnotationsNamesInTwoObjects
class  GTest_CheckAnnotationsNumInTwoObjects
class  GTest_CheckAnnotationsQualifiersInTwoObjects
class  GTest_CheckNumAnnotations
class  GTest_CompareMAlignment
class  GTest_DiPropertyCheckAttribs
class  GTest_DNACompeareMulSequencesAlphabetIdInTwoObjects
class  GTest_DNACompeareMulSequencesInTwoObjects
class  GTest_DNACompeareMulSequencesNamesInTwoObjects
class  GTest_DNACompeareSequencesAlphabetsInTwoObjects
class  GTest_DNACompeareSequencesInTwoObjects
class  GTest_DNACompeareSequencesNamesInTwoObjects
class  GTest_DNAMulSequenceAlphabetId
class  GTest_DNAMulSequencePart
class  GTest_DNAMulSequenceSize
class  GTest_DNASequenceAlphabet
class  GTest_DNASequenceAlphabetId
class  GTest_DNASequenceAlphabetType
class  GTest_DNASequencePart
class  GTest_DNASequenceSize
class  GTest_DNASequencInMulSequence
class  GTest_DNATranslation3to1Test
class  GTest_DocumentNumObjects
class  GTest_DocumentObjectNames
class  GTest_DocumentObjectTypes
class  GTest_FindAnnotationByNum
class  GTest_FindGObjectByName
class  GTest_hmmCompare
class  GTest_LoadBrokenDocument
class  GTest_LoadDocument
class  GTest_ORFMarkerTask
class  GTest_PDBFormatStressTest
class  GTest_RemoteRequest
class  GTest_SaveDocument
class  GTest_SiteconSearchTask
class  GTest_SW_CheckRegion
class  GTest_TaskAddSubtaskTest
class  GTest_TaskCancelTest
class  GTest_TaskCheckFlag
class  GTest_TaskCheckState
class  GTest_TaskCreateTest
class  GTest_TaskExec
class  GTest_TaskStateOrder
class  GTest_uHMMERBuild
class  GTest_uHMMERCalibrate
class  GTest_uHMMERSearch
class  GTest_uMuscle
class  GTest_uMuscleAddUnalignedSequenceToProfile
class  GTest_Wait
class  GTestAnnotationDataItem
class  GTestEnvironment
class  GTestFormat
class  GTestFormatRegistry
class  GTestRef
class  GTestState
class  GTestSuite
class  GUIUtils
class  GzippedHttpFileAdapterFactory
class  GzippedLocalFileAdapterFactory
class  GzipUtil
class  HBar
struct  Header
class  Helix3D
 Alpha Helix 3D representation. More...
class  HMMADVContext
class  HMMBuildDialogController
class  HMMBuildTask
class  HMMBuildToFileTask
class  HMMCalibrateAbstractTask
class  HMMCalibrateDialogController
class  HMMCalibrateParallelSubTask
class  HMMCalibrateParallelTask
class  HMMCalibrateTask
class  HMMCalibrateToFileTask
class  HMMIO
class  HMMMSAEditorContext
class  HMMReadTask
class  HMMSearchDialogController
class  HMMSearchTask
class  HMMSearchTaskCachedResult
class  HMMSearchTaskResult
class  HMMSearchToAnnotationsTask
class  HMMWriteTask
class  HttpFileAdapter
class  HttpFileAdapterFactory
class  IdRegistry
class  Index3To1
class  IndexedMapping3To1
class  InfiniteTestTask
class  IOAdapter
class  IOAdapterFactory
class  IOAdapterRegistry
class  IOAdapterRegistryImpl
class  ItemStyles
class  ItemViewStyle
class  IterationListModel
class  IterationListWidget
class  KarlinGraphAlgorithm
class  KarlinGraphFactory
class  LargeModePreset
class  LastOpenDirHelper
class  ListDataType
class  LoadDocumentTask
class  LoadDocumentTaskProvider
class  LoadProjectTask
 LoadProjectTask. More...
class  LoadTestTask
class  LoadUnloadedDocumentAndOpenViewTask
class  LoadUnloadedDocumentTask
class  LoadWorkflowSchemaTask
class  LocalFileAdapter
class  LocalFileAdapterFactory
class  LogCache
class  LogCategory
class  LogCategoryPrototype
struct  LogCategorySettings
class  LogMessage
class  LogServer
class  LogSettings
class  LogSettingsPageController
class  LogSettingsPageState
class  LogSettingsPageWidget
class  LogSettingsTopLineWidget
class  LogViewDockWidget
class  LRegion
class  LRegionsSelection
class  MainWindow
class  MainWindowImpl
class  MAlignment
class  MAlignmentItem
class  MAlignmentObject
class  Mapping3To1
struct  MatchScores
class  Matrix4x4
class  MDIItem
class  MinMaxSelectorWidget
class  MoleculeData
class  MSAEditor
class  MSAEditorColorScheme
class  MSAEditorConsensusArea
class  MSAEditorFactory
class  MSAEditorNameList
class  MSAEditorSequenceArea
class  MSAEditorState
class  MSAEditorUI
class  MSASymStatItem
class  MSAUtils
class  MultiGSelection
class  MultiPartDocFormatConfigurator
class  MultiTask
class  MuscleAction
class  MuscleAdapter
class  MuscleAddSequencesToProfileTask
class  MuscleAlignDialogController
class  MuscleAlignPreset
class  MuscleContextTLSRef
class  MuscleGObjectTask
class  MuscleMSAEditorContext
class  MuscleParamsHelper
class  MusclePlugin
class  MuscleTask
class  MuscleTaskSettings
class  MWDockManager
class  MWDockManagerImpl
class  MWMDIManager
class  MWMDIManagerImpl
class  MWMDIWindow
class  MWMenuManager
class  MWMenuManagerImpl
class  MWStub
class  MWToolBarManager
class  MWToolBarManagerImpl
class  NetworkConfiguration
class  NetworkSettingsPageController
class  NetworkSettingsPageState
class  NetworkSettingsPageWidget
class  NewickFormat
class  NextPieceLabel
class  Object3D
 OpenGL drawable object. More...
