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15 Commits (f39d0008bc5558c06786d2c3b8cbbaa537ca49b2)

Author SHA1 Message Date
Mark DePristo f2a05af356 Fixed layout problem with advanced arguments 2011-08-18 21:59:44 -04:00
Mark DePristo cca0930517 Better formatting for GATKDocs 2011-08-18 21:24:23 -04:00
Mark DePristo ce009bd4a4 Works without related data 2011-08-18 14:05:09 -04:00
Mark DePristo b984b7aa9b Missing default values are now NA 2011-08-10 22:22:57 -04:00
Mauricio Carneiro 321afac4e8 Updates to the help layout. 
*New style.css, new template for the walker auto-generated html. Short description is no longer repeated in the long description of the walker.

 *Updated DiffObjectsWalker and ContigStatsWalker as "reference" documented walkers.
 2011-07-26 19:29:25 -04:00
Mark DePristo 2039ce6102 Default values now displayed in arguments 
DiffEngine fixed so that newInstance() would work.  Pretty quickly encountered a situation where newInstance() failed.  Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
 2011-07-24 22:56:55 -04:00
Mark DePristo 83996f7951 Enumerated types are working. 2011-07-24 18:14:21 -04:00
Mark DePristo 3c34e9fa65 Cleanup emuns and tables 2011-07-24 17:45:58 -04:00
Mark DePristo c620d96c96 Inline enum documentation is working 2011-07-24 17:22:14 -04:00
Mark DePristo 793e7d3d1d Improved header and argument details 
Argument detail structure cleaned up. Only relevant pieces of information are shown now, and in a cleaner layout.
Misc. cleanup in the code.
 2011-07-24 16:36:25 -04:00
Mark DePristo c6af4efcdc Implemented see also and version header 2011-07-24 16:10:17 -04:00
Mark DePristo 5e0fe2d0f9 Support for style.css via refactored common.html included in all files 2011-07-24 15:42:39 -04:00
Mark DePristo d0ab6bf7a9 Now links to sub and superclass documentation, where possible. 2011-07-24 09:56:17 -04:00
Mark DePristo 7420ed098e Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another 
Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
 2011-07-23 22:07:30 -04:00
Mark DePristo f0be7348be Generalized handler to allow it to be used with any arbitrary class structure. 
DocumentedGATKFeature now includes a field for the group name.
Build.xml works with public / private now.
 2011-07-22 14:07:40 -04:00