Patch Notes

This page documents all known issues, bug fixes, issues and implementation changes that have been addressed.

Contents:

• Known issues
• Latest patch fixes
• Patch history

Known issues

Below lists known issues or bugs that need to be address.

• Flag options in OraclePainter preferences do not work as intended.

Latest patch fixes

Below lists the latest fixes, updates or implementation changes. Note that fixes or changes may not necessarily be committed immediately.

Patch history

v1.00

• Example networks updated
  • Added human literature network
  • Updated columns for each network
  • Tooltips added for each network
• New model for defining features. Feature now referred to as Property
• New PTMOracle file format
  • Properties can now be defined for edges!
• New model for IO
  • XML parser changed to DOM
  • Added summary of properties to be imported
  • Protein data in a tab-separated files (TSV) can now be imported
  • Multiple regex-keyword mappings of properties are now handled by user upon import
• New GUI for panels. More effective use of tunables and tasks
  • Import, Export and preferences panels are now tunables
  • File choosers are now tunables and open from the directory they ended with
  • Updated tooltips for actions
  • Panel designs updated
  • All 'high level' actions are now tasks
• New database schema
  • Added new table for mapping properties to networks
  • Added new table for holding edge properties
  • Added mergeable flag column to property types
  • Added color column to keywords. This is only used by PTMs.
  • Protein sequences are now handled as normal properties
  • Extended regex-keyword mappings to other property types
  • Properties (excluding Sequence) which do not relate to a specific keyword will no longer present in any Oracle component. They remain hidden from the user until re-introduced
  • Updated regex-keyword mappings for case-sensitive descriptions, eg. Phosphorylation vs phosphorylation
  • Fixed collation of properties from different sources. Status and comments are appended if there are
  • Allowed more customisation of properties and keywords. User controls properties recognised by Oracle
  • Allowed properties to be shared across networks
• New OraclePainter
  • New OraclePainter file format.
  • Added option to switch between painters. Only colour scheme on visible painter will be applied
  • Added option to colour all nodes or only selected nodes
  • Added option to change the proportion of the graphic
  • Added feature allowing users to reset the colours of ModPainter to the default setting
  • MultiPainter updated to use pie-chart representation
  • Updated implementation for import, export and legend
  • Legend is now outputted in alphabetical order
  • Fixed issue where the colour scheme does not stay applied when Cytoscape's visual style changes.
  • Resized the OraclePainter panel to be more visually appealing
• New OracleResults
  • Added column for additional comments / information
  • Added option to show a legend panel to help distinguish between different properties
  • Added option to change delimiters
  • Added option to change search column. Only default Cytoscape columns can be searched (eg. SUID and shared name)
  • Improved error handling. Only displays 1 error message for multiple invalid inputs.
• New OracleTools
  • Improved GUIs. All OracleTools panels are now tunables.
  • Updated OracleTool labels and tooltips. Now referenced by name rather than by function.
  • New Calculator
    • All node and edge properties can be counted
    • Added brief description onto the GUI panel
    • Added error for invalid parameters
  • New MotifFinder
    • Added option to import identified motifs into Oracle
    • Added brief description onto the GUI panel
    • Added error for invalid parameters
  • New RegionFinder
    • Added option to search for PTMs on specific residues
    • Added brief description onto the GUI panel
    • Added error for invalid parameters
  • New PairFinder
    • Added brief description onto the GUI panel
    • Added error for invalid parameters

v0.10

• Changed stringAccs columns in example networks to ptmcodeAccs
• Fixed string replacement bug that occurred during sequence validation
• Remove column now added to global info table
• Painter colours now stay the same if color chooser has been cancelled
• Added color legend for sequence output on local info panel
• Renamed label on global info to 'Num. of modified residues'
• Importing painter file no longer removes a component
• Revamped GUI for info panel with tunables
• Revamped GUI for query tools with tunables