class  ObjectViewTask
class  ObjectViewTreeController
class  OpenAnnotatedDNAViewTask
class  OpenMSAEditorTask
class  OpenProjectTask
class  OpenSavedAnnotatedDNAViewTask
class  OpenSavedMSAEditorTask
class  OpenSimpleTextObjectViewTask
class  OpenViewContext
class  OpenWorkflowViewTask
class  ORFAlgorithmSettings
class  ORFDialog
class  ORFFindAlgorithm
class  ORFFindResult
class  ORFFindResultsListener
class  ORFFindTask
class  ORFListItem
class  ORFMarkerPlugin
class  ORFMarkerTests
class  ORFViewContext
class  OVTItem
class  OVTStateItem
class  OVTViewItem
struct  PairVector
class  PaletteDelegate
class  PanView
class  PanViewRenderArea
class  PDBFormat
class  PercentValidator
class  PhyBranch
class  PhyNode
class  PhyTreeData
class  PhyTreeObject
class  PlainTextFormat
class  Plugin
class  PluginRef
class  PluginSupport
class  PluginSupportImpl
class  PluginViewer
class  PluginViewerController
class  PluginViewerImpl
class  PlugViewPluginItem
class  PlugViewServiceItem
class  PlugViewTreeItem
class  PositionSelector
class  Project
 Project model. More...
class  ProjectDialogController
class  ProjectDocumentComboBoxController
class  ProjectImpl
class  ProjectLoader
 Service responsible for project loading / unloading. More...
class  ProjectLoaderImpl
class  ProjectManagedHints
class  ProjectService
class  ProjectServiceDisableTask
class  ProjectServiceEnableTask
class  ProjectServiceImpl
class  ProjectTreeController
class  ProjectTreeControllerModeSettings
class  ProjectTreeItemSelectorDialog
class  ProjectView
class  ProjectViewDocTree
class  ProjectViewImpl
class  ProjectViewWidget
class  ProjViewDocumentTreeItem
class  ProjViewObjectTreeItem
class  ProjViewTreeItem
class  PrompterBase
class  PrompterBaseImpl
class  PropertyDelegate
class  ProxyConfig
class  ProxyDelegate
class  PVRowData
class  PVRowsManager
class  Qualifier
class  QualifierModification
class  QVariantUtils
class  RangeSelector
class  RawDNASequenceFormat
class  RefineModePreset
class  RegisterServiceTask
class  ReloadScriptTask
class  RemoteRequestPlugin
class  RemoteRequestPluginTests
class  RemoteRequestSubtask
class  RemoteRequestTask
class  RemoteRequestViewContext
class  RemoveMultipleDocumentsTask
class  RepeatFinder
class  RepeatFinderDiagonalBase
class  RepeatFinderDiagonalWK
class  RepeatFinderPlugin
class  RepeatFinderSArrayW
class  RepeatFinderSArrayWK
struct  RepeatResult
class  RepeatViewContext
class  ResidueData
class  ResourceTracker
class  RingBuffer
class  RollingArray
class  RollingMatrix
class  SArrayIndex
class  SaveDocumentTask
class  SaveMiltipleDocuments
class  SaveProjectTask
 SaveProjectTask schema:. More...
class  SaveWorkflowSchemaTask
class  SceneSerializer
class  SCFFormat
class  SchemaConfigurationDialog
class  ScreenedParamValidator
class  Script
class  ScriptHttpAnnotatorContext
class  ScriptManagerDialog
class  ScriptManagerView
class  ScriptManagerWidgetImpl
class  ScriptRegistryEnableTask
class  ScriptRegistryService
class  ScriptTypes
class  SecondaryStructureData
class  SecStructColorScheme
class  SelectionUtils
class  SendSelectionDialogImpl
class  SequenceWalkerCallback
class  SequenceWalkerConfig
class  SequenceWalkerSubtask
class  SequenceWalkerTask
class  SequenceWalkerTests
class  Service
class  ServiceRegistry
class  ServiceRegistryImpl
class  Settings
class  SettingsImpl
class  ShutdownTask
class  SimpleProcStyle
class  SimpleTextObjectView
class  SimpleTextObjectViewFactory
class  SiteconADVContext
class  SiteconAlgorithm
class  SiteconAlgorithmTests
class  SiteconBuildDialogController
class  SiteconBuildSettings
class  SiteconBuildTask
class  SiteconBuildToFileTask
class  SiteconIO
class  SiteconModel
class  SiteconPlugin
class  SiteconReadTask
class  SiteconResultItem
class  SiteconSearchDialogController
class  SiteconSearchResult
class  SiteconSearchTask
class  SiteconWriteTask
class  SpinBoxDelegate
class  SplitterHeaderWidget
class  StateLock
class  StateLockableItem
class  StateLockableTreeItem
class  StateOrderTestTask
class  StateOrderTestTaskCallback
class  StockholmFormat
class  Strand3D
 Beta Strand 3D representation. More...
