ABItype | Reads files in ABI format |
AlignmentAppearanceDialog | The class implementing the "Alignment appearance" dialog in the alignment module |
aln_pos | Part of the ClustalW package |
AutoAnnotate | Scans database(s) for known features in the current sequence |
blastThread | A wxThreadHelper class to run BLAST queries in the background |
CGdialog | This class contains the settings dialog for the CGviewer export function |
CGview | This class manages the CGview export |
ChildBase | The base class for all modules |
cmd_line_data | Part of the ClustalW package |
color | Part of the ClustalW package |
EILB | The External Interface List Box class, a specialized wxHtmlListBox |
EIpanel | The External Interface panel class |
element | Part of the IPC package |
ExternalInterface | The External Interface ChildBase class |
FindSequenceDialog | The class implementing the "Find" dialog in various ChildBase modules |
fit_dat | |
GPOUT | Part of the IPC package |
hept_pref | |
ipc_compound | Part of the IPC package |
isotope | Part of the IPC package |
MatMenu | Part of the ClustalW package |
MatMenuEntry | Part of the ClustalW package |
menu_item | Part of the ClustalW package |
MyApp | Application class |
MyChild | The very, very, *very* important module to handle DNA in all its beauty! |
myExternal | This class is a wrapper around HTTP GET commands |
MyFrame | Frame class |
MyFrameDropTarget | The class that handles drag'n'drop events for MyFrame |
MySplitter | Specialized class based on wxSplitterWindow; used in MyChild to separate the different parts of the module |
node | Part of the ClustalW package |
panel_data | Part of the ClustalW package |
PCR_troubleshoot_dialog | The class implementing the PCR troubleshooting dialog |
PlasmidCanvas | The class to draw the DNA map, as well as the mini-map in the amino acid module |
prettyopts | Part of the ClustalW package |
ProgramOptionsDialog | The dialog containing program end enzyme global settings |
range | Part of the ClustalW package |
rangeNum | Part of the ClustalW package |
ReadSeqVars | Part of the ClustalW package |
SeqAA | Sequence display class showing amino acids |
SeqAAstructure | Sequence display class showing amino acids |
SeqABI | Sequence display class showing ABI sequencer peaks |
SeqAlign | Sequence display class showing alignments |
SeqBasic | The parent class for all sequence types, including DNA, amino acids, features, restriction sites, ABI peaks, etc |
SeqBlank | Sequence display class showing a blank line |
SeqDivider | Sequence display class showing a horizontal divider |
SeqDNA | Sequence display class showing DNA |
SeqFeature | Sequence display class showing annotated features |
SeqNum | Sequence display class showing numbers "inline" |
SeqPlot | Sequence display class showing plot data in the amino acid module |
SeqPos | SeqPos manages the positions of all items for a single "type" (for example, DNA) |
SeqPrimer | Sequence display class showing primers |
SeqRestriction | Sequence display class showing restriction sites |
SequenceCanvas | The main sequence display class |
SequenceCharMarkup | This class contains the markup of a single character (borders, fore- and background) |
SequencePartList | This class assists in the restriction site layout |
SeriesMat | Part of the ClustalW package |
spanel | Part of the ClustalW package |
spec_points | Part of the IPC package |
TAAProp | This class manages amino acid properties; so 20 total. Used by the static part of TVector |
TABIviewer | The ABI (sequencer data) viewer module class |
TAlignLine | Helper class for TAlignment; represents a line (a sequence) in the alignment |
TAlignment | The alignment module class. Note: this is actually a child class of both ChildBase and wxThreadHelper! |
TAlignmentDialog | The alignment settings dialog |
TAminoAcids | The amino acid sequence display module |
TAutoAnnotateDialog | The dialog class for the AutoAnnotate class/function |
TCalculator | The calculator module |
TClone | The CLONE format import/export class |
TClone_Enzyme | Temporarily stores an enzyme |
TClone_Gene | Temporarily stores an item |
TCloneManager | |
TCloningAssistant | The cloning assistant module |
TCloningAssistantPanel | |
TDDR | |
TDDR_Timer | |
Tdna2aa | This class stores a codon and the corresponding amino acid. Used by TVector |
TEnzymeDialog | A dialog to display/edit enzyme properties |
TEnzymeRules | Stores, loads, stores, and compares enzyme settings |
