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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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ACH.pm  1.7  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
ACHserver.pm  1.16  9 years  parrello  Removed from the SAS distribution.
ANNO.pm  1.8  9 years  olson  kmer info changes
ANNOserver.pm  1.20  9 years  parrello  Fixed a POD error.
AT.pm  1.5  9 years  fangfang  always return psiblast search history
ATserver.pm  1.2  9 years  fangfang  default url set to biobig
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  1.10  9 years  parrello  Fixed the LocusTag match pattern.
AlignTree.pm  1.19  9 years  fangfang  update comments
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.
BerkTable.pm  1.2  9 years  olson  fix arg
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  1.6  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
COPYING.TXT  1.1  14 years  olson  add license file
COserver.pm  1.13  9 years  parrello  Removed from the SAS distribution.
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
Classes.pm  1.1  13 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.
ClientThing.pm  1.17  9 years  olson  More analysis fixes; user-agent setting.
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.
Clustering.pm  1.6  9 years  overbeek  added double and triple linkage
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
CorrTableEntry.pm  1.4  9 years  olson  Add num_matching_functions for column 19
Correspondence.pm  1.4  9 years  overbeek  correct the identity check
CorrespondenceCache.pm  1.1  9 years  parrello  Updates for new expression-data method.
DBKernel.pm  1.63  10 years  parrello  Server database recovery fix.
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.
ErrorMessage.pm  1.2  9 years  olson  remove unused use CGI.
FBAMODEL.pm  1.14  9 years  dejongh  fix return
FBAMODELserver.pm  1.3  9 years  parrello  Allow alternate forms of parameters to client-side modules.
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
FF.pm  1.35  9 years  disz  FigFam 6 digit fix
FFs.pm  1.49  9 years  olson  Clean up errors.
FFserver.pm  1.23  9 years  parrello  Removed from the SAS distribution.
FIG.pm  1.820  9 years  disz  FIGFAM 6 digit problem
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  1.18  9 years  olson  Add FIGV and FIGM function_of_bulk
FIGMODEL.pm  1.70  9 years  dejongh  use a colon to split environmental variable fields rather than a semi-colon, bec...
FIGMODELObject.pm  1.4  9 years  chenry  Implemented new function to change the name of a date header.
FIGMODELTable.pm  1.15  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
FIGMODELmodel.pm  1.30  9 years  chenry  Bug fixes to pipeline.
FIGMODELweb.pm  1.15  9 years  chenry  Adding code to support model curation via upload.
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  1.96  9 years  gdpusch  Modified to gracefully handle Organism directories with no or empty Subsystems/ ...
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  1.31  9 years  olson  re-redirect nap stdout to /dev/null. here's hoping it works on windows still
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FileIOFunctions.pm  1.14  9 years  chenry  Moving some functions over to FIGMODEL.
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
FullLocation.pm  1.25  10 years  parrello  Added a method to compute the total location length.
GenoGraphics.pm  1.24  9 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
GenomeLists.pm  1.2  11 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeMeta.pm  1.16  9 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
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  1.27  9 years  olson  add id to diagnostic
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
ListServerScripts.pm  1.1  9 years  parrello  Added to support server script listing.
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
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
NCBI_genetic_code.pm  1.3  9 years  olson  add SAS 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
Phage.pm  1.3  9 years  redwards  minor correction
PickFeatureSet.pm  1.2  10 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.34  9 years  olson  fix unlink here too
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  1.18  9 years  olson  Further uniquify temp files.
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
RAST_submission.pm  1.26  9 years  olson  Support -determineFamily
RASTserver.pm  1.23  9 years  gdpusch  Fixed bugs in and added more support for Viral and Euk jobs.
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  1.125  9 years  parrello  New compare-regions support.
SAPserver.pm  1.13  9 years  parrello  Allow alternate forms of parameters to client-side modules.
SAPtutorial.pm  1.10  9 years  parrello  Fixed some errors in examples of ID types.
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
SS.pm  1.13  10 years  parrello  More documentation cleanup.
SSU_rRNA_reps.pm  1.3  9 years  golsen  Adjust end of one reference sequence by padding it slightly.
SSserver.pm  1.17  9 years  parrello  Removed from the SAS distribution.
SUP.pm  1.2  9 years  parrello  New methods for alignment data.
SUPserver.pm  1.1  9 years  parrello  New Sapling update support.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
SampleDir.pm  1.4  9 years  olson  More analysis fixes; user-agent setting.
SapCompareRegions.pm  1.2  9 years  parrello  New compare-regions support.
Scenario.pm  1.9  10 years  dejongh  new methods
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
SeedAware.pm  1.5  9 years  golsen  Minor change in temporary file name code.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedEnv.pm  1.3  9 years  parrello  Added ANNOserver. Removed deprecated servers.
SeedHTML.pm  1.3  9 years  olson  More distro fixes.
SeedSims.pm  1.1  10 years  overbeek  additions to support partitioning of sims
SeedUtils.pm  1.58  9 years  gdpusch  Added support for Genetic Code 1.
SeedV.pm  1.9  9 years  gdpusch  Changed a debugging line to print to STDERR, not STDOUT; print only if VERBOSE.
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
ServerThing.pm  1.58  9 years  parrello  New Sapling update support.
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
Sim.pm  1.14  9 years  olson  Distro fixups
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  1.147  9 years  overbeek  minor fix
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  1.11  10 years  parrello  Fixed display glitch for pure white space.
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  1.131  9 years  parrello  Changed a "die" to a "confess".
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  1.14  9 years  paczian  added 'circle' color scheme
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  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
compare_coding.pm  1.9  10 years  overbeek  gene calling stuff
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
fastDNAml.pm  1.2  14 years  olson  Added license words.
ffxtree.pm  1.10  9 years  fangfang  update sas component
find_homologs.pm  1.3  10 years  overbeek  update from Gary
find_special_proteins.pm  1.12  9 years  olson  typod the declaration
gd_tree_0.pm  1.5  9 years  golsen  Extensive reworking of color management.
gjoalign2html.pm  1.5  9 years  fangfang  SAS component
gjoalignandtree.pm  1.7  9 years  fangfang  change to verify_db
gjoalignment.pm  1.35  9 years  fangfang  use SeedAware::run_gathering_output to handle muscle version information
gjocolorlib.pm  1.6  9 years  overbeek  fixes to gray
gjogenbank.pm  1.5  9 years  golsen  Handle BASE COUNT Handle entries without a date on the LOCUS line.
gjolib.pm  1.3  10 years  olson  Add more modules to the SAS toolkit.
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
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.
gjophylip.pm  1.6  9 years  fangfang  SAS component
gjoseqlib.pm  1.23  9 years  overbeek  get rid of Dumper
gjostat.pm  1.2  9 years  golsen  Integrate the function descriptions into a string returned by the function gjost...
model.pm  1.35  9 years  olson  make it not a fatal error to not load hope_supersets; this was causing a crash o...
proml.pm  1.9  9 years  golsen  Minor updates to SEED awareness.
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  1.16  9 years  fangfang  handle undefined return value from pack_sequences in req_seq and rep_