class  StrandContext
class  StyledItem
class  SuperDelegate
class  SyncHTTP
class  Task
class  TaskInfo
class  TaskLocalData
class  TaskScheduler
class  TaskSchedulerImpl
class  TaskSignalMapper
class  TaskStateInfo
class  TaskStateInfoPrototype
class  TaskStatusBar
class  TaskTests
class  TaskThread
class  TaskTimeInfo
class  TaskViewDockWidget
class  TBoard
class  TestFramework
class  TestRunnerPlugin
class  TestRunnerService
class  TestRunnerTask
class  TestViewController
class  TestViewReporter
class  TextObject
class  TextSelection
class  TextUtils
class  TPiece
class  Translations
class  Translator
class  TreeSorter
struct  Triplet
class  TubeGLRenderer
class  TVButton
class  TVItem
class  TVReportWindow
class  TVTestItem
class  TVTreeItem
class  TVTSItem
class  TypeMapEditor
class  UHMMBuild
class  UHMMBuildSettings
class  UHMMCalibrate
class  UHMMCalibrateSettings
class  UHMMERTests
class  uHMMPlugin
class  UHMMSearch
class  UHMMSearchResult
class  UHMMSearchSettings
class  UMUSCLETests
class  UnloadDocumentTask
class  UnregisterServiceTask
class  UpdateAnnotatedDNAViewTask
class  UpdateMSAEditorTask
class  UpdateSimpleTextObjectViewTask
class  URLDelegate
class  URLLineEdit
class  UserApplicationsSettingsPageController
class  UserApplicationsSettingsPageState
class  UserApplicationsSettingsPageWidget
class  UserAppsSettings
class  Vector3D
class  WBusItem
class  WindowStepSelectorDialog
class  WindowStepSelectorWidget
class  WorkflowDesignerPlugin
class  WorkflowDesignerService
class  WorkflowDocFormat
class  WorkflowEditor
class  WorkflowGObject
class  WorkflowIterationRunTask
class  WorkflowMetaDialog
class  WorkflowPalette
class  WorkflowPortItem
class  WorkflowProcessItem
class  WorkflowRunTask
class  WorkflowScene
class  WorkflowView
class  WorkflowViewFactory
struct  WorkPool_s
class  WormsGLRenderer
class  XMLMultiTest
class  XMLTestFactory
class  XMLTestFormat
class  XMLTestUtils
class  ZlibAdapter

Typedefs

typedef QString ActorId
typedef QFlags< ATVAnnUpdateFlag > ATVAnnUpdateFlags
typedef
QExplicitlySharedDataPointer
< DataType > 
DataTypePtr
typedef QString DocumentFormatId
typedef QString GObjectType
typedef QString GObjectViewFactoryId
typedef QList< GSelection * > GSelections
typedef QString GSelectionType
typedef QFlags< GSLV_FeatureFlag > GSLV_FeatureFlags
typedef QFlags< GSLV_UpdateFlag > GSLV_UpdateFlags
typedef QString GTestFormatId
typedef QString IOAdapterId
typedef QList< MDIItem * > MDIItems
typedef QSharedDataPointer
< PhyTreeData > 
PhyTree
typedef Plugin *(* PLUG_INIT_FUNC )()
typedef QVector< DiStat > PositionStats
typedef QNetworkProxy::ProxyType Proxy_t
typedef QVector< QVector< float > > PWVector
typedef int ServiceType
typedef QSharedDataPointer
< AnnotationData > 
SharedAnnotationData
typedef QSharedDataPointer
< AtomData > 
SharedAtom
typedef QSharedDataPointer
< MoleculeData > 
SharedMolecule
typedef QSharedDataPointer
< ResidueData > 
SharedResidue
typedef QSharedDataPointer
< SecondaryStructureData > 
SharedSecondaryStructure
typedef QFlags
< StateLockableTreeItemBranchFlag
StateLockableTreeItemBranchFlags
typedef QFlags< StateLockFlag > StateLockFlags
typedef QString StyleId
typedef QFlags< TaskFlag > TaskFlags

Enumerations

enum  { DelegateRole = Qt::UserRole + 100, DescriptorRole }
enum  { WorkflowProcessItemType = QGraphicsItem::UserType + 1, WorkflowPortItemType, WorkflowBusItemType }
enum  AnnotationModificationType {
  AnnotationModification_NameChanged, AnnotationModification_QualifierAdded, AnnotationModification_QualifierRemoving, AnnotationModification_QualifierValueChanged,
