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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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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
HTML.pm  1.130  10 years  arodri7  added links to set_prot_links
ProtFamLite.pm  1.2  10 years  arodri7  added functions and made functions work
GenomeLists.pm  1.2  11 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
FIGMODELweb.pm  1.15  9 years  chenry  Adding code to support model curation via upload.
TimeZone.pm  1.1  10 years  chenry  *** empty log message ***
FIGMODELObject.pm  1.4  9 years  chenry  Implemented new function to change the name of a date header.
FIGMODELmodel.pm  1.30  9 years  chenry  Bug fixes to pipeline.
FIGMODELTable.pm  1.15  9 years  chenry  Bug fixes to pipeline.
JulianDay.pm  1.1  10 years  chenry  *** empty log message ***
FileIOFunctions.pm  1.14  9 years  chenry  Moving some functions over to FIGMODEL.
ParseDate.pm  1.1  10 years  chenry  *** empty log message ***
Scenario.pm  1.9  10 years  dejongh  new methods
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
FIGMODEL.pm  1.70  9 years  dejongh  use a colon to split environmental variable fields rather than a semi-colon, bec...
FIGMODELdatabase.pm  1.21  9 years  dejongh  Get config info from the FIGMODEL instead of duplicating it in FIGMODELdatabase
FBAMODEL.pm  1.14  9 years  dejongh  fix return
FIG.pm  1.820  9 years  disz  FIGFAM 6 digit problem
ACH.pm  1.7  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
FF.pm  1.35  9 years  disz  FigFam 6 digit fix
CO.pm  1.6  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
README  1.1.1.1  15 years  efrank   import
gjoalignandtree.pm  1.7  9 years  fangfang  change to verify_db
AT.pm  1.5  8 years  fangfang  always return psiblast search history
ATserver.pm  1.2  9 years  fangfang  default url set to biobig
representative_sequences.pm  1.16  9 years  fangfang  handle undefined return value from pack_sequences in req_seq and rep_seq_2
ffxtree.pm  1.10  8 years  fangfang  update sas component
gjophylip.pm  1.6  8 years  fangfang  SAS component
AlignTree.pm  1.19  8 years  fangfang  update comments
gjoalign2html.pm  1.5  8 years  fangfang  SAS component
gjoalignment.pm  1.35  9 years  fangfang  use SeedAware::run_gathering_output to handle muscle version information
FIGV.pm  1.96  8 years  gdpusch  Modified to gracefully handle Organism directories with no or empty Subsystems/ ...
RASTserver.pm  1.23  9 years  gdpusch  Fixed bugs in and added more support for Viral and Euk jobs.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
SeedUtils.pm  1.58  9 years  gdpusch  Added support for Genetic Code 1.
ToCall.pm  1.11  10 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
SeedV.pm  1.9  9 years  gdpusch  Changed a debugging line to print to STDERR, not STDOUT; print only if VERBOSE.
proml.pm  1.9  9 years  golsen  Minor updates to SEED awareness.
selenoprotein_ref_seq.pm  1.5  9 years  golsen  Add some reference sequences and replace ; with @ in functions.
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
protdist_neighbor.pm  1.1  12 years  golsen  A package for protdist and neighbor PHYLIP trees.
SSU_rRNA_reps.pm  1.3  9 years  golsen  Adjust end of one reference sequence by padding it slightly.
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
gjonewicklib.pm  1.25  9 years  golsen  Change behavior of reroot_tree() to ignore distance if there is only one node.
gjoparseblast.pm  1.8  9 years  golsen  Fix two minor typographical errors in the documentation.
gd_tree_0.pm  1.5  9 years  golsen  Extensive reworking of color management.
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
GenoGraphics.pm  1.24  9 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
ButtonArray.pm  1.1  11 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
gjostat.pm  1.2  9 years  golsen  Integrate the function descriptions into a string returned by the function gjost...
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
ParalogResolution.pm  1.5  10 years  golsen  Modifications to support line-drawing character set in tree printer plots.
SeedAware.pm  1.5  9 years  golsen  Minor change in temporary file name code.
gjogenbank.pm  1.5  9 years  golsen  Handle BASE COUNT Handle entries without a date on the LOCUS line.
