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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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README  1.1.1.1  16 years  efrank   import
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.
clustaltree.pm  1.1  12 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
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.
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
selenoprotein_ref_seq.pm  1.4  11 years  golsen  Add to the list of reference proteins.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
Stats.pm  1.6  11 years  parrello  Added a method to facilitate periodic tracing.
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
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.
BasicLocation.pm  1.16  12 years  parrello  Added some new methods for the backfill gaps code in RAST.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
gjonewicklib.pm  1.11  11 years  golsen  Allow matched [ ... ] inside Newick tree comment. This violates the standard, b...
gjoparseblast.pm  1.2  13 years  golsen  Bug fix in parse error message (blast outputs invalid query and database sizes f...
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.
AliasAnalysis.pm  1.3  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.
ApplyTransactions.pm  1.7  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.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
Tracer.pm  1.110  11 years  parrello  Clarified a comment.
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
FigFams.pm  1.46  11 years  arodri7  Figfams update
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.
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
Makefile  1.10  11 years  golsen  Fix to path for pod2html
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
HTML.pm  1.129  11 years  parrello  Fixed URL references.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
DocUtils.pm  1.17  11 years  parrello  Fixed a bug in the config file modification method and added tracing.
PinnedRegions.pm  1.12  11 years  parrello  Fixed a compiler warning.
NewGenome.pm  1.75  11 years  gdpusch  Fixed bug in ORF::seq(); minor changes in debugging output. -- /gdp
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
SFXlate.pm  1.108  11 years  parrello  Fixed search to be able to find an organism by name.
WikiTools.pm  1.5  11 years  parrello  Fixed table generator to remove line-feeds that would break the table.
model.pm  1.18  11 years  dejongh  Fixes for excluding . and .. when reading directories for paths
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  12 years  olson  Hope college modifications.
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
TestUtils.pm  1.6  11 years  parrello  Improved display of undefined and empty strings.
DBKernel.pm  1.52  11 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
gjoalign2html.pm  1.2  12 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
FIGRules.pm  1.41  11 years  disz  New wording in structured english
GenoGraphics.pm  1.18  11 years  parrello  Not sure. The DIFF says there was no change.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
find_special_proteins.pm  1.9  12 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjocolorlib.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
display_related_genomes.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
COPYING.TXT  1.1  14 years  olson  add license file
representative_sequences.pm  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
FileLocking.pm  1.2  12 years  olson  add shared locking
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
PHOB.pm  1.14  12 years  overbeek  add utilities for computing alignments
Classes.pm  1.1  14 years  mkubal  added Organism class
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
UnvSubsys.pm  1.20  11 years  paczian  added missing "use HTML;"
WebColors.pm  1.7  11 years  paczian  added palette 'excel' with the default excel color palette minus black, white an...
tree_utilities.pm  1.17  11 years  disz  added subsyste display on hover
raelib.pm  1.44  11 years  redwards  adding a randomizer function
AnnoClearinghouse.pm  1.36  11 years  wilke  changed names for db tables
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
FFs.pm  1.25  11 years  arodri7  corrected errors for merge_figfams
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
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
Observation.pm  1.73  11 years  arodri7  fixed functional coupling data retrieval
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...
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FIG.pm  1.724  11 years  overbeek  get rid of warning and update conditionally_assign
FIGV.pm  1.63  11 years  paczian  getting the subsystem bindings from bindings file again, since annotators can no...
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
Subsystem.pm  1.137  11 years  bartels  inserted code to save rules and definitions for check variants
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
GenomeMeta.pm  1.15  11 years  olson  oops, these need updated.
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
Diagram.pm  1.15  11 years  paczian  scaled images will now have better quality scaled images will now always have gr...
GenomeMetaDB.pm  1.2  11 years  olson  touch the meta file when a change is written to the db.
FigFam.pm  1.75  11 years  arodri7  updated and corrected sub new

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