  AnnotationModification_LocationChanged, AnnotationModification_AddedToGroup, AnnotationModification_RemovedFromGroup
}
enum  ATVAnnUpdateFlag { ATVAnnUpdateFlag_BaseColumns = 0x1, ATVAnnUpdateFlag_QualColumns = 0x2 }
enum  AVItemType { AVItemType_Group, AVItemType_Annotation, AVItemType_Qualifier }
enum  DNAAlphabetType { DNAAlphabet_RAW, DNAAlphabet_NUCL, DNAAlphabet_AMINO }
enum  DNATranslationRole {
  DNATranslationRole_Unknown, DNATranslationRole_Start, DNATranslationRole_Start_Alternative, DNATranslationRole_Stop,
  DNATranslationRole_Num
}
enum  DNATranslationType {
  DNATranslationType_UNKNOWN, DNATranslationType_NUCL_2_NUCL, DNATranslationType_NUCL_2_COMPLNUCL, DNATranslationType_NUCL_2_AMINO,
  DNATranslationType_AMINO_2_AMINO, DNATranslationType_RAW_2_NUCL, DNATranslationType_RAW_2_AMINO
}
enum  DocumentModLock {
  DocumentModLock_IO, DocumentModLock_USER, DocumentModLock_FORMAT_AS_CLASS, DocumentModLock_FORMAT_AS_INSTANCE,
  DocumentModLock_UNLOADED_STATE, DocumentModLock_NUM_LOCKS
}
enum  FindAlgorithmStrand { FindAlgorithmStrand_Both, FindAlgorithmStrand_Direct, FindAlgorithmStrand_Complement }
enum  GSLV_FeatureFlag { GSLV_FF_SupportsCustomRange = 0x1 }
enum  GSLV_UpdateFlag {
  GSLV_UF_NeedCompleteRedraw = 1<<0, GSLV_UF_ViewResized = 1<<1, GSLV_UF_VisibleRangeChanged = 1<<2, GSLV_UF_SelectionChanged = 1<<3,
  GSLV_UF_FocusChanged = 1<<4, GSLV_UF_FrameChanged = 1<<5, GSLV_UF_AnnotationsChanged = 1<<6
}
enum  HMMBuildStrategy { P7_BASE_CONFIG, P7_LS_CONFIG, P7_FS_CONFIG, P7_SW_CONFIG }
enum  HttpAnnotatorAlphabet { HttpAnnotatorAlphabet_Any, HttpAnnotatorAlphabet_Nucleo, HttpAnnotatorAlphabet_Amino }
enum  HttpAnnotatorStrand { HttpAnnotatorStrand_Unknown, HttpAnnotatorStrand_Single, HttpAnnotatorStrand_Both }
enum  IOAdapterMode { IOAdapterMode_Read, IOAdapterMode_Write }
enum  LogLevel {
  LogLevel_TRACE, LogLevel_DETAILS, LogLevel_INFO, LogLevel_ERROR,
  LogLevel_NumLevels
}
enum  MSAConsensusType { MSAConsensusType_Default, MSAConsensusType_ClustalW }
enum  MuscleTaskOp { MuscleTaskOp_Align, MuscleTaskOp_Refine, MuscleTaskOp_AddUnalignedToProfile, MuscleTaskOp_ProfileToProfile }
enum  MWDockArea { MWDockArea_Left, MWDockArea_Right, MWDockArea_Bottom, MWDockArea_MaxDocks }
enum  ORFAlgorithmStrand { ORFAlgorithmStrand_Both, ORFAlgorithmStrand_Direct, ORFAlgorithmStrand_Complement }
enum  p7_weight {
  WGT_NONE, WGT_GSC, WGT_BLOSUM, WGT_PB,
  WGT_VORONOI, WGT_ME
}
enum  PluginState { PluginState_Loaded, PluginState_FailedToLoad }
enum  SaveProjectTaskKind { SaveProjectTaskKind_SaveProjectOnly, SaveProjectTaskKind_SaveProjectAndDocuments, SaveProjectTaskKind_SaveProjectAndDocumentsAskEach }
enum  ScriptState { ScriptState_Invalid = -1, ScriptState_Unloaded, ScriptState_Ready }
enum  SendSelectionAlphabet { SendSelectionAlphabet_Any, SendSelectionAlphabet_Nucleo, SendSelectionAlphabet_Amino }
enum  SendSelectionStrand { SendSelectionStrand_Both, SendSelectionStrand_Direct, SendSelectionStrand_Complement }
enum  ServiceState {
  ServiceState_Enabled, ServiceState_Disabled_New, ServiceState_Disabled_Manually, ServiceState_Disabled_ParentDisabled,
  ServiceState_Disabled_CircularDependency, ServiceState_Disabled_FailedToStart
}
enum  SiteconWeightAlg { SiteconWeightAlg_None, SiteconWeightAlg_Alg2 }
enum  StateLockableTreeItemBranchFlag { StateLockableTreeItemBranch_Item = 0x1, StateLockableTreeItemBranch_Parents = 0x2, StateLockableTreeItemBranch_Children = 0x4 }
enum  StateLockFlag { StateLockFlag_NoFlags = 0x00, StateLockFlag_LiveLock = 0x01, StateLockFlag_AnyFlags = 0xFF }
enum  TaskFlag {
  TaskFlag_None = 0x0, TaskFlag_NoRun = 1<<1, TaskFlag_DeleteWhenFinished = 1<<2, TaskFlag_RunAfterAllSubtasksFinished = 1<<3,
