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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