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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  1.20  10 years  olson  Add more modules to the SAS toolkit.
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  1.5  10 years  golsen  Add some reference sequences and replace ; with @ in functions.
representative_sequences.pm  1.11  10 years  golsen  Minor changes in style.
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  1.9  10 years  golsen  Minor updates to SEED awareness.
model.pm  1.34  10 years  dejongh  fix reference
gjostat.pm  1.1  10 years  golsen  Adding a library of useful statistical functions.
gjoseqlib.pm  1.17  10 years  golsen  Add new function for assessing similarity of aligned sequences. Fix a bug in pri...
gjophylip.pm  1.2  10 years  golsen  Add and/or update routines to support bootstrapping and bootstrap consensus tree...
gjoparseblast.pm  1.7  10 years  overbeek  add as SAS components
gjonewicklib.pm  1.17  10 years  olson  Add more modules to the SAS toolkit.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjolib.pm  1.3  10 years  olson  Add more modules to the SAS toolkit.
gjocolorlib.pm  1.3  10 years  golsen  Added more named colors from X11, but these are almost certainly based on a diff...
gjoalignment.pm  1.28  10 years  overbeek  mark as SAS component
gjoalign2html.pm  1.4  10 years  golsen  Fix problem with line wrap in the alignment. Change all #abc colors to #aabbcc f...
gd_tree_0.pm  1.2  10 years  golsen  Add PNG format trees to fid_checked.cgi. Add support elsewhere. Some code clea...
find_special_proteins.pm  1.10  11 years  overbeek  add the ability to find TIF3
find_homologs.pm  1.3  11 years  overbeek  update from Gary
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
compare_coding.pm  1.9  10 years  overbeek  gene calling stuff
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
__init__.py  1.2  14 years  olson  Added license words.
WikiTools.pm  1.8  11 years  parrello  Fixed a glitch in list rendering.
WebColors.pm  1.12  10 years  dejongh  add many_except_gray and rgb_to_hex
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  1.129  10 years  parrello  Fixed race condition while checking the emergency tracing file.
ToCall.pm  1.11  10 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
TimeZone.pm  1.1  10 years  chenry  *** empty log message ***
TestUtils.pm  1.11  10 years  parrello  Fixed display glitch for pure white space.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TBLstuff.pm  1.2  10 years  overbeek  minor fixes
Subsystem.pm  1.145  10 years  redwards  moving error messages from STDOUT to STDERR
Stats.pm  1.8  10 years  parrello  Added a method to extract saved messages.
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.
SimFC.pm  1.3  11 years  overbeek  handle deleted FIDs and failure to get translations
Sim.pm  1.14  10 years  olson  Distro fixups
ServerThing.pm  1.34  10 years  parrello  Fixed so that the ETracing parameter overrides the environment variable.
ServerScripts.pm  1.2  10 years  parrello  Final server updates.
SeedV.pm  1.2  10 years  olson  remove Tracer ref
SeedUtils.pm  1.29  10 years  dejongh  Removed extraneous curly bracket causing compilation error
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
SeedEnv.pm  1.3  10 years  parrello  Added ANNOserver. Removed deprecated servers.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
ScriptThing.pm  1.3  10 years  parrello  Added a column parameter to GetBatch.
Scenario.pm  1.9  10 years  dejongh  new methods
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
SSU_rRNA_reps.pm  1.2  10 years  golsen  Update to the variable names (for more universal application).
SS.pm  1.13  10 years  parrello  More documentation cleanup.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
SAPtutorial.pm  1.9  10 years  parrello  More documentation cleanup.
SAPserver.pm  1.11  10 years  parrello  Changed to use the default URL if an empty string is specified, for compatibilit...
SAP.pm  1.62  10 years  parrello  Added ids_to_annotations method.
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.
