This is a complete rewrite of the framework, and is still in progress. See the Design page for a description of the new framework and the ToDo page for what still needs to be done.
BioCocoa 1.7 -- (found in Tags / 1.7)
This is the final release update of the classic BioCocoa code. This release contains the following new features:
- BCReader, the standalone BCReader classes for sequence file IO (original version Peter Schols)
- EntrezController, a controller plus view for browsing and fetching NCBI's Entrez Database
- BCSequenceView, a custom NSTextView for displaying biological sequences.
BioCocoa 1.6 -- (found in Tags / 1.6)
This folder contains:
- the ProjectBuilder project of the SequenceConverter utility application (BioCocoa util.pbproj), which can be opened in Xcode on Mac OS X or in the GNUstep ProjectCenter on Linux/Windows (see www.gnustep.org)
- the compiled utility application SequenceConverter, ready to run on Mac OS X 10.2 or higher
- the ProjectBuilder project of the BioCocoa framework (BioCocoa Framework), which can be opened in ProjectBuilder on Mac OS X or in the GNUstep ProjectCenter on Linux/Windows (see www.gnustep.org)
- the compiled BioCocoa framework (BioCocoa.framework), which can be opened in ProjectBuilder on Mac OS X or in the GNUstep ProjectCenter on Linux/Windows (see www.gnustep.org)
- the GNU GPL
If you are not a developer and you are only interested in the SequenceConverter utility application (to convert between sequence file formats), you can remove everything in this package except for the SequenceConverter application itself.
Changes since version 1.2:
- BC now reads SwissProt, NCBI, and PDB files
- To be consistent when reading all filetypes, 'taxon' and 'taxa' were changed to 'item' and 'items' respectively in BCReader. BCCreator still uses 'taxon' and 'taxa'.
- Added a 'fileType' key-value
Changes since version 1.1:
- BC now reads and writes the GCG-MSF format
- Added Unix and Windows line break methods for cross-platform compatibility
- BC now recognizes the Trees Nexus block and stores all Newick strings in the root dictionary
- BC returns all Nexus blocks in the root dictionary
- BC now stores the line break of the original source file in the root dictionary
For more information on how to use BioCocoa (version 1.x) in your own app, see the API docs at: http://bioinformatics.org/biococoa/docs/ and the header files in the framework.