Detailed Roadmap

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Detailed Roadmap to version 1.0:

Transition to 1.0 requires:

(Timescale: around May)


== Bioclipse == (Ola)

  • adapt TextEditor for editing and saving subParts individually [Postponed to >1.0]
  • Change BioResource to Abstract and make folders FolderResources with FileResource as PersistedResource [Postponed to >1.0]
  • Remove the IFileBuffers and use plain old java.io.File instead [Postponed to >1.0]
  • Intro page [OPTIONAL]
  • Reference web service action [DONE]
  • Decouple TextEditor from file system [DONE]
  • Decouple XMLEditor from file system [DONE]
  • Action "Open" and "Open with" in context menu of BioResourceView [DONE]
  • use byte[] instead of String as localResource to fix XML problems [DONE]
  • Open XML/TextEditor and not JCPMPE if 2D [DONE]
  • Get export to work for Linux [DONE]
  • Get export to work for Windows [DONE]
  • Get export to work for Mac[DONE, but will not run]
  • Create new file, folder (using NewWizards) [DONE]
  • Implement 'lazy parsing' of dir structure of BioResourceView so that dir is read on first expand [DONE]
  • Unload() should remove from 2DStructureView also (Ola) [DONE]
  • Duplicate properties on unload [DONE]
  • Listener for model changes to BioResources (Tobias) [DONE]
  • Global toolbar cleanup (Ola) [DONE]
  • Fix ApplicationRunner and Preferences (Ola) [DONE]
  • Fix Filters for unwanted filenames and endings e.g. '~' (Ola) [DONE]
  • Delete folder fails if containing not shown files (like .SVN etc)(Ola) [DONE]
  • Unload should close open editors for selected BioResource [DONE]
  • ExternalApplication should catch output and echoes to Bioclipse Console [DONE]
  • Open with... should close any open editors for same BioResource before new open [DONE]
  • Editor open of correct types does not work properly (Ola) [DONE, but pending CDK RFE]
  • Remove BioSearch for later usage (Ola) [DONE]
  • Fix menu look/move menus (Ola) [DONE]
  • Update and fix help system (Ola)
  • Use an Installer (nsis at nsis.sf.net looks promising for windows installer, linux might have to settle for archive) (Ola)
  • Find and install a profiler capable of handling eclipse rcp applications (Tobias)

bc_biojava

(Ola, Egon)

  • Reference Biojava actions [Postponed to >1.0]
  • Use RichSequences instead of Sequences [Postponed to >1.0]
  • Fix sequence I/O for multiple formats [DONE, but needs testing]
  • Sequence visualization in table (Ola) [DONE]
  • Get SequenceViewer to work again (Egonw) [DONE]
  • Allow for Biojava-supported formats (Ola) [DONE]

com.tools.logging

No current activities

== bc_cdk == (CUBIC, Ola)

  • COT icons add/make transparent (Egon) [Doesn´t work]
  • Scanner that tests for data features [IN PROGRESS]
  • Finish the "New molecules" wizards (requires the "Save As..." action to be fixed (tohel) [IN PROGRESS]
  • Have IChemObject properties be shown [DONE]
  • A BioPolymer hierarchy viewer [DONE]
  • get CDK Protein to work again with Jmol View (Egon, Martin) [DONE]
  • ChemObjectTreeView is not recursing anymore (Egon) [DONE]
  • Scanner that is able to do a fast scan of files to determine format (Egon) [DONE]
  • Update getter/setter in CDKResource to not cache but work directly on ChemFile [DONE]
  • convert to/Save as ... action (Tohel) more or less [DONE]
  • "Fix molecule from smiles wizard" [DONE]
  • 2DStructureView should be empty if only 3D-coords is available [DONE]
  • SDGAction to generate 2D-coordinates if missing + ask on parse if no 2D-coordinates [DONE]
  • test and fix reading of all PDB files in Jmol SVN (see PdbTesting, Egon) [DONE]

== bc_cml == (PMR, CUBIC)

  • Add CMLEditor with syntax highlighting and code completion and possibly show line numbers (Ola) [Postponed to >1.0]
  • Allow for CML-validation of CDKResources and SpectrumResources that originate from CML-files (Ola) [Postponed to >1.0]
  • to be fixed and working with jumbo5.2 [DONE]
  • move CMLResource to bc_cml [DONE]
  • finish/repair cml validation action (Tobias, Miguel) [DONE]
  • fix namespace problem on construction of CMLResource [DONE]