TEnzymeSettingsTab | The "tab" for global and per-sequence enzyme/methylation/etc. settings |
TextImportDialog | The dialog where one can enter a sequence manually |
TFLAG | Helper class for ABItype |
TFragment | A restriction fragment (from, to, length) |
TGelLane | This class represents a lane on a virtual gel |
TGenBank | GenBank format import/export class |
TGenBankFeature | Helper class for TGenBank |
TGraph | The graph drawing module |
TGraphData | The class containing xy-data for graph drawing |
TGraphDialog | |
TGraphDisplay | The display class, containing graphs and scales; essentially, a "tab" |
TGraphScale | The class containing a scale used in the graph |
TGridBasic | The base class for each calculator submodule (grid/sheet) |
TGridData | The codon table calculator submodule |
TGridDNA | The DNA concentration/purity calculator submodule |
TGridLigation | The ligation calculator submodule |
TGridProtein | The protein concentration calculator submodule |
TImageDisplay | The image display module |
TIMGitem | Annotation drawing class |
TIMGreader | This class can read the ancient BioRad IMG format (most of the time...) |
TIPC | Part of the IPC package |
TIPC_ELEMENT | Part of the IPC package |
TIPC_PARS | Part of the IPC package |
TIPCDialog | The dialog handling the TIPC settings |
TItemEditDialog | Dialog to set item/feature color, offset, type etc.; called from TVectorEditor |
TiXmlAttribute | |
TiXmlAttributeSet | |
TiXmlBase | |
TiXmlBase::Entity | |
TiXmlBase::StringToBuffer | |
TiXmlComment | |
TiXmlCursor | |
TiXmlDeclaration | |
TiXmlDocument | |
TiXmlElement | |
TiXmlHandle | |
TiXmlNode | |
TiXmlParsingData | |
TiXmlText | |
TiXmlUnknown | |
TLigationDialog | The ligation dialog class |
TMainTree | The main tree class |
TMainTreeItem | Item in TMainTree |
TManageDatabaseDialog | The database interface dialog; opening, storing, searching sequences |
TMarkMem | This helper class of SequenceCanvas can memorize a marking of the sequences, and restore it |
TMyDropTarget | Handles drag'n'drop events for items dragged between the two database lists in TManageDatabaseDialog |
TMyGelControl | This class handles a single virtual gel for TVirtualGel, using TGelLane lanes |
TMyImagePanel | This class represents the actual image displayed by TImageDisplay |
TMyMultipleChoiceDialog | A dialog for multiple choices |
TMySQLDialog | Creates the dialog for entering parameters to add a MySQL database |
TOnlineTools | TOnlineTools class |
TORF | This class manages open reading frames (ORFs) |
TPDB | Can parse PDB files and generated annotated TVector sequences |
TPhylip | |
TPhyloTree | The phylogenetic tree module |
TPhyloTreeBox | |
TPrimer | This class holds and generates information about a primer |
TPrimerDesign | The virtual PCR/primer design module |
TPrimerDialog | The dialog to optimize primers |
TProject | Project class |
TProtease | Class to store a protease |
TProteaseCut | Class to store a protease cut |
TProteolysis | |
TProteolysisGel | |
TProteolysisSuggestion | |
TPTree | |
TransformSequenceDialog | Tiny dialog for transforming a DNA sequence |
TREcache | Restriction enzyme site cache |
TRestrictionCut | Stores a specific cut of a restriction enzyme |
TRestrictionEditor | The restriction editor dialog class |
TRestrictionEnzyme | Stores a restriction enzyme |
TSantaLucia | The class implementing a "Santa Lucia" free energy set |
tseqres | Helper class for TPDB, holds the TVector objects for each parsed PDB chain |
TSequencingAssistantDialog | |
TSequencingPrimerDialog | The dialog for settings when searching for sequencing primers |
TSilmutDialog | Silent mutation dialog |
TSilmutItem | Helper class for TSilmutDialog |
TsiRNA | |
TSpeakDialog | |
TSQLresult | This class stores the results from SQL queries |
TStorage | This is the famous storage class. It manages all MySQL and sqlite traffic |
TTreeItem | Item in TVectorTree |
TUndo | This class stores TVector objects for the undo function |
TUReadSeq | This is a wrapper class for ureadseq, which can read many sequence formats |
TURLtext | A text control highlighting URLs |
TVector | This class stores all sequence information, both DNA and amino acids |
TVectorEditor | The sequence edit dialog |
TVectorItem | This class stores a vector item |
TVectorTree | The vector items tree class |
TVirtualGel | The virtual gel module |
TXMLfile | This class is a wrapper around the tinyxml software, specialized for GenBankXML format |
UserMatSeries | Part of the ClustalW package |