Outstanding Issues

User level problems

No undo
- All changes destructive and irreversible
- Nearly impossible to retrofit existing structure to support undo
Confusing selection model
- Difficult to tell what's selected / active - does it affect my current analysis?
- No ability to have different components operate on different selections
No repeatability of experiments
No workflow support
Confusing connection between components - what affects what? Where did my results go?
Large Memory footprint
- Just the framework and component initialization, over 200 megs
- Large overhead for data
- Every datapoint stored as multiple objects
- Means probably unable to load, let alone analyze mid to large sized datasets
Performance problems
- All components receive every event whether used or not, many components recompute something upon reception of those events - leads to poor interface responsiveness
- Complex object structures cause unnecessary and large processing overhead for analyses
- Roughly 10x speedup was gained by Hierarchical clustering in routing around data structures
Lack of adequate data import export functionality
- Most components should export to tab delimited text file at a minimum
No built in standards or support for progress monitoring or cancellation of long running processes

Non-standard event system
- Runtime extension model causes non-standard CGLib exceptions
- Mid level Java developers not familiar with annotations
Overwhelming and only semi-functional data object structure
- Many objects extending Java Collections classes, but not fully implementing their interface contracts - leads to subtle and confusing errors
Selection model confusing
- Many objects maintaining their own internal selected data structures