Table 1 Summary of user-accessible classes and functions
From: Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization
Class name | Subject | Example of functions |
|---|---|---|
AppService | Miscellaneous application service (6 functions) | - Export data to clipboard - Access to Workspace window - Show instant message |
GeneService | Sequence manipulation, analysis, optimization (62 functions) | - Parse, translate, reverse, etc. - Calculate CAI, Nc, GC contents - Search query/repeated sequences - Do codon/mRNA optimization - Remove undesired sequences silently |
GeneConstruct | Access Gene construct and components (12 functions) | - Manipulate gene construct components - Get current gene construct index - Access to a real time analysis table |
mRNApredict | Prediction of mRNA secondary structure (18 functions) | - Predict mRNA structure and binding energy - Visualize predicted structure - Read raw data of mRNA structure |
NeuralNet | Artificial neural network prediction module (6 functions) | - Open trained network map file - Set input variables - Predict outputs |
CustomUI | Custom GUI form and graphics engine (27 functions) | - Draw line, circle, rectangles, pie, arc, and text - Export raw data and image |
NetComService | Network and multi-threaded computing module (23 functions) | - Connect/disconnect service - Get information about server, client, jobs |
PropertyBag | Manipulation of Property Bag (11 functions) | - Clear and add property - Read/write parameter values |
ScriptService | Execution of user defined module (6 functions) | - Load/run user-defined script module - Assign parameter array - Retrieve results |