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
Classes.pm  1.1  13 years  mkubal  added Organism class
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
ANNO.pm  1.8  9 years  olson  kmer info changes
GenomeMeta.pm  1.16  9 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
gjolib.pm  1.3  9 years  olson  Add more modules to the SAS toolkit.
__init__.py  1.2  13 years  olson  Added license words.
fastDNAml.pm  1.2  13 years  olson  Added license words.
GenomeIDMap.pm  1.4  13 years  olson  Added license words.
KmersOld.pm  1.1  9 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
FIGrpc.pm  1.3  13 years  olson  Added license words.
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
P2P.pm  1.31  13 years  olson  Added license words.
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
FIGGenDB.pm  1.6  13 years  olson  Added license words.
RAST_submission.pm  1.26  9 years  olson  Support -determineFamily
SproutSearch.pm  1.11  13 years  olson  Added license words.
FIGM.pm  1.18  9 years  olson  Add FIGV and FIGM function_of_bulk
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
SampleDir.pm  1.4  9 years  olson  More analysis fixes; user-agent setting.
ProtSims.pm  1.18  9 years  olson  Further uniquify temp files.
FFs.pm  1.49  9 years  olson  Clean up errors.
ClusterWorker.pm  1.2  13 years  olson  Added license words.
Sim.pm  1.14  9 years  olson  Distro fixups
RC.pm  1.2  13 years  olson  Added license words.
Construct.pm  1.2  13 years  olson  Added license words.
UserDB.pm  1.2  13 years  olson  Added license words.
FIGnet.pm  1.2  13 years  olson  Added license words.
SeedHTML.pm  1.3  9 years  olson  More distro fixes.
ErrorMessage.pm  1.2  9 years  olson  remove unused use CGI.
HtmlPageParser.pm  1.2  13 years  olson  Added license words.
FS_RAST.pm  1.31  9 years  olson  re-redirect nap stdout to /dev/null. here's hoping it works on windows still
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
FIGRules.pm  1.54  10 years  olson  Optimize to_structured_english.
KGML.pm  1.4  12 years  olson  Hope college modifications.
Cluster.pm  1.11  13 years  olson  Added license words.
FIGUtilities.pm  1.2  13 years  olson  Added license words.
BerkTable.pm  1.2  9 years  olson  fix arg
NRTools.pm  1.4  10 years  olson  update to new metadata standard
FIG.py  1.13  13 years  olson  Added license words.
FIGtree.pm  1.3  13 years  olson  Added license words.
PinnedRegions.pm  1.34  9 years  olson  fix unlink here too
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
COPYING.TXT  1.1  13 years  olson  add license file
find_special_proteins.pm  1.12  9 years  olson  typod the declaration
FIG2.py  1.2  13 years  olson  Added license words.
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
NCBI_genetic_code.pm  1.3  9 years  olson  add SAS header
Kmers.pm  1.27  8 years  olson  add id to diagnostic
HTML.py  1.6  13 years  olson  Added license words.
tree_utilities.pm  1.20  9 years  olson  Add more modules to the SAS toolkit.
CorrTableEntry.pm  1.4  9 years  olson  Add num_matching_functions for column 19
SproutFIG.pm  1.10  13 years  olson  Added license words.
ClientThing.pm  1.17  9 years  olson  More analysis fixes; user-agent setting.
model.pm  1.35  9 years  olson  make it not a fatal error to not load hope_supersets; this was causing a crash o...
