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Index of /FigKernelPackages

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File (rev) Rev. Age Author Last log entry
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tree_utilities.pm  1.17  11 years  disz  added subsyste display on hover
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
set_utilities.pm  1.2  14 years  olson  Added license words.
selenoprotein_ref_seq.pm  1.4  12 years  golsen  Add to the list of reference proteins.
representative_sequences.pm  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
raelib.pm  1.44  12 years  redwards  adding a randomizer function
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
proml.pm  1.8  13 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
model.pm  1.22  11 years  dejongh  assume supersets are loaded
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
gjoparseblast.pm  1.3  11 years  overbeek  updates from Gary
gjonewicklib.pm  1.11  12 years  golsen  Allow matched [ ... ] inside Newick tree comment. This violates the standard, b...
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjolib.pm  1.2  14 years  olson  Added license words.
gjocolorlib.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
gjoalignment.pm  1.17  11 years  golsen  Fixed a bug introduced into align_with_clustal() that caused it to return [ id, ...
gjoalign2html.pm  1.2  12 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
find_special_proteins.pm  1.10  11 years  overbeek  add the ability to find TIF3
fastDNAml.pm  1.2  14 years  olson  Added license words.
display_related_genomes.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
clustaltree.pm  1.1  12 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
__init__.py  1.2  14 years  olson  Added license words.
WikiTools.pm  1.5  11 years  parrello  Fixed table generator to remove line-feeds that would break the table.
WebColors.pm  1.7  11 years  paczian  added palette 'excel' with the default excel color palette minus black, white an...
UserData.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
UserDB.pm  1.2  14 years  olson  Added license words.
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
Tracer.pm  1.114  11 years  olson  When tracing CGIs run at the command line, make the tracing code honor the TRACI...
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
TestUtils.pm  1.7  11 years  parrello  Quoted values in string comparisons to avoid an error when working with sim obje...
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
Subsystem.pm  1.140  11 years  dejongh  Changes to get_hope_reactions for a genome even if it isn't active in a subsyste...
Stats.pm  1.7  11 years  parrello  Changed to round floating-point stats to integer values.
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
SproutSearch.pm  1.11  14 years  olson  Added license words.
SproutFIG.pm  1.10  14 years  olson  Added license words.
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
SFXlate.pm  1.111  11 years  parrello  Fixed subsystems_for_pegs. Changed to fail more gracefully if the attribute data...
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
README  1.1.1.1  16 years  efrank   import
RC.pm  1.2  14 years  olson  Added license words.
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
PinnedRegions.pm  1.15  11 years  paczian  added functional coupling pin
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
PHOB.pm  1.14  12 years  overbeek  add utilities for computing alignments
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
P2P.pm  1.31  14 years  olson  Added license words.
Overlap.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
Observation.pm  1.73  11 years  arodri7  fixed functional coupling data retrieval
NewGenome.pm  1.75  11 years  gdpusch  Fixed bug in ORF::seq(); minor changes in debugging output. -- /gdp
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
MergeTransactions.pm  1.3  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.
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
Makefile  1.10  11 years  golsen  Fix to path for pod2html
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  12 years  olson  Hope college modifications.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
HtmlPageParser.pm  1.2  14 years  olson  Added license words.
HTML.py  1.6  14 years  olson  Added license words.
HTML.pm  1.129  11 years  parrello  Fixed URL references.
GenomeMetaDB.pm  1.3  11 years  olson  Fix database version of GenomeMeta's get_log output to match the old format, so ...
GenomeMeta.pm  1.15  11 years  olson  oops, these need updated.
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
GenoGraphics.pm  1.18  11 years  parrello  Not sure. The DIFF says there was no change.
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
FileLocking.pm  1.2  12 years  olson  add shared locking
FileIOFunctions.pm  1.1  11 years  chenry  These modules are for interacting with the modeling database Chris Henry and Mat...
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FigFams.pm  1.48  11 years  gdpusch  Added POD block listing the methods within this module.
FigFam.pm  1.75  11 years  arodri7  updated and corrected sub new
FS_RAST.pm  1.19  11 years  overbeek  fixes to detecting consistent fragments
FIGtree.pm  1.3  14 years  olson  Added license words.
FIGrpc.pm  1.3  14 years  olson  Added license words.
FIGnet.pm  1.2  14 years  olson  Added license words.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGV.pm  1.70  11 years  paczian  added support for FIGM
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FIGRules.pm  1.48  11 years  paczian  moved encoded_annotation_to_natural_english to this module to be self contained
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGMODEL.pm  1.2  11 years  chenry  Fixing bug in CpdLink function.
FIGM.pm  1.3  11 years  paczian  added support for FIGM
FIGGenDB.pm  1.6  14 years  olson  Added license words.
FIGAttributes.pm  1.3  14 years  olson  Added license words.
FIG2.py  1.2  14 years  olson  Added license words.
FIG.py  1.13  14 years  olson  Added license words.
FIG.pm  1.733  11 years  overbeek  add routine to get close pegs in the same subsystem
FFs.pm  1.25  11 years  arodri7  corrected errors for merge_figfams
FF.pm  1.22  11 years  olson  Fix bug where return of should_be_member is lost.
DocUtils.pm  1.17  11 years  parrello  Fixed a bug in the config file modification method and added tracing.
Diagram.pm  1.16  11 years  parrello  Fixed a bad URL.
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
DBKernel.pm  1.52  11 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
Construct.pm  1.2  14 years  olson  Added license words.
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
CompareMR.pm  1.6  11 years  parrello  Changed to avoid an unnecessary creation of the FIG object at load time.
ClusterWorker.pm  1.2  14 years  olson  Added license words.
Cluster.pm  1.11  14 years  olson  Added license words.
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
Classes.pm  1.1  14 years  mkubal  added Organism class
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
COPYING.TXT  1.1  14 years  olson  add license file
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
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.
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
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.
AnnoClearinghouse.pm  1.36  11 years  wilke  changed names for db tables
AliasAnalysis.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions

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