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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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FIG.pm  1.780  11 years  overbeek  fix operator in SQL
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
Kmers.pm  1.9  11 years  overbeek  fix blast to add ln2
Observation.pm  1.77  11 years  arodri7  made fixes to graphic view, fixed table issues with checkboxes
ACHserver.pm  1.3  11 years  olson  mods for production ACH server
DBKernel.pm  1.57  11 years  olson  prepare_command(): Pass attribute variable through to $dbh->prepare()
NewGenome.pm  1.77  11 years  gdpusch  Fixed failure to remove overlaps of initial ORF candidates against "special" or ...
FIGV.pm  1.88  11 years  dejongh  Force reloading of subsystem info when functional annotations change
FFserver.pm  1.9  11 years  arodri7  added FIGfam functions org_of, function_of, seq_of, aliases_of, and more
FigFams.pm  1.55  11 years  arodri7  updated non-essential functions
FFs.pm  1.38  11 years  arodri7  updated non-essential functions
SAP.pm  1.1  11 years  overbeek  initial version
SSserver.pm  1.3  11 years  olson  fixes to use the canonical server url
COserver.pm  1.2  11 years  olson  fixes to use the canonical server url
FC.pm  1.14  11 years  overbeek  updates to co_occurrence rtns
FIGM.pm  1.14  11 years  paczian  fixed call to seqs_with_role to match FIG.pm invocation
TimeZone.pm  1.1  11 years  chenry  *** empty log message ***
JulianDay.pm  1.1  11 years  chenry  *** empty log message ***
ParseDate.pm  1.1  11 years  chenry  *** empty log message ***
FileIOFunctions.pm  1.8  11 years  chenry  *** empty log message ***
FIGMODELTable.pm  1.3  11 years  chenry  *** empty log message ***
FIGMODELObject.pm  1.3  11 years  chenry  *** empty log message ***
FIGMODEL.pm  1.15  11 years  chenry  *** empty log message ***
AliasAnalysis.pm  1.9  11 years  parrello  Fixed the pattern for CMR IDs.
FF.pm  1.31  11 years  arodri7  updates for release 9 FIGfams
gjoalignment.pm  1.19  11 years  golsen  Slight clean-up of code.
gjoseqlib.pm  1.15  11 years  golsen  Improve the comments and descriptions of functions.
FIGRules.pm  1.52  11 years  paczian  removed STDERR for wikipedia
compare_coding.pm  1.9  11 years  overbeek  gene calling stuff
gjoparseblast.pm  1.6  11 years  golsen  Fix to bug that caused failure in reading alignments with an entire row of gaps....
TBLstuff.pm  1.2  11 years  overbeek  minor fixes
FS_RAST.pm  1.24  11 years  overbeek  force frameshifts to be of longer chunks
model.pm  1.32  11 years  parrello  Fixed a bunch of compiler warnings.
Tracer.pm  1.117  11 years  parrello  Added code for memory tracing.
TestUtils.pm  1.9  11 years  parrello  Added code to detect circular references.
Stats.pm  1.8  11 years  parrello  Added a method to extract saved messages.
Scenario.pm  1.8  11 years  parrello  Added a line to suppress spurious warnings.
Diagram.pm  1.17  11 years  parrello  Fixed some bad links.
AnnoClearinghouse.pm  1.44  11 years  wilke  Modified sql query to ? syntax
FigFam.pm  1.78  11 years  arodri7  changed to check if is_deleted_fid in sub new
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.19  11 years  paczian  fixed display of subsystems
HTML.pm  1.130  11 years  arodri7  added links to set_prot_links
WikiTools.pm  1.8  11 years  parrello  Fixed a glitch in list rendering.
tree_utilities.pm  1.18  11 years  parrello  Added tracing support.
SFXlate.pm  1.117  11 years  parrello  Added support for get_representative_genome and is_exchangable_subsystem.
GenomeMetaDB.pm  1.4  11 years  parrello  Fixed an error in the POD documentation. Fixed a compiler warning.
SimFC.pm  1.3  11 years  overbeek  handle deleted FIDs and failure to get translations
FIGAttributes.pm  1.4  11 years  overbeek  get rid of something
ProtFams.pm  1.3  11 years  arodri7  added functions and made functions work
ProtFamLite.pm  1.2  11 years  arodri7  added functions and made functions work
ProtFamsLite.pm  1.2  11 years  arodri7  added functions and made functions work
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
find_homologs.pm  1.3  11 years  overbeek  update from Gary
CompareMR.pm  1.8  11 years  paczian  cutting comments off of functional roles
SSU_rRNA_reps.pm  1.1  11 years  overbeek  fixes to support search for rRNAs
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
Subsystem.pm  1.144  11 years  parrello  Added a new method-- all_functions-- that allows SproutSubsys to retrieve role i...
Makefile  1.11  11 years  olson  attempt at fixing pod2html bug
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
find_special_proteins.pm  1.10  11 years  overbeek  add the ability to find TIF3
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
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.
WebColors.pm  1.7  11 years  paczian  added palette 'excel' with the default excel color palette minus black, white an...
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.
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
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.
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
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.
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;"
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.
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...
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  13 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
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.
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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