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
Subsystem.pm  1.147  9 years  overbeek  minor fix
FIGAttributes.pm  1.4  10 years  overbeek  get rid of something
tree_neighborhood.pm  1.1  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
gjocolorlib.pm  1.6  9 years  overbeek  fixes to gray
TBLstuff.pm  1.2  10 years  overbeek  minor fixes
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
Clustering.pm  1.6  9 years  overbeek  added double and triple linkage
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
Contigs.pm  1.1  10 years  overbeek  new Contigs.pm and compare_coding.pm
compare_coding.pm  1.9  10 years  overbeek  gene calling stuff
SimFC.pm  1.3  10 years  overbeek  handle deleted FIDs and failure to get translations
SameFunc.pm  1.17  11 years  overbeek  fix to SameFunc.pm
Blast.pm  1.5  11 years  overbeek  close TMP files in Blast.pm
Correspondence.pm  1.4  9 years  overbeek  correct the identity check
PickFeatureSet.pm  1.2  10 years  overbeek  add .html to HTML files
SeedSims.pm  1.1  10 years  overbeek  additions to support partitioning of sims
gjoseqlib.pm  1.23  9 years  overbeek  get rid of Dumper
find_homologs.pm  1.3  10 years  overbeek  update from Gary
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
set_utilities.pm  1.3  9 years  overbeek  make SAS components
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
UnvSubsys.pm  1.20  11 years  paczian  added missing "use HTML;"
Observation.pm  1.82  10 years  paczian  fixed hit and query length (cannot be null)
CompareMR.pm  1.8  10 years  paczian  cutting comments off of functional roles
WebColors.pm  1.14  9 years  paczian  added 'circle' color scheme
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
SS.pm  1.13  9 years  parrello  More documentation cleanup.
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.
Quality.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
Overlap.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
FullLocation.pm  1.25  9 years  parrello  Added a method to compute the total location length.
Markups.pm  1.2  11 years  parrello  Changed POD format for better compatability with Wiki.
ServerThing.pm  1.58  9 years  parrello  New Sapling update support.
BasicLocation.pm  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
PageBuilder.pm  1.14  11 years  parrello  Changed POD format for better compatability with Wiki.
CorrespondenceCache.pm  1.1  9 years  parrello  Updates for new expression-data method.
TransactionProcessor.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
SSserver.pm  1.17  9 years  parrello  Removed from the SAS distribution.
SAPtutorial.pm  1.10  9 years  parrello  Fixed some errors in examples of ID types.
DBKernel.pm  1.63  9 years  parrello  Server database recovery fix.
FFserver.pm  1.23  9 years  parrello  Removed from the SAS distribution.
UserData.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
AliasAnalysis.pm  1.10  9 years  parrello  Fixed the LocusTag match pattern.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
SUPserver.pm  1.1  9 years  parrello  New Sapling update support.
raedraw.pm  1.14  11 years  parrello  Changed POD heading levels.
FudgeTransactions.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
BadCall.pm  1.4  11 years  parrello  Replaced obsolete AddToListMap method.
RemoteCustomAttributes.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
Tracer.pm  1.131  9 years  parrello  Changed a "die" to a "confess".
TestUtils.pm  1.11  9 years  parrello  Fixed display glitch for pure white space.
ACHserver.pm  1.16  9 years  parrello  Removed from the SAS distribution.
SAP.pm  1.125  8 years  parrello  New compare-regions support.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
Stats.pm  1.8  10 years  parrello  Added a method to extract saved messages.
MergeTransactions.pm  1.3  11 years  parrello  Changed POD format for better compatability with Wiki.
ApplyTransactions.pm  1.7  11 years  parrello  Changed POD format for better compatability with Wiki.
Annotation.pm  1.4  11 years  parrello  Added a TITLE statement for the Wiki.
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
Makefile  1.12  10 years  parrello  Removed POD stuff.
FBAMODELserver.pm  1.3  9 years  parrello  Allow alternate forms of parameters to client-side modules.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SAPserver.pm  1.13  9 years  parrello  Allow alternate forms of parameters to client-side modules.
WikiTools.pm  1.8  10 years  parrello  Fixed a glitch in list rendering.
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
NewGenome.pm  1.80  10 years  parrello  Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.
TemplateObject.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
SUP.pm  1.2  9 years  parrello  New methods for alignment data.
SeedEnv.pm  1.3  9 years  parrello  Added ANNOserver. Removed deprecated servers.
SapCompareRegions.pm  1.2  8 years  parrello  New compare-regions support.
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
COserver.pm  1.13  9 years  parrello  Removed from the SAS distribution.
ANNOserver.pm  1.20  8 years  parrello  Fixed a POD error.
ListServerScripts.pm  1.1  9 years  parrello  Added to support server script listing.
JobScheduler.pm  1.8  11 years  parrello  Changed POD headers to work better with the new system.
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
Phage.pm  1.3  9 years  redwards  minor correction
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
raelib.pm  1.44  11 years  redwards  adding a randomizer function
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
AnnoClearinghouse.pm  1.44  10 years  wilke  Modified sql query to ? syntax

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