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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  1.3  10 years  overbeek  make SAS components
selenoprotein_ref_seq.pm  1.5  10 years  golsen  Add some reference sequences and replace ; with @ in functions.
representative_sequences.pm  1.16  9 years  fangfang  handle undefined return value from pack_sequences in req_seq and rep_seq_2
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  1.35  9 years  olson  make it not a fatal error to not load hope_supersets; this was causing a crash o...
gjostat.pm  1.2  9 years  golsen  Integrate the function descriptions into a string returned by the function gjost...
gjoseqlib.pm  1.23  9 years  overbeek  get rid of Dumper
gjophylip.pm  1.6  9 years  fangfang  SAS component
gjoparseblast.pm  1.8  9 years  golsen  Fix two minor typographical errors in the documentation.
gjonewicklib.pm  1.25  9 years  golsen  Change behavior of reroot_tree() to ignore distance if there is only one node.
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.
gjogenbank.pm  1.5  9 years  golsen  Handle BASE COUNT Handle entries without a date on the LOCUS line.
gjocolorlib.pm  1.6  9 years  overbeek  fixes to gray
gjoalignment.pm  1.35  9 years  fangfang  use SeedAware::run_gathering_output to handle muscle version information
gjoalignandtree.pm  1.7  9 years  fangfang  change to verify_db
gjoalign2html.pm  1.5  9 years  fangfang  SAS component
gd_tree_0.pm  1.5  10 years  golsen  Extensive reworking of color management.
find_special_proteins.pm  1.12  9 years  olson  typod the declaration
find_homologs.pm  1.3  11 years  overbeek  update from Gary
ffxtree.pm  1.10  9 years  fangfang  update sas component
fastDNAml.pm  1.2  14 years  olson  Added license words.
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
compare_coding.pm  1.9  11 years  overbeek  gene calling stuff
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
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  1.14  9 years  paczian  added 'circle' color scheme
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  1.131  9 years  parrello  Changed a "die" to a "confess".
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  11 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  11 years  overbeek  minor fixes
Subsystem.pm  1.147  10 years  overbeek  minor fix
Stats.pm  1.8  11 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
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
ServerThing.pm  1.58  9 years  parrello  New Sapling update support.
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
SeedV.pm  1.9  9 years  gdpusch  Changed a debugging line to print to STDERR, not STDOUT; print only if VERBOSE.
SeedUtils.pm  1.58  9 years  gdpusch  Added support for Genetic Code 1.
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.
SeedAware.pm  1.5  9 years  golsen  Minor change in temporary file name code.
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
Scenario.pm  1.9  10 years  dejongh  new methods
SapCompareRegions.pm  1.2  9 years  parrello  New compare-regions support.
SampleDir.pm  1.4  9 years  olson  More analysis fixes; user-agent setting.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
SUPserver.pm  1.1  9 years  parrello  New Sapling update support.
SUP.pm  1.2  9 years  parrello  New methods for alignment data.
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
SSU_rRNA_reps.pm  1.3  9 years  golsen  Adjust end of one reference sequence by padding it slightly.
SS.pm  1.13  10 years  parrello  More documentation cleanup.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
SAPtutorial.pm  1.10  10 years  parrello  Fixed some errors in examples of ID types.
SAPserver.pm  1.13  9 years  parrello  Allow alternate forms of parameters to client-side modules.
SAP.pm  1.125  9 years  parrello  New compare-regions support.
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  1.23  9 years  gdpusch  Fixed bugs in and added more support for Viral and Euk jobs.
RAST_submission.pm  1.26  9 years  olson  Support -determineFamily
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
ProtSims.pm  1.18  9 years  olson  Further uniquify temp files.
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  1.34  9 years  olson  fix unlink here too
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
Phage.pm  1.3  9 years  redwards  minor correction
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
ParseDate.pm  1.1  11 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  1.3  9 years  olson  add SAS header
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
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  12 years  parrello  Added to facilitate reading the error log.
ListServerScripts.pm  1.1  9 years  parrello  Added to support server script listing.
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
Kmers.pm  1.27  9 years  olson  add id to diagnostic
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  13 years  olson  Hope college modifications.
JulianDay.pm  1.1  11 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  1.16  10 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
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  1.24  10 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
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  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
FileIOFunctions.pm  1.14  10 years  chenry  Moving some functions over to FIGMODEL.
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FS_RAST.pm  1.31  9 years  olson  re-redirect nap stdout to /dev/null. here's hoping it works on windows still
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  13 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  1.96  9 years  gdpusch  Modified to gracefully handle Organism directories with no or empty Subsystems/ ...
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  1.15  9 years  chenry  Adding code to support model curation via upload.
FIGMODELmodel.pm  1.30  9 years  chenry  Bug fixes to pipeline.
FIGMODELdatabase.pm  1.21  9 years  dejongh  Get config info from the FIGMODEL instead of duplicating it in FIGMODELdatabase
FIGMODELTable.pm  1.15  9 years  chenry  Bug fixes to pipeline.
FIGMODELObject.pm  1.4  10 years  chenry  Implemented new function to change the name of a date header.
FIGMODEL.pm  1.70  9 years  dejongh  use a colon to split environmental variable fields rather than a semi-colon, bec...
FIGM.pm  1.18  9 years  olson  Add FIGV and FIGM function_of_bulk
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  1.820  9 years  disz  FIGFAM 6 digit problem
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
FFs.pm  1.49  9 years  olson  Clean up errors.
FF.pm  1.35  9 years  disz  FigFam 6 digit fix
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
FBAMODELserver.pm  1.3  9 years  parrello  Allow alternate forms of parameters to client-side modules.
FBAMODEL.pm  1.14  9 years  dejongh  fix return
ErrorMessage.pm  1.2  10 years  olson  remove unused use CGI.
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
Diagram.pm  1.17  11 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.
CorrespondenceCache.pm  1.1  9 years  parrello  Updates for new expression-data method.
Correspondence.pm  1.4  9 years  overbeek  correct the identity check
CorrTableEntry.pm  1.4  9 years  olson  Add num_matching_functions for column 19
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
ContigMD5.pm  1.3  13 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
Clustering.pm  1.6  9 years  overbeek  added double and triple linkage
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  1.17  9 years  olson  More analysis fixes; user-agent setting.
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
BerkTable.pm  1.2  9 years  olson  fix arg
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
AlignTree.pm  1.19  9 years  fangfang  update comments
AliasAnalysis.pm  1.10  10 years  parrello  Fixed the LocusTag match pattern.
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
ATserver.pm  1.2  9 years  fangfang  default url set to biobig
AT.pm  1.5  9 years  fangfang  always return psiblast search history
ANNOserver.pm  1.20  9 years  parrello  Fixed a POD error.
ANNO.pm  1.8  9 years  olson  kmer info changes
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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