  TaskFlag_SerialSubtasks = 1<<4, TaskFlag_StopOnSubtaskError = 1<<5, TaskFlag_FailOnSubtaskError = 1<<6, TaskFlag_FailOnSubtaskCancel = 1<<7
}
enum  TriState { TriState_Unknown, TriState_Yes, TriState_No }
enum  TVColumns {
  TVColumns_Name, TVColumns_Desc, TVColumns_Progress, TVColumns_Actions,
  TVColumns_NumCols
}
enum  TVItemType { TVItem_TestSuite, TVItem_Test }
enum  UnloadDocumentTask_SaveMode { UnloadDocumentTask_SaveMode_Ask, UnloadDocumentTask_SaveMode_NotSave, UnloadDocumentTask_SaveMode_Save }

Functions

static QSet< GObject * > _findObjects (GObjectType t, const QList< GObject * > &objs)
static bool _registerMeta ()
static void addSequenceToMSA (MAlignment &ma, const QByteArray &path, QByteArray &msaPathChanges, const QByteArray &seq, const QString &name)
static void align (int start, int end, int win, int step, int seqLen, int &alignedFirst, int &alignedLast)
static bool allNucleic (const QList< ADVSequenceObjectContext * > &seqs)
static bool alphabetComplexityComparator (const DNAAlphabet *a1, const DNAAlphabet *a2)
static QScriptValue annotation_data_ctor (QScriptContext *ctx, QScriptEngine *engine)
bool annotationLessThanByRegion (const Annotation *a1, const Annotation *a2)
static float ascii2prob (char *s, float null)
void averagingRes (LRegion &res, const LRegion &min, const LRegion &max, int distance, const LRegion &searchRegion)
QPair< Vector3D, Vector3D > calcBestAxisThroughPoints (const QVector< Vector3D > &points)
 Calculates axis through points using least linear square method.
Vector3D calcMiddlePoint (const QVector< Vector3D > &points)
 Calculates average point.
static bool canDrop (const QMimeData *m, QList< ActorPrototype * > &lst)
static bool checkAllParentsEnabled (ServiceRegistryImpl *sr, Service *s)
static void checkFinishedState (TaskInfo *ti)
static bool checkModel (const MAlignment &al, TaskStateInfo &ti)
static void checkQuotes (const char *str, int len, bool &outerQuotes, bool &doubleQuotes)
static void checkSerialPromotion (TaskInfo *pti, Task *serialSubtask)
static void checkThread ()
static void checkThread (StateLockableItem *i)
static bool checkTypes (Port *p1, Port *p2)
bool compare_rows (PVRowData *x, PVRowData *y)
static ALPHA convertAlpha (DNAAlphabet *al)
static void convertMAlignment2MSA (MSA &muscleMSA, const MAlignment &ma, bool fixAlpha)
static void convertMAlignment2SecVect (SeqVect &sv, const MAlignment &ma, bool fixAlpha)
static void convertMSA2MAlignment (MSA &msa, DNAAlphabet *al, MAlignment &res)
static CorePlugin * createCorePlugin ()
static Task * createOpenViewTask (const MultiGSelection &ms)
static Task * createRegisterProjectTask (Project *proj)
double critchi (double p, int df)
static void drawArrow (QPainter *painter, const QPen &pen, const QPointF &p1, const QPointF &p2)
static void drawNum (QPainter &p, int x1, int x2, const QString &num, int lBorder, int rBorder, int y1, int y2)
static bool eq (float v1, float v2, int degree)
static bool existsCovalentBond (double r1, double r2, double distance)
static void fill (QBitArray &map, const char *s, Qt::CaseSensitivity caseMode)
static void fill3To1 (QList< Mapping3To1< char > > &map, QMap< DNATranslationRole, QList< Triplet > > &codons, const DNAAlphabet *srcAl, const DNAAlphabet *dstAl, const char *amino, const char *role, const char *n1, const char *n2, const char *n3)
static void fillBitArray (QBitArray &map, const char *str, Qt::CaseSensitivity caseMode)
static QList< Descriptorfilter (DataTypePtr set, DataTypePtr el)
void filterReadyScripts (QList< Script * > *all_scripts)
