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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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Tracer.pm  1.110  11 years  parrello  Clarified a comment.
FIG.pm  1.724  11 years  overbeek  get rid of warning and update conditionally_assign
SFXlate.pm  1.108  11 years  parrello  Fixed search to be able to find an organism by name.
AnnoClearinghouse.pm  1.36  11 years  wilke  changed names for db tables
FIGV.pm  1.62  11 years  paczian  RAST genomes now always compute the pegs for subsystems on the fly (ignoring the...
FIGRules.pm  1.41  11 years  disz  New wording in structured english
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
CompareMR.pm  1.5  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
FS_RAST.pm  1.18  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
DocUtils.pm  1.17  11 years  parrello  Fixed a bug in the config file modification method and added tracing.
Observation.pm  1.73  11 years  arodri7  fixed functional coupling data retrieval
Subsystem.pm  1.136  11 years  olson  Add support for $fig->change_funcrole()
GenomeMetaDB.pm  1.2  11 years  olson  touch the meta file when a change is written to the db.
WebColors.pm  1.7  11 years  paczian  added palette 'excel' with the default excel color palette minus black, white an...
FFs.pm  1.25  11 years  arodri7  corrected errors for merge_figfams
HTML.pm  1.129  11 years  parrello  Fixed URL references.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
gjoalignment.pm  1.15  11 years  golsen  Fix FIG dependencies so that it is FIG-aware, but not FIG-dependent.
FF.pm  1.22  11 years  olson  Fix bug where return of should_be_member is lost.
TestUtils.pm  1.6  11 years  parrello  Improved display of undefined and empty strings.
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
Diagram.pm  1.15  11 years  paczian  scaled images will now have better quality scaled images will now always have gr...
Stats.pm  1.6  11 years  parrello  Added a method to facilitate periodic tracing.
WikiTools.pm  1.5  11 years  parrello  Fixed table generator to remove line-feeds that would break the table.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGM.pm  1.1  11 years  olson  Add annotation support to FIGV. Add FIGM.
GenomeMeta.pm  1.15  11 years  olson  oops, these need updated.
Makefile  1.10  11 years  golsen  Fix to path for pod2html
FigFams.pm  1.46  11 years  arodri7  Figfams update
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
NewGenome.pm  1.75  11 years  gdpusch  Fixed bug in ORF::seq(); minor changes in debugging output. -- /gdp
PinnedRegions.pm  1.12  12 years  parrello  Fixed a compiler warning.
FigFam.pm  1.75  12 years  arodri7  updated and corrected sub new
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
GenoGraphics.pm  1.18  12 years  parrello  Not sure. The DIFF says there was no change.
DBKernel.pm  1.52  12 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
tree_utilities.pm  1.17  12 years  disz  added subsyste display on hover
model.pm  1.18  12 years  dejongh  Fixes for excluding . and .. when reading directories for paths
selenoprotein_ref_seq.pm  1.4  12 years  golsen  Add to the list of reference proteins.
gjonewicklib.pm  1.11  12 years  golsen  Allow matched [ ... ] inside Newick tree comment. This violates the standard, b...
raelib.pm  1.44  12 years  redwards  adding a randomizer function
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
find_special_proteins.pm  1.9  12 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
BasicLocation.pm  1.16  12 years  parrello  Added some new methods for the backfill gaps code in RAST.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
Overlap.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
Markups.pm  1.2  12 years  parrello  Changed POD format for better compatability with Wiki.
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
UserData.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
MergeTransactions.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
ApplyTransactions.pm  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
AliasAnalysis.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
FileLocking.pm  1.2  12 years  olson  add shared locking
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
KGML.pm  1.4  13 years  olson  Hope college modifications.
representative_sequences.pm  1.9  13 years  overbeek  add make_trimmed_alignment_from_ids
PHOB.pm  1.14  13 years  overbeek  add utilities for computing alignments
ContigMD5.pm  1.3  13 years  olson  clone the digest so that checksum() may be called multiple times
FIGgjo.pm  1.3  13 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
clustaltree.pm  1.1  13 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
gjoalign2html.pm  1.2  13 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
gjocolorlib.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
display_related_genomes.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
proml.pm  1.8  13 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
gjoparseblast.pm  1.2  14 years  golsen  Bug fix in parse error message (blast outputs invalid query and database sizes f...
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
Classes.pm  1.1  14 years  mkubal  added Organism class
COPYING.TXT  1.1  14 years  olson  add license file
gjolib.pm  1.2  14 years  olson  Added license words.
__init__.py  1.2  14 years  olson  Added license words.
fastDNAml.pm  1.2  14 years  olson  Added license words.
FIGAttributes.pm  1.3  14 years  olson  Added license words.
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
FIGrpc.pm  1.3  14 years  olson  Added license words.
P2P.pm  1.31  14 years  olson  Added license words.
FIGGenDB.pm  1.6  14 years  olson  Added license words.
SproutSearch.pm  1.11  14 years  olson  Added license words.
ClusterWorker.pm  1.2  14 years  olson  Added license words.
RC.pm  1.2  14 years  olson  Added license words.
Construct.pm  1.2  14 years  olson  Added license words.
UserDB.pm  1.2  14 years  olson  Added license words.
FIGnet.pm  1.2  14 years  olson  Added license words.
HtmlPageParser.pm  1.2  14 years  olson  Added license words.
Cluster.pm  1.11  14 years  olson  Added license words.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIG.py  1.13  14 years  olson  Added license words.
FIGtree.pm  1.3  14 years  olson  Added license words.
FIG2.py  1.2  14 years  olson  Added license words.
HTML.py  1.6  14 years  olson  Added license words.
SproutFIG.pm  1.10  14 years  olson  Added license words.
set_utilities.pm  1.2  14 years  olson  Added license words.
README  1.1.1.1  16 years  efrank   import

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