RASTserver.pm  1.16  10 years  disz  Submit doc
RAST_submission.pm  1.20  10 years  olson  bugfix
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
ProtSims.pm  1.10  10 years  olson  Distro fixups
ProtFamsLite.pm  1.2  11 years  arodri7  added functions and made functions work
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
PinnedRegions.pm  1.28  10 years  paczian  added location for artificial features
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
ParseDate.pm  1.1  10 years  chenry  *** empty log message ***
ParalogResolution.pm  1.5  10 years  golsen  Modifications to support line-drawing character set in tree printer plots.
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
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  1.82  10 years  paczian  fixed hit and query length (cannot be null)
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
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
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  1.12  10 years  parrello  Removed POD stuff.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
Kmers.pm  1.19  10 years  olson  Support constructor that takes friDB/setIDB/table.binary instead of a kmers dir....
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  12 years  olson  Hope college modifications.
JulianDay.pm  1.1  10 years  chenry  *** empty log message ***
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  1.130  11 years  arodri7  added links to set_prot_links
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
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  1.22  10 years  golsen  Remove superfluous references to CGI. Add png format as comments.
FullLocation.pm  1.25  10 years  parrello  Added a method to compute the total location length.
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  1.11  10 years  chenry  *** empty log message ***
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FigFams.pm  1.56  10 years  overbeek  fixes to support Kmer analysis
FigFam.pm  1.78  11 years  arodri7  changed to check if is_deleted_fid in sub new
FS_RAST.pm  1.24  10 years  overbeek  force frameshifts to be of longer chunks
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  1.92  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FIGRules.pm  1.54  10 years  olson  Optimize to_structured_english.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGMODELweb.pm  1.1  10 years  chenry  *** empty log message ***
FIGMODELmodel.pm  1.4  10 years  chenry  *** empty log message ***
FIGMODELdatabase.pm  1.3  10 years  chenry  *** empty log message ***
FIGMODELTable.pm  1.12  10 years  chenry  *** empty log message ***
FIGMODELObject.pm  1.3  10 years  chenry  *** empty log message ***
FIGMODEL.pm  1.42  10 years  chenry  *** empty log message ***
FIGM.pm  1.17  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIGGenDB.pm  1.6  14 years  olson  Added license words.
FIGAttributes.pm  1.4  11 years  overbeek  get rid of something
FIG2.py  1.2  14 years  olson  Added license words.
FIG.py  1.13  14 years  olson  Added license words.
FIG.pm  1.810  10 years  redwards  adding load_dlits to load_all
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
FFs.pm  1.46  10 years  paczian  fixed rast figfam display
FF.pm  1.33  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
FBAMODELserver.pm  1.2  10 years  parrello  *** empty log message ***
FBAMODEL.pm  1.3  10 years  chenry  *** empty log message ***
ErrorMessage.pm  1.1  10 years  parrello  Error handling restructure.
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
Diagram.pm  1.17  10 years  parrello  Fixed some bad links.
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
DBKernel.pm  1.63  10 years  parrello  Server database recovery fix.
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
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  1.8  11 years  paczian  cutting comments off of functional roles
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
ClientThing.pm  1.13  10 years  parrello  Fixed to produce a less ugly message when there is no response content from a se...
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
COserver.pm  1.13  10 years  parrello  Removed from the SAS distribution.
COPYING.TXT  1.1  14 years  olson  add license file
CO.pm  1.6  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
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  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
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  1.44  11 years  wilke  Modified sql query to ? syntax
AliasAnalysis.pm  1.9  10 years  parrello  Fixed the pattern for CMR IDs.
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
ANNOserver.pm  1.11  10 years  disz  Fixed doc for assign_using_prot
ANNO.pm  1.3  10 years  parrello  Fixed an obscure metabolic reconstruction problem.
ACHserver.pm  1.16  10 years  parrello  Removed from the SAS distribution.
ACH.pm  1.7  10 years  disz  changed doc to say XXserver->new() insetad of XX->new

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