static void find_subst (FindAlgorithmResultsListener *rl, DNATranslation *aminoTT, DNATranslation *complTT, FindAlgorithmStrand strand, const char *seq, const LRegion &range, const char *pattern, int patternLen, bool singleShot, int maxErr, bool &stopFlag, int &percentsCompleted, int &currentPos)
static void findAllAnnotationsNamesInProject (QSet< QString > &allAnnotations)
static void findAllAnnotationsNamesInSettings (QSet< QString > &allAnnotations)
static QStringList findAllFiles (const QString &dirPath, const QString &ext, bool recursive, int rec)
static QStringList findAllPluginsInDefaultPluginsDir ()
static DNAChromatogramObject * findChromaObj (ADVSingleSequenceWidget *sw)
static bool findCircular (ServiceRegistryImpl *sr, Service *s, int currentDepth=0)
static void findInAmino (FindAlgorithmResultsListener *rl, DNATranslation *aminoTT, DNATranslation *complTT, FindAlgorithmStrand strand, bool insDel, const char *seq, const LRegion &range, const char *pattern, int patternLen, bool singleShot, int maxErr, bool &stopFlag, int &percentsCompleted, int &currentPos)
static void findInAmino_subst (FindAlgorithmResultsListener *rl, DNATranslation *aminoTT, DNATranslation *complTT, FindAlgorithmStrand strand, const char *seq, const LRegion &range, const char *pattern, int patternLen, bool singleShot, int maxErr, bool &stopFlag, int &percentsCompleted, int &currentPos)
static int findItem (QComboBox *cb, GObject *obj)
static FRListItem * findItem (const FindAlgorithmResult &r, QListWidget *lv)
static Service * findServiceToDisable (ServiceRegistry *sr)
static void fixAnnotationData (AnnotationData *ad)
static TaskFlags flagsFromString (QString str, bool *ok=NULL)
static QString formatDoc (const Descriptor &s, const Descriptor &d)
static float frag_trace_score (struct plan7_s *hmm, unsigned char *dsq, struct p7trace_s *tr, float *pernode, float expected)
Q_DECL_EXPORT Plugin * GB2_PLUGIN_INIT_FUNC ()
static QString genLocusString (AnnotationTableObject *ao, DNASequenceObject *so)
static qint64 genTaskId ()
static QString genUniqueName (const QSet< QString > &names, QString prefix)
static QBitArray getAlphaNums ()
static QBitArray getAlphas ()
static QBitArray getBinary ()
static quint8 getByteAtSCF (const char *buff, int pointer)
static QList< WorkflowPortItem * > getCandidates (WorkflowPortItem *port)
static QString getDate ()
static QList< Service * > getDirectChilds (ServiceRegistryImpl *sr, ServiceType st)
static QBitArray getEmptyBitMap ()
static int getIndex (char nucl)
static int getIntAt (const char *buff, int pointer)
static int getIntAtSCF (const char *buff, int pointer)
static QBitArray getLines ()
static QByteArray getLowerCaseMap ()
static QBitArray getNums ()
static GObjectReference getObjRef (const QVariantMap &stateData, const QString &key)
static int getShortAt (const char *buff, int pointer)
static quint16 getShortAtSCF (const char *buff, int ptr)
static QByteArray getSpaceLine ()
static QString getStateName (const GTestState *testState)
static QStringList getStrProperties ()
static QByteArray getUpperCaseMap ()
static QBitArray getWhites ()
void glCreateArrowPrimitive (float width, float height, float length)
 Draw arrow.
void glDrawAtom (GLUquadric *pObj, const Vector3D &pos, double r)
 Draw atom as sphere with center = pos and radius = r.
void glDrawCylinder (GLUquadric *pObj, const Vector3D &p1, const Vector3D &p2, double thickness)
 Draw cylinder from one point to another.
void glDrawHalfBond (GLUquadric *pObj, const Vector3D &p1, const Vector3D &p2, double thickness)
void glDrawHalfWorm (const Vector3D *p0, const Vector3D &p1, const Vector3D &p2, const Vector3D *p3, double radius, bool cap1, bool cap2, double tension)
 Draw a spline (worm).
