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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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ACHserver.pm  1.5  10 years  disz  FIxed bad run_query
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliasAnalysis.pm  1.9  10 years  parrello  Fixed the pattern for CMR IDs.
AnnoClearinghouse.pm  1.44  10 years  wilke  Modified sql query to ? syntax
Annotation.pm  1.4  11 years  parrello  Added a TITLE statement for the Wiki.
ApplyTransactions.pm  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
BadCall.pm  1.4  11 years  parrello  Replaced obsolete AddToListMap method.
BasicLocation.pm  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
Blast.pm  1.5  11 years  overbeek  close TMP files in Blast.pm
ButtonArray.pm  1.1  11 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
CO.pm  1.2  10 years  parrello  Fixed some documentation errors.
COPYING.TXT  1.1  14 years  olson  add license file
COserver.pm  1.3  10 years  olson  server fixes
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
Classes.pm  1.1  14 years  mkubal  added Organism class
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
Cluster.pm  1.11  14 years  olson  Added license words.
ClusterWorker.pm  1.2  14 years  olson  Added license words.
CompareMR.pm  1.8  10 years  paczian  cutting comments off of functional roles
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
Construct.pm  1.2  14 years  olson  Added license words.
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
Contigs.pm  1.1  10 years  overbeek  new Contigs.pm and compare_coding.pm
DBKernel.pm  1.60  10 years  parrello  Removed connect_cached.
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
Diagram.pm  1.17  10 years  parrello  Fixed some bad links.
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
FC.pm  1.19  10 years  parrello  Converted co-occurrence server to new technology.
FF.pm  1.32  10 years  arodri7  replaced backticks for reading files
FFs.pm  1.46  10 years  paczian  fixed rast figfam display
FFserver.pm  1.19  10 years  olson  increase request size in non-blast case so we don't drown in overhead.
FIG.pm  1.804  10 years  olson  Add rewrite-loop breaking to the role rewrite process.
FIG.py  1.13  14 years  olson  Added license words.
FIG2.py  1.2  14 years  olson  Added license words.
FIGAttributes.pm  1.4  10 years  overbeek  get rid of something
FIGGenDB.pm  1.6  14 years  olson  Added license words.
FIGM.pm  1.17  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIGMODEL.pm  1.36  10 years  devoid  Added functions get_role_id, get_role_name, deprecate_role for converting functi...
FIGMODELObject.pm  1.3  10 years  chenry  *** empty log message ***
FIGMODELTable.pm  1.10  10 years  chenry  Added html_print function to simplify the printing of FIGMODELTables in webpages...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGRules.pm  1.54  10 years  olson  Optimize to_structured_english.
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGV.pm  1.92  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
FIGnet.pm  1.2  14 years  olson  Added license words.
FIGrpc.pm  1.3  14 years  olson  Added license words.
FIGtree.pm  1.3  14 years  olson  Added license words.
FS_RAST.pm  1.24  10 years  overbeek  force frameshifts to be of longer chunks
FigFam.pm  1.78  10 years  arodri7  changed to check if is_deleted_fid in sub new
FigFams.pm  1.56  10 years  overbeek  fixes to support Kmer analysis
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FileIOFunctions.pm  1.10  10 years  chenry  *** empty log message ***
FileLocking.pm  1.2  12 years  olson  add shared locking
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
GenoGraphics.pm  1.18  11 years  parrello  Not sure. The DIFF says there was no change.
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeMeta.pm  1.15  11 years  olson  oops, these need updated.
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
HTML.pm  1.130  10 years  arodri7  added links to set_prot_links
HTML.py  1.6  14 years  olson  Added license words.
HtmlPageParser.pm  1.2  14 years  olson  Added license words.
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
JobScheduler.pm  1.8  11 years  parrello  Changed POD headers to work better with the new system.
JulianDay.pm  1.1  10 years  chenry  *** empty log message ***
KGML.pm  1.4  12 years  olson  Hope college modifications.
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
Kmers.pm  1.15  10 years  olson  Add assign_functions_to_prot_set. Use ProtSims::blastP instead of blast for prot...
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
Makefile  1.12  10 years  parrello  Removed POD stuff.
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
Markups.pm  1.2  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.
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
NRTools.pm  1.4  10 years  olson  update to new metadata standard
NewGenome.pm  1.80  10 years  parrello  Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.
Observation.pm  1.82  10 years  paczian  fixed hit and query length (cannot be null)
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
Overlap.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
P2P.pm  1.31  14 years  olson  Added license words.
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
ParalogResolution.pm  1.5  10 years  golsen  Modifications to support line-drawing character set in tree printer plots.
