| AceWriter | |
| Algo | |
| AlgoMaker | |
| AlgoMakerTP< AlgoType, algoName, algoShouldPopup > | |
| AlgoMoveParam | |
| AlgoParam | |
| ChromatData | The chromatogram data for the read |
| ChromatGui | The visual appearance of a ChromatData |
| ChromatParser | |
| ConsAlgo | |
| Database::Creator< T > | To create records in the berkeley db |
| Destroyer | |
| DnaStrData | The nucleotide sequence for the read, e.g. "atag*ct*cgcg" |
| DnaStrGui | The visual appearance of a DnaStrData |
| DnaStrInfo | |
| DnpAlgo | |
| DNPclass | |
| DnpData | A "dnp", i.e. a defined nucleotype position |
| DnpGui | The visual appearance of a DnpData |
| DnpInfo | |
| DnpSearchAlgo | |
| DnpSortAlgo | |
| FeatureData | Provides a abstract feature object representing a feature, i.e. an attribute to a read. Holds its corresponding read index (recno) and geometric placement relative to its read |
| FeatureData::StorageData | To keep the order of the data members when serializing/unserializing |
| FeatureGui | Abstract class for the visual appereance of a feature. Each FeatureData derived class will have a corresponding FeatureGui derived class with a specialized paintMe() method |
| FeatureInfo | Base class for displaying info about reads and features |
| FeatureItem | Used in view modes edit dialog. Is there to reuse some code for the QListView |
| FindMatesAlgo | |
| GeneralData | This class is the base class for all data items that are to be stored in the Berkeley Db databases. It has methods for serializing its data to and from a bytestream and has methods for writing the same data to and from a xml dom tree. It also let you specify how this data should be indexed in the Berkeley Db databases for very fast retrieval |
| GeneralMaker | This is a factory class for GeneralData objects |
| GeneralMakerTP< Data, str_ > | |
| gengetopt_args_info | |
| Item | Used in view modes edit dialog. Is there to reuse some code for the QListView |
| Iterator< Wrappee > | |
| Layer | To hold the configuration of a single layer in a view mode ( ViewMode ). It knows its height and which features that should be painted in this layer |
| LayerEditDlg | Used in view modes edit dialog. A dialog window for that uses the ui file ui_layereditwidget.ui |
| LayerItem | Used in view modes edit dialog. Is there to reuse some code for the QListView |
| MAl | Writeable version of the multi alignment class |
| MAl_addon | |
| MAl_addon::cons_struct | |
| MAl_Readonly | |
| MAl_Readonly::dnp_struct | |
| MAlWrapper< alphabet > | |
| MateParser | |
| ModeEditDlg | |
| ModeItem | Used in view modes edit dialog. Is there to reuse some code for the QListView |
| MoveAlgo | |
| PhdParser | |
| Database::PrimaryIterator< T > | |
| PrintAlgo | |
| QualityData | Quality values of the meassurements/predicted bases |
| QualityGui | The visual appearance of a QualityData |
| QualityInfo | |
| RAlgo | Base class for algorithms that reads data. Nota bene! Read-only! |
| ReadData | Representing a read stored in the berkeley db. Holds its name and geometric placement in the contig |
| ReadData::StorageData | To keep the order of the data members when serializing/unserializing |
| ReadDrag | Drag object representing selected reads. Is created when a drag in TrapperView is initiated |
| ReadListAlgo | |
| ReadnamesAlgo | |
| ReadsInRect | |
| RealignerAlgo | |
| RemoveAlgo | |
| RootItem | Used in view modes edit dialog. Is there to reuse some code for the QListView |
| RWAlgo | Base class for algorithms that reads and writes data |
| Database::SecondaryIterator< T > | To search records and iterate over a secondary index |
| ShowModesDlg | Used in view modes edit dialog. Main window and handles the parsing of the trapperconf.xml file |
| SortAlgo | |
| SortAlgo::compBeg | |
| SortAlgo::compEnd | |
| SortAlgo::sort_struct | |
| StrandsAlgo | |
| SubsetAlgo | |
| TrapperApp | The base class of the application. It sets up the main window and providing a menubar, toolbar and statusbar. For the main view, an instance of class TrapperView is created which creates your view |
| TrapperConf | Load and saves the trapperconf.xml file |
| TrapperDoc | TrapperDoc provides a document object for a document-view model |
| TrapperParser | |
| TrapperVector< T > | To store an array of values. It's a template class to be used in the serializing bytearray and import/export to dom tree |
| TrapperView | The view to graphically present the reads and their features. The user will mainly interact with this window |
| TrashAlgo | |
| TrashRemoveAlgo | |
| TrDb | Opens and closes the primary and all secondary Berkeley dbs that are the underlying storage for a single GeneralData class |
| TrDb::Index | This defines a secondary index |
| ViewMode | To hold the configuration of a single view mode. A view mode specifies which features should be shown and how each read should be sliced in layers |
| ViewModes | To hold all configured view modes ( of class ViewMode ) |
| ViewParam |
1.4.4