static bool groupDepthInverseComparator (const AVGroupItem *i1, const AVGroupItem *i2)
static bool hasAminoForAll (const QSet< GObject * > &set)
static bool hasComplementForAll (const QSet< GObject * > &set)
bool HMMSearchResultEValLessThan (const HMMSearchTaskResult &r1, const HMMSearchTaskResult &r2)
static void initProcMap (QMap< ActorId, WorkflowProcessItem * > &procMap, WorkflowScene *scene)
static bool isComplement (ORFAlgorithmStrand s)
static bool isComplement (FindAlgorithmStrand s)
static bool isDirect (ORFAlgorithmStrand s)
static bool isDirect (FindAlgorithmStrand s)
static bool isHyperLink (const QString &str)
static bool isNewQStart (const char *s, int l)
static bool isReadyToBeDisabled (Service *s, ServiceRegistry *sr)
static QString itemText (GObject *o)
static bool ksInUse (const QKeySequence &ks, const QList< DockData * > &docks)
static void least_squares (int n, const float *x, float *a, float *b)
static void load (IOAdapter *io, QList< GObject * > &objects, TaskStateInfo &ti)
static void load (IOAdapter *io, const QString &docUrl, QList< GObject * > &objects, TaskStateInfo &ti, int gapSize, int predictedSize, QString &writeLockReason)
static QString loadTextFromUrl (const QString &url)
static LogCategory log (ULOG_CAT_TASKS)
static LogCategory log (ULOG_CAT_MUSCLE)
static LogCategory log (ULOG_CAT_SITECON)
static LogCategory log (ULOG_CAT_WD)
static LogCategory log (ULOG_CAT_PLUGIN_TEST_RUNNER)
static LogCategory log (ULOG_CAT_PLUGIN_REMOTE_REQUEST)
static LogCategory log (ULOG_CAT_PLUGIN_BIOSTRUCT_3D)
static LogCategory log (ULOG_CAT_TEXT)
static LogCategory log (ULOG_CAT_MSA)
static LogCategory log (ULOG_CAT_ADV)
static LogCategory log (ULOG_CAT_IO)
static LogCategory log (ULOG_CAT_SCRIPTS)
static LogCategory log (ULOG_CAT_USER_INTERFACE)
static LogCategory log (ULOG_CAT_CORE_SERVICES)
static LogCategory logPerf (ULOG_CAT_PERFORMANCE)
static void main_loop_serial (struct plan7_s *hmm, const char *seq, int seqLen, struct threshold_s *thresh, int do_forward, int do_null2, int do_xnu, struct histogram_s *histogram, struct tophit_s *ghit, struct tophit_s *dhit, int *ret_nseq, TaskStateInfo &ti)
static void main_loop_serial (struct plan7_s *hmm, int seed, int nsample, float lenmean, float lensd, int fixedlen, struct histogram_s **ret_hist, float *ret_max, bool &cancelFlag, int &progress)
static QString map2String (const QVariantMap &map)
static bool matches (DNAAlphabet *al, const QByteArray &ba, const LRegion &r)
static bool matches (DNAAlphabet *al, const QByteArray &ba)
static void maximum_entropy (struct alphabet_s *al, struct plan7_s *hmm, unsigned char **dsq, MSA *msa, float eff_nseq, struct p7prior_s *prior, struct p7trace_s **tr)
static void multiline (QString &res, const QString &prefix, const char *s)
static QString nameByType ()
static QString nameByType (DeviationGraphFactory::GDeviationType t)
static QString nameByType (CumulativeSkewGraphFactory::GCumulativeSkewType t)
static QString nameByType (BaseContentGraphFactory::GType t)
static void normalize (DiProperty *p)
Vector3D operator* (double f, const Vector3D &v)
Vector3D operator* (const Vector3D &v, double f)
Vector3D operator+ (const Vector3D &a, const Vector3D &b)
Vector3D operator- (const Vector3D &a, const Vector3D &b)
Vector3D operator- (const Vector3D &a)
Vector3D operator/ (const Vector3D &v, double f)
QDataStream & operator<< (QDataStream &out, const LRegion &myObj)
QDataStream & operator<< (QDataStream &out, const GObjectRelation &myObj)
QDataStream & operator<< (QDataStream &out, const GObjectReference &myObj)
QDataStream & operator>> (QDataStream &in, LRegion &myObj)
QDataStream & operator>> (QDataStream &in, GObjectRelation &myObj)
QDataStream & operator>> (QDataStream &in, GObjectReference &myObj)
static void originalMSAToCurrent (const QByteArray &adjPath, const QByteArray &origPath, QByteArray &resPath)
static PhyTree parseTree (const QByteArray &text, TaskStateInfo &si)
static QByteArray path2Str (const PWPath &path)
double pochisq (double x, int df)
static void position_average_score (struct plan7_s *hmm, unsigned char **dsq, float *wgt, int nseq, struct p7trace_s **tr, float *pernode, float *ret_avg)
double poz (double z)
static void prepareAlignResults (MSA &msa, DNAAlphabet *al, MAlignment &ma, bool mhack)
static QVector< QColor > prepareColors ()
static void prepareMultiline (QString &lineToChange, int spacesOnLineStart, bool newLineAtTheEnd=true, int maxLineLen=79)
static QString prepareURL (QString url)
static const char * prob2ascii (float p, float null)
static ProfPos * ProfileFromMSALocal_ProfileCPP (MSA &msa, Tree &tree)
Vector3D projectPointOnAxis (const Vector3D &point, const Vector3D &axisUnitVector, const Vector3D &axisPoint)
 Project point on axis.
static bool registerMetas1 ()
static bool registerMetas2 ()
static void saveObjRef (QVariantMap &stateData, const QString &key, const GObjectReference &ref)
static QList< AVAnnotationItem * > selectAnnotationItems (const QList< QTreeWidgetItem * > &items, TriState readOnly)
static QSet< Document * > selectDocuments (Project *p, const QList< GObjectReference > &refs)
QSet< int > selectedIndexes (const QList< QTableWidgetItem * > &items)
static QList< AVGroupItem * > selectGroupItems (const QList< QTreeWidgetItem * > &items, TriState readOnly, TriState rootOnly)
static void setupAlphaAndScore (DNAAlphabet *al, TaskStateInfo &ti)
static QString state2String (Task::State state)
static Task::State stateFromString (QString str, bool *ok=NULL)
ActorId str2aid (const QString &s)
static QVariantMap string2Map (const QString &string, bool emptyMapIfError)
static QByteArray translate (DNATranslation *t, const char *seq, int seqLen)
static bool TreeNeededForWeighting (SEQWEIGHT s)
static QString triplet2str (const Triplet &t)
static int ugene_printf (FILE *f, const char *format,...)