== bc_jmol == (Ola, CUBIC)

  • add all actions from jmol (Ola) [DONE]
  • synced with latest Jmol from SVN [DONE]
  • implement a proper JmolStatusListener [DONE]
  • Fix recognition of protein atoms by Jmol [DONE]
  • Fix 'Run Jmol Script' action to be in editor [DONE]
  • Adapt to display BioPolymers-specific commands (Egon) [DONE]
  • Add console for scripting commands (Ola) [DONE]
  • Echo "No 3D-coordinates" instead of empty frame (Ola) [DONE]
  • Fix Jmol repaint when Jmol window is covered and then displayed [DONE]
  • Add action to change background to black/white (Ola) [DONE]
  • Add surface actions (Ola)
  • Fix 'New Jmol Script file' wizard (Ola)
  • if editor is inactive, clicking onto drawingPanel should activate the editor and not edit anything (Tobias)

== bc_cmlrss == (Egon)

  • extracts CML content and present as CMLResource (worked around by removing prefixes) [DONE]
  • add more meta data [DONE]
  • read Atom 0.3 feeds [DONE]
  • read Atom 1.0 feeds [DONE]
  • read RSS 1.0 feeds [DONE]
  • read RSS 2.0 feeds [DONE]
  • add GUI for adding feeds [Postponed to >1.0]
  • extraction of CML automatically when a feed is read [DONE]
  • adding option to edit the OPML file using the XML editor [DONE]
  • add HTML view for feed entry content [DONE]
  • add action to reload feed(s) (e.g. happens upon saving of OPML file in Text/XML editor) [DONE]
  • NewWizard: New OPMLResource (Egon, Ola) [DONE]
  • merge r728,729-733 into b1/ branch: bit of refactoring, Atom 1.0 support, Logger, NPE fixes [DONE]

== bc_spectrum post 1.0 == (CUBIC)

  • create new editor being build by a 2dmolViewer and a peakView for assignment... (Stefan, Tobias)
  • this editor should be connected to one cml file containing a mol and several spectra, where the mol part is fixed and the spectrum could be changed by selecting another spectrum from inside this cml file (Stefan, Tobias)
  • there should be methods for adding new spectra/molecule to an existing "multiItem-cml" file and a way of creating a new empty one to be filled with spectra and a mol (Tobias, Stefan)
  • propably include a "new multiItem-cml file" wizard for selecting a mol and several spectra from the file sys and create a new multiItem-cml file... (Tobias Stefan)
  • include Metadata to Properties View (Tobias)
  • "peak-molecule assignment" (into version 1.0?) including the new peak assignment editor (Stefan. Tobias)

== bc_jchempaint == (CUBIC)

  • transport context menu to swt (Tobias) [Doesn´t work]
  • rename to bc_jchempaint and remove old bc_jcp [DONE]
  • transparency of icons (redesign them) [DONE]
  • jcpEditor title should show molecule title (See TextEditor) [DONE]
  • sync of editor in multiPageEditor (Stefan) [DONE]
  • Remove all File dependencies of editor [DONE]
  • Editor should not open but throw an exception if molecule does not contain 2D-coordinates or is a valid 2D-molecule [DONE]
  • if editor is inactiv, clicking onto drawingPanel should activate the editor and not edit anything [DONE]
  • hook in the life cycle to global keys (save, undoRedo(use global eclipse way)) [DONE]
  • Save as action (Tobias) [DONE] -> but not working for many formats at the moment...
  • Fix highlighting when collections of IAtoms and/or IBonds are selected in ChemObjectTreeView (also in 2DStructureView) [DONE]
  • Cut and paste using the eclipse way as global actions [DONE]
  • Fix scaling of molecule to fit window on load, add scrollbars, center on load (shk3) [DONE]
  • Fix JCP SRC tab to open in dedicated editors e.g. CMLEditor. Now only XMLEditor is used (Ola will assist) [DONE]
  • Force english localization [DONE]
  • If user edits in Source-tab, add msgbox if unallowed editions are made that will be lost on save (Tobias) [DONE]
  • Integrate rendering prefs with RCP preference system (Egon)
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