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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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ServerThing.pm  1.51  10 years  parrello  *** empty log message ***
SAP.pm  1.86  10 years  parrello  Added "all_proteins" method.
FIG.pm  1.813  10 years  overbeek  turn off recognition of locks
FBAMODEL.pm  1.7  10 years  chenry  Corrected bugs in the FBA classify function.
FIGMODELweb.pm  1.4  10 years  chenry  Reoganization of model viewer.
FIGMODELdatabase.pm  1.9  10 years  chenry  Bug fixes and reorganization for model viewer.
FIGMODEL.pm  1.51  10 years  chenry  More bug fixes for the model viewer.
PinnedRegions.pm  1.31  10 years  olson  use bulk lookups
FIGMODELmodel.pm  1.12  10 years  chenry  Minor corrections.
FIGMODELObject.pm  1.4  10 years  chenry  Implemented new function to change the name of a date header.
gd_tree_0.pm  1.5  10 years  golsen  Extensive reworking of color management.
gjonewicklib.pm  1.19  10 years  golsen  Fixed bug introduced yesterday (a spurious newline).
gjoalignandtree.pm  1.2  10 years  fangfang  fixed a small bug in representative_for_profile()
FileIOFunctions.pm  1.12  10 years  chenry  Removed some functions that were placed in FIGMODEL instead.
FIGMODELTable.pm  1.14  10 years  chenry  A small number of new functions were introduced to support improved database acc...
SeedUtils.pm  1.35  10 years  parrello  Changed boundaries_of to allow comma-delimited strings.
representative_sequences.pm  1.12  10 years  fangfang  check if formatdb and blastall exist in $FIG_Config::ext_bin
ErrorMessage.pm  1.2  10 years  olson  remove unused use CGI.
RAST_submission.pm  1.24  10 years  olson  Allow anyone with access to the job to be able to upload data. Unlink the spoole...
RASTserver.pm  1.19  10 years  olson  Add chunked upload and directory support.
ANNOserver.pm  1.16  10 years  parrello  Fixed a POD error.
ANNO.pm  1.4  10 years  parrello  Updates for glimmer training and special-protein finder.
Subsystem.pm  1.147  10 years  overbeek  minor fix
ProtSims.pm  1.12  10 years  overbeek  allow use of just blast
Clustering.pm  1.4  10 years  overbeek  make SAS components
set_utilities.pm  1.3  10 years  overbeek  make SAS components
AliasAnalysis.pm  1.10  10 years  parrello  Fixed the LocusTag match pattern.
ServerScripts.pm  1.3  10 years  parrello  Updated the POD.
SAPtutorial.pm  1.10  10 years  parrello  Fixed some errors in examples of ID types.
GenomeMeta.pm  1.16  10 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
FileLocking.pm  1.3  10 years  olson  Add support for File::FcntlLock
GenoGraphics.pm  1.24  10 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
FigFams.pm  1.57  10 years  bartels  added a function
FFs.pm  1.47  10 years  bartels  added a function
model.pm  1.34  10 years  dejongh  fix reference
proml.pm  1.9  10 years  golsen  Minor updates to SEED awareness.
SSU_rRNA_reps.pm  1.2  10 years  golsen  Update to the variable names (for more universal application).
Kmers.pm  1.19  10 years  olson  Support constructor that takes friDB/setIDB/table.binary instead of a kmers dir....
selenoprotein_ref_seq.pm  1.5  10 years  golsen  Add some reference sequences and replace ; with @ in functions.
gjoseqlib.pm  1.17  10 years  golsen  Add new function for assessing similarity of aligned sequences. Fix a bug in pri...
gjostat.pm  1.1  10 years  golsen  Adding a library of useful statistical functions.
ScriptThing.pm  1.3  10 years  parrello  Added a column parameter to GetBatch.
Tracer.pm  1.129  10 years  parrello  Fixed race condition while checking the emergency tracing file.
gjoalignment.pm  1.28  10 years  overbeek  mark as SAS component
gjoparseblast.pm  1.7  10 years  overbeek  add as SAS components
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
SeedV.pm  1.2  10 years  olson  remove Tracer ref
Sim.pm  1.14  10 years  olson  Distro fixups
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
ACHserver.pm  1.16  10 years  parrello  Removed from the SAS distribution.
COserver.pm  1.13  10 years  parrello  Removed from the SAS distribution.
SeedEnv.pm  1.3  10 years  parrello  Added ANNOserver. Removed deprecated servers.
ClientThing.pm  1.13  10 years  parrello  Fixed to produce a less ugly message when there is no response content from a se...
FBAMODELserver.pm  1.2  10 years  parrello  *** empty log message ***
DBKernel.pm  1.63  10 years  parrello  Server database recovery fix.
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
SS.pm  1.13  10 years  parrello  More documentation cleanup.
ACH.pm  1.7  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
FF.pm  1.33  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
CO.pm  1.6  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
SAPserver.pm  1.11  10 years  parrello  Changed to use the default URL if an empty string is specified, for compatibilit...
TestUtils.pm  1.11  10 years  parrello  Fixed display glitch for pure white space.
FullLocation.pm  1.25  10 years  parrello  Added a method to compute the total location length.
gjolib.pm  1.3  10 years  olson  Add more modules to the SAS toolkit.
tree_utilities.pm  1.20  10 years  olson  Add more modules to the SAS toolkit.
Scenario.pm  1.9  10 years  dejongh  new methods
WebColors.pm  1.12  10 years  dejongh  add many_except_gray and rgb_to_hex
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
gjophylip.pm  1.2  10 years  golsen  Add and/or update routines to support bootstrapping and bootstrap consensus tree...
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
FIGV.pm  1.92  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIGM.pm  1.17  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
Observation.pm  1.82  10 years  paczian  fixed hit and query length (cannot be null)
FIGRules.pm  1.54  10 years  olson  Optimize to_structured_english.
gjoalign2html.pm  1.4  10 years  golsen  Fix problem with line wrap in the alignment. Change all #abc colors to #aabbcc f...
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
BasicLocation.pm  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
NewGenome.pm  1.80  10 years  parrello  Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.
NRTools.pm  1.4  10 years  olson  update to new metadata standard
ToCall.pm  1.11  10 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
ParalogResolution.pm  1.5  10 years  golsen  Modifications to support line-drawing character set in tree printer plots.
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
gjocolorlib.pm  1.3  10 years  golsen  Added more named colors from X11, but these are almost certainly based on a diff...
Makefile  1.12  10 years  parrello  Removed POD stuff.
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
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 ***
compare_coding.pm  1.9  11 years  overbeek  gene calling stuff
TBLstuff.pm  1.2  11 years  overbeek  minor fixes
FS_RAST.pm  1.24  11 years  overbeek  force frameshifts to be of longer chunks
Stats.pm  1.8  11 years  parrello  Added a method to extract saved messages.
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
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.
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
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
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
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.
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
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
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.
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...
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
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.
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 ...
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.
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
__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.
README  1.1.1.1  16 years  efrank   import

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