static void updateLabel (DockData *d, bool active)
QScriptValue url_get (QScriptContext *ctx, QScriptEngine *engine)
Vector3D vector_cross (const Vector3D &a, const Vector3D &b)
double vector_dot (const Vector3D &a, const Vector3D &b)
static void writeAnnotations (IOAdapter *io, AnnotationTableObject *ao, TaskStateInfo &si)
static void writeQualifier (const QString &name, const QString &val, IOAdapter *io, TaskStateInfo &si, const char *spaceLine)
static void writeSequence (IOAdapter *io, DNASequenceObject *ao, TaskStateInfo &si)

Variables

const qreal A = 8
static AppContextImpl appContext
static const int bl = (int) A/4
static int count = 0
static const QString DATAFLOW_EL = "dataflow"
const float Deg2Rad = 0.017453293f
static const QString DST_PORT_ATTR = "dprt"
static const QString DST_PROC_ATTR = "dprc"
static QList< Annotation * > emptyAnnotations
static QList< Document * > emptyDocs
static QList< AnnotationGroup * > emptyGroups
static QList< LRegion > emptyLRegions
static QList< GObject * > emptyObjs
static const float FLOAT_MIN = 0.000000001f
static const char * HTTP_SCRIPT_ALPHABET_AMINO = "amino"
static const char * HTTP_SCRIPT_ALPHABET_NUCLEO = "nucleic"
static const char * HTTP_SCRIPT_ANNOTATION_DATA = "AnnotationData"
static const char * HTTP_SCRIPT_PROPERTY_ALPHABET = "alphabet"
static const char * HTTP_SCRIPT_PROPERTY_ANNOTATIONS = "annotations"
static const char * HTTP_SCRIPT_PROPERTY_CUSTOM_SETTINGS = "configure"
static const char * HTTP_SCRIPT_PROPERTY_GET = "get"
static const char * HTTP_SCRIPT_PROPERTY_LOG = "log"
static const char * HTTP_SCRIPT_PROPERTY_MAX_QUERY_LEN = "max_query_len"
static const char * HTTP_SCRIPT_PROPERTY_MAXRESLEN = "max_res_len"
static const char * HTTP_SCRIPT_PROPERTY_MINRESLEN = "min_res_len"
static const char * HTTP_SCRIPT_PROPERTY_QUERY = "query"
static const char * HTTP_SCRIPT_PROPERTY_STRAND = "strand"
static const char * HTTP_SCRIPT_PROPERTY_TASK_STATE_INFO = "stateInfo"
static const char * HTTP_SCRIPT_STRAND_BOTH = "both"
static const char * HTTP_SCRIPT_STRAND_SINGLE = "single"
static const QString ID_ATTR = "id"
static const QString NAME_ATTR = "name"
static const QString PARAMS_EL = "params"
static QString percentStr = WorkflowView::tr("%")
const float PI = 3.14159265f
static const QString PORT_EL = "port"
static const int portRotationModifier = Qt::AltModifier
static const QString POSITION_ATTR = "pos"
static const QString PROCESS_EL = "process"
const qreal R = 30
const float Rad2Deg = 57.2957795f
static const char * SCRIPT_PROPERTY_CONFIGURE = "configure"
static const char * SCRIPT_PROPERTY_GLOBAL = "U_GLOBAL"
static const char * SCRIPT_PROPERTY_MAIN = "main"
static const char * SCRIPT_PROPERTY_NAME = "name"
static const char * SCRIPT_PROPERTY_SETUP = "setup"
static const char * SCRIPT_PROPERTY_TYPE = "type"
const ServiceType Service_DNAExport = 11
const ServiceType Service_DNAGraphPack = 10
const ServiceType Service_MaxCoreServiceId = 1000
const ServiceType Service_MinCoreServiceId = 500
const ServiceType Service_PluginViewer = 1
const ServiceType Service_Project = 2
const ServiceType Service_ProjectView = 3
const ServiceType Service_ScriptRegistry = 13
const ServiceType Service_TestRunner = 12
static const char * SETTINGS_HTTP_PROXY_ENABLED = "network_settings/http_proxy/enabled"
static const char * SETTINGS_HTTP_PROXY_HOST = "network_settings/http_proxy/host"
static const char * SETTINGS_HTTP_PROXY_PORT = "network_settings/http_proxy/port"
static const char * SETTINGS_PROXY_EXCEPTED_URLS = "network_settings/proxy_exc_urls"
static const char * SETTINGS_PROXY_EXCEPTED_URLS_ENABLED = "network_settings/proxy_exc_urls_enabled"
static const char * SETTINGS_SCRIPT_MAX_RESULT_LEN = "http_annotator/max_res_len"
static const char * SETTINGS_SCRIPT_MIN_RESULT_LEN = "http_annotator/min_res_len"
static const QString SRC_PORT_ATTR = "sprt"
static const QString SRC_PROC_ATTR = "sprc"
static const QString TYPE_ATTR = "type"
static int windowCounter = 0
static const QString WORKFLOW_EL = "workflow"


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