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CHANGELOG.txt
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121 lines (108 loc) · 4.27 KB
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** TODO **
+ General
- Write tutorials (see TeMV developer documentation).
- Write documention (see TeMV developer documentation).
- Write more unit tests.
- Write an article.
- Update cvs/subversion.
+ Platform
- Workflow graph optimization.
- Move parameters tests to the discover module section.
- Save data container.
- Synchronization, Multithreading.
- Networking.
- Algorithm must be used without Workflow.
- Write tests : BioAssay Filter
- Write tests : Experiement design
- RomdeData must be serializable.
+ OM
- Finish wrappers for Genepix GPR and GAL.
- Write object to handle GAL data.
- New object : Expression Matrix.
- Finish writing javascript annotation reader for Genepix data import.
- New object : Experiment description. [In progress]
- New object : Translator (e.g. GeneID / Locuslink)
- BioAssay object setLocation with Genepix block numerotation
- Write IO for BiologicalLists.
- JAVA 5.0 : BioAssayBase can remove rows.
- JAVA 5.0 : BioAssayBaseImpl use ArrayList<T> than array of ints, doubles or strings.
- JAVA 5.0 : Optimize BioAssayReader and BioAssayWriter.
- JAVA 5.0 : Next BioAssayBase version : use Collections.unmodifiableSet(Set s)
- Create a thread safe version of bioAssayBase
- Find memory leaks, find automaticaly bugs
- Optimize Containts
- Optimize BioAssay writer.
- New BioAssay transformation : concat 2 bioAssay object (columns or lines)
- New BioAssay transformation : remove a list of column
+ Util
- Parameters can be cloned.
- R integration.
- Interface TeMV algorithm with algorithms.
+ Laucher
- Change the name of the application under Mac OS X (standalone), actualy : fr.ens.transcriptome.launcher.Launcher.
- mosquitos
- Real testing
- Clean GUI code.
- New Graph : Array visualisation.
- new input results : Database.
- new input arra list : Database.
- new result output : Report in database.
- new array list output : Database.
- BUG : Safari problem.
- make a sample plugin : test windows batch.
- make a logo and an icon.
- Windows sample plugin compilation script must works
** DONE **
+ General
- New name: Nividic
- Backup sources.
- Change Romde licence : LGPL. Mosquitos license still in GPL.
+ Platform
- Workflow stop/start/pause/resume must use Listeners.
- Automatic instanciation of the algorithm while add to a workflow.
- Read configuration files for the registery.
- New file structure organisation (bin,lib,conf,plugins).
- Plugins operational
- log file in /log if user can create it.
- Use threads for Workflows.
+ Romdeom
- Test data new BioAssayImpl for loading data directly from Genepix.
- rewrite BioAssayLoadDataWhenNeed.
- Rewrite ATF IO, more generic like Genespring file reader.
- Interface BioAssay : add field description, M and A for MA plots.
- Translate javadoc in french (BioAssay and BioAssayBase Interfaces).
- Manage list of gene operations(intersections, exclusion, uniq) load/save.
- BioAssay filtering interface and implementation.
- Write tests : Biological list.
- Spot object.
- GPR reader : use initial capacity with ArrayList
- Use RomdeRuntimeException when needed.
- Replace new RomdeException("foo is null") with new RomdeRuntimeException(NullPointerException,"toto").
- Replace new RomdeException("foo : invalid argument") with new RomdeRuntimeException(IllegalArgumentException).
- New Object : BioAssayIterator
- Factory must have statics methods.
+ Util
+ RomdeLaucher
- True CLI test with mosquitos.
- make an executable jar without shell script
+ Mosquitos
- New Graph : Distribution graph.
- New test: Spot size.
- New test: Empty spot.
- New test: Heterogenous spot.
- New result output : HTML report.
- GUI : Save result array list button.
- GUI : Save report button.
- new array list output : GAL File.
- Change the background of the graph : lighter color
- Show the test suite name in test suite tab and report tab
- Show the units of the thresholds
- Show the threshold on the graphs
- windows testing
- Remove freezing actions from applet mode
- New test: Valid spotting.
- Polish Report tab
- GUI : Print report button.
- clear testsuite and result tab when start a workflow.
- make a sample plugin (jar + source in docs)
- add a progress bar.