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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
 Parent Directory        
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tests/        
Annotation.pm  1.2  14 years  parrello  Converted tabs to spaces. Added parentheses to an assignment in the "new" method...
ApplyTransactions.pm  1.4  14 years  parrello  Changed to index the subsystems before applying transactions.
Assignments.pm  1.3  14 years  overbeek  fixes to automated assignments
BadCall.pm  1.1  14 years  parrello  Added as a place in which to put methods related to analyzing gene calls.
BasicLocation.pm  1.4  14 years  parrello  Fixed a bug in the Peel method for backward locations.
Blast.pm  1.2  15 years  olson  Force blastall and formatdb to be run using a full path to $FIG_Config::ext_bin....
Clearinghouse.pm  1.3  14 years  parrello  Changed attributes to capital-case in order to prevent the avalanche of compile-...
Clearinghouse.py  1.9  14 years  olson  Feh. host specifier for DBI is different in mysql and postgres.
Cluster.pm  1.10  14 years  olson  More cluster fixes.
ClusterWorker.pm  1.1  14 years  olson  Split the Cluster::Worker package out to its own file so it can be used on hosts...
Construct.pm  1.1  15 years  olson  add higher-level construct support
CountTransactions.pm  1.1  14 years  parrello  Converted the transaction processor to an object-oriented module in order to sim...
DBKernel.pm  1.17  14 years  overbeek  RAE: adding a drop_index method
DBrtns.pm  1.22  14 years  overbeek  NMPDR updates
DocUtils.pm  1.2  14 years  parrello  *** empty log message ***
FIG.pm  1.392  14 years  efrank   move cv files from Global to Global/CV
FIG.py  1.12  14 years  overbeek  Make cgi_url return a proper relative path if possible.
FIG2.py  1.1  15 years  olson  First cut at python FIG module that uses the CallPerl direct call interface.
FIGAttributes.pm  1.2  14 years  parrello  Changed attributes to capital-case in order to prevent the avalanche of compile-...
FIGGenDB.pm  1.5  14 years  redwards  Fixed lost username in protein.cgi and removed Bound/Find uncalled gene from FIG...
FIGRules.pm  1.1  15 years  olson  Move this here from Sprout.
FIGUtilities.pm  1.1  14 years  olson  some standalone (don't need a FIG object) utility routines.
FIG_CGI.pm  1.2  14 years  olson  remove debug warns
FIGjs.pm  1.10  14 years  golsen  Do some cleanup, and covert to relative URL for the javascript libraray.
FIGnet.pm  1.1.1.1  16 years  efrank   import
FIGrpc.pm  1.2  15 years  olson  Don't need to create a new fig at the toplevel; it was breaking import
FIGtree.pm  1.2  14 years  golsen  Major update of FIGtree package
FigGFF.pm  1.19  14 years  parrello  Converted tabs to spaces. Removed a redundant "my" that was causing a compiler w...
FudgeTransactions.pm  1.1  14 years  parrello  Cleaned up the transaction-processing stuff.
FullLocation.pm  1.9  14 years  parrello  Fixed the Search method to handle cases where it must search more than 9000 base...
GenoGraphics.pm  1.12  14 years  golsen  Heavy workover of generate_html to support: Pop-up tool tips when there is n...
GenomeIDMap.pm  1.3  14 years  overbeek  NMPDR updates
HTML.pm  1.71  14 years  parrello  Fixed a bug in "show_page". The "last" directive had been coded as "$last".
HTML.py  1.5  14 years  olson  anther dumb typo
HtmlPageParser.pm  1.1  14 years  olson  HTML parsing code for diagram generator.
InterfaceRoutines.pm  1.10  14 years  overbeek  show curator of subsystem on protein page
JobScheduler.pm  1.5  14 years  redwards  Allow deleting jobs from seed_ctl.cgi
KGML.pm  1.1  14 years  dejongh  CGIs, Perl modules, and help page to support KEGG integration into subsystems pa...
KGMLData.pm  1.1  14 years  dejongh  CGIs, Perl modules, and help page to support KEGG integration into subsystems pa...
Makefile  1.7  15 years  olson  Fix makefiles for change in releasetools.
MergeTransactions.pm  1.1  14 years  parrello  Cleaned up the transaction-processing stuff.
Overlap.pm  1.2  14 years  parrello  Modified CheckOverlap to allow full locations as input.
P2P.pm  1.30  14 years  olson  Move P2PQueue and JobQueue out of FIG/Data into FIG/var.
P2Pupdate.pm  1.55  14 years  olson  Make annotations_made_fast return new Annotation objects instead of arrays of da...
PageBuilder.pm  1.2  14 years  overbeek  finally
RC.pm  1.1.1.1  16 years  efrank   import
README  1.1.1.1  16 years  efrank   import
SFXlate.pm  1.47  14 years  parrello  Fixed a case error in the specification of the EC field.
SameFunc.pm  1.8  14 years  parrello  Changed to remove deprecated use of implicit split to @_.
SeedDas.pm  1.19  14 years  parrello  Converted tabs to spaces. Fixed a compiler warning.
Sim.pm  1.6  14 years  olson  Add methods: $sim = Sim->new_from_line($line): create a new sim object from a t...
SproutFIG.pm  1.9  14 years  olson  Make SproutFIG immune to errors when Sprout code is not present. It will throw a...
SproutSearch.pm  1.10  14 years  overbeek  NMPDR seed fixes
Subsystem.pm  1.74  14 years  overbeek  Broad minor fixes to make the SEED use relative paths throughout. (The motivati...
Tracer.pm  1.28  14 years  parrello  Changed to delete CRs instead of escaping them.
TransactionProcessor.pm  1.4  14 years  parrello  Added a method for creating statistic categories.
UnvSubsys.pm  1.13  14 years  olson  add missing argument to active_genomes
UserDB.pm  1.1  15 years  olson  Simple user database. Initializes state from assignments and annotations existin...
UserData.pm  1.1  14 years  parrello  Added with documentation.
__init__.py  1.1  15 years  olson  New file needed to make this a python module.
fastDNAml.pm  1.1  15 years  overbeek  add tree manipulation utilities
gjoalignment.pm  1.1  14 years  golsen  Add a module with some routines for adding sequences to alignments.
gjolib.pm  1.1.1.1  16 years  efrank   import
gjoseqlib.pm  1.1.1.1  16 years  efrank   import
raedraw.pm  1.9  14 years  redwards  changing raedraw and raelib
raelib.pm  1.27  14 years  redwards  Initial release of cookies code, including myseed
set_utilities.pm  1.1.1.1  16 years  efrank   import
tree_utilities.pm  1.4  15 years  overbeek  minor fixes to subsys.cgi and tree_utilities.pm

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