ParseDate.pm  1.1  10 years  chenry  *** empty log message ***
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
PickFeatureSet.pm  1.2  10 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.28  10 years  paczian  added location for artificial features
ProtFamLite.pm  1.2  10 years  arodri7  added functions and made functions work
ProtFams.pm  1.3  10 years  arodri7  added functions and made functions work
ProtFamsLite.pm  1.2  10 years  arodri7  added functions and made functions work
ProtSims.pm  1.7  10 years  overbeek  condensing sets of hits against a sequence
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
RC.pm  1.2  14 years  olson  Added license words.
README  1.1.1.1  16 years  efrank   import
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
SAP.pm  1.16  10 years  parrello  Added "genes_in_region" method.
SAPserver.pm  1.8  10 years  parrello  Changed to allow specification of 'localhost" for the server URL. When this is d...
SAPtutorial.pm  1.7  10 years  parrello  Converted to use leading "-" in parameters.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
SS.pm  1.1  10 years  parrello  Converted subsystem server to new technology.
SSU_rRNA_reps.pm  1.1  10 years  overbeek  fixes to support search for rRNAs
SSserver.pm  1.10  10 years  parrello  Converted subsystem server to new technology.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
Scenario.pm  1.8  10 years  parrello  Added a line to suppress spurious warnings.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedSims.pm  1.1  10 years  overbeek  additions to support partitioning of sims
SeedUtils.pm  1.8  10 years  parrello  Added "verify_dir".
ServerThing.pm  1.7  10 years  parrello  Fixed CSS link.
Sim.pm  1.13  11 years  overbeek  implemented new version of dsims based on partitions
SimFC.pm  1.3  10 years  overbeek  handle deleted FIDs and failure to get translations
SproutFIG.pm  1.10  14 years  olson  Added license words.
SproutSearch.pm  1.11  14 years  olson  Added license words.
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
Stats.pm  1.8  10 years  parrello  Added a method to extract saved messages.
Subsystem.pm  1.145  10 years  redwards  moving error messages from STDOUT to STDERR
TBLstuff.pm  1.2  10 years  overbeek  minor fixes
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TestUtils.pm  1.10  10 years  parrello  Added new functions to support the seed viewer debug console.
TimeZone.pm  1.1  10 years  chenry  *** empty log message ***
ToCall.pm  1.11  10 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
Tracer.pm  1.124  10 years  parrello  Added ability to turn off automatic CGI parm trace in ETracing method.
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
UnvSubsys.pm  1.20  11 years  paczian  added missing "use HTML;"
UserDB.pm  1.2  14 years  olson  Added license words.
UserData.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
WebColors.pm  1.11  10 years  devoid  Added functions for converting colors from RGB values to HSL values.
WikiTools.pm  1.8  10 years  parrello  Fixed a glitch in list rendering.
__init__.py  1.2  14 years  olson  Added license words.
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
compare_coding.pm  1.9  10 years  overbeek  gene calling stuff
display_related_genomes.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
fastDNAml.pm  1.2  14 years  olson  Added license words.
find_homologs.pm  1.3  10 years  overbeek  update from Gary
find_special_proteins.pm  1.10  11 years  overbeek  add the ability to find TIF3
gd_tree_0.pm  1.2  10 years  golsen  Add PNG format trees to fid_checked.cgi. Add support elsewhere. Some code clea...
gjoalign2html.pm  1.4  10 years  golsen  Fix problem with line wrap in the alignment. Change all #abc colors to #aabbcc f...
gjoalignment.pm  1.27  10 years  golsen  Add and/or update routines to support bootstrapping and bootstrap consensus tree...
gjocolorlib.pm  1.3  10 years  golsen  Added more named colors from X11, but these are almost certainly based on a diff...
gjolib.pm  1.2  14 years  olson  Added license words.
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
gjonewicklib.pm  1.16  10 years  golsen  Add ability to put internal node labels in printer plot trees. (requires dy >= 2...
gjoparseblast.pm  1.6  10 years  golsen  Fix to bug that caused failure in reading alignments with an entire row of gaps....
gjophylip.pm  1.2  10 years  golsen  Add and/or update routines to support bootstrapping and bootstrap consensus tree...
gjoseqlib.pm  1.15  10 years  golsen  Improve the comments and descriptions of functions.
model.pm  1.32  10 years  parrello  Fixed a bunch of compiler warnings.
proml.pm  1.8  12 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
protdist_neighbor.pm  1.1  12 years  golsen  A package for protdist and neighbor PHYLIP trees.
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
raedraw.pm  1.14  11 years  parrello  Changed POD heading levels.
raelib.pm  1.44  11 years  redwards  adding a randomizer function
representative_sequences.pm  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
selenoprotein_ref_seq.pm  1.4  11 years  golsen  Add to the list of reference proteins.
set_utilities.pm  1.2  14 years  olson  Added license words.
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
tree_utilities.pm  1.18  10 years  parrello  Added tracing support.

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