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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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Observation.pm  1.73  11 years  arodri7  fixed functional coupling data retrieval
FFs.pm  1.25  11 years  arodri7  corrected errors for merge_figfams
FigFams.pm  1.46  11 years  arodri7  Figfams update
FigFam.pm  1.75  11 years  arodri7  updated and corrected sub new
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
FIGMODEL.pm  1.2  11 years  chenry  Fixing bug in CpdLink function.
FileIOFunctions.pm  1.1  11 years  chenry  These modules are for interacting with the modeling database Chris Henry and Mat...
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
model.pm  1.19  11 years  dejongh  Support for model curation tools
tree_utilities.pm  1.17  11 years  disz  added subsyste display on hover
FIGV.pm  1.69  11 years  dsouza  peg hash from btree has contig and peg ids as keys -- filter them out in pegs_of...
README  1.1.1.1  16 years  efrank   import
DBKernel.pm  1.52  11 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
find_special_proteins.pm  1.9  12 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
NewGenome.pm  1.75  11 years  gdpusch  Fixed bug in ORF::seq(); minor changes in debugging output. -- /gdp
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
proml.pm  1.8  13 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
selenoprotein_ref_seq.pm  1.4  11 years  golsen  Add to the list of reference proteins.
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
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...
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
Makefile  1.10  11 years  golsen  Fix to path for pod2html
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
clustaltree.pm  1.1  12 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
gjoalign2html.pm  1.2  12 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
gjoalignment.pm  1.15  11 years  golsen  Fix FIG dependencies so that it is FIG-aware, but not FIG-dependent.
Classes.pm  1.1  14 years  mkubal  added Organism class
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
GenomeMeta.pm  1.15  11 years  olson  oops, these need updated.
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
gjolib.pm  1.2  14 years  olson  Added license words.
__init__.py  1.2  14 years  olson  Added license words.
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
fastDNAml.pm  1.2  14 years  olson  Added license words.
FIG.pm  1.730  11 years  olson  Add FIG.pm caching of all-subsystem data, and use that for subsystem-classificat...
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.
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
P2P.pm  1.31  14 years  olson  Added license words.
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
FIGGenDB.pm  1.6  14 years  olson  Added license words.
SproutSearch.pm  1.11  14 years  olson  Added license words.
FIGM.pm  1.2  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
Tracer.pm  1.114  11 years  olson  When tracing CGIs run at the command line, make the tracing code honor the TRACI...
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.
FF.pm  1.22  11 years  olson  Fix bug where return of should_be_member is lost.
KGML.pm  1.4  12 years  olson  Hope college modifications.
Cluster.pm  1.11  14 years  olson  Added license words.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
FIG.py  1.13  14 years  olson  Added license words.
FIGtree.pm  1.3  14 years  olson  Added license words.
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
FileLocking.pm  1.2  12 years  olson  add shared locking
COPYING.TXT  1.1  14 years  olson  add license file
FIG2.py  1.2  14 years  olson  Added license words.
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
GenomeMetaDB.pm  1.2  11 years  olson  touch the meta file when a change is written to the db.
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.
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
gjocolorlib.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
display_related_genomes.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
representative_sequences.pm  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
FS_RAST.pm  1.18  11 years  overbeek  fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic rec...
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
PHOB.pm  1.14  12 years  overbeek  add utilities for computing alignments
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
UnvSubsys.pm  1.20  11 years  paczian  added missing "use HTML;"
Diagram.pm  1.15  11 years  paczian  scaled images will now have better quality scaled images will now always have gr...
WebColors.pm  1.7  11 years  paczian  added palette 'excel' with the default excel color palette minus black, white an...
DocUtils.pm  1.17  11 years  parrello  Fixed a bug in the config file modification method and added tracing.
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
SFXlate.pm  1.110  11 years  parrello  Changed to fail gracefully if an invalid subsystem ID is passed in to get_subsys...
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.
Subsystem.pm  1.139  11 years  parrello  Fixed a bad URL.
BasicLocation.pm  1.16  12 years  parrello  Added some new methods for the backfill gaps code in RAST.
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.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
HTML.pm  1.129  11 years  parrello  Fixed URL references.
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
CompareMR.pm  1.6  11 years  parrello  Changed to avoid an unnecessary creation of the FIG object at load time.
GenoGraphics.pm  1.18  11 years  parrello  Not sure. The DIFF says there was no change.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TestUtils.pm  1.7  11 years  parrello  Quoted values in string comparisons to avoid an error when working with sim obje...
FIGRules.pm  1.42  11 years  parrello  Fixed bad subsystem call.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
Stats.pm  1.7  11 years  parrello  Changed to round floating-point stats to integer values.
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.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
PinnedRegions.pm  1.12  11 years  parrello  Fixed a compiler warning.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
WikiTools.pm  1.5  11 years  parrello  Fixed table generator to remove line-feeds that would break the table.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
raelib.pm  1.44  11 years  redwards  adding a randomizer function
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
AnnoClearinghouse.pm  1.36  11 years  wilke  changed names for db tables

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