A set of useful tools leveraging JavaCycO

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@1 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
A set of tools leveraging JavaCycO

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@2 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Improved the createAffyProbeIDTranslationFile function.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@3 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Added functions to print stoichiometric matrix and reaction enzymes.  Edits to comments.  Print tab functions still unfinished.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@4 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Various updates and new functions.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@5 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
printFrameSlotsTab and printGeneInfo

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@6 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Backup

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@7 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Latest Updates

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@8 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
SBML Model
Circos format of gene info

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@9 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
SBML Model Support added

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@10 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Switched to new JavaCycO respository.
Moved SBML model code to new class, CycModeler.
Rewrote much of the SBML model code.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@11 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Switched to new JavaCycO respository.
Moved SBML model code to new class, CycModeler.
Rewrote much of the SBML model code.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@12 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Switched to new JavaCycO respository.
Moved SBML model code to new class, CycModeler.
Rewrote much of the SBML model code.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@13 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Switched to new JavaCycO respository.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@14 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Switched to new JavaCycO respository.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@15 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@16 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Multiple updates to existing methods.  New methods to compare iAF1260 model to ecocyc (very rough methods).

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@17 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Updates to genomeStructureAtLocation method, as well as other insignificant changes to test code.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@18 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
Moved cycModeler into a separate project file.

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@21 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6
A class for updating a pgdb

git-svn-id: https://subversion.vrac.iastate.edu/Subversion/jrwalsh/svn/jrwalsh/BioCycTool@24 2cdb7f3e-855d-47db-aa0b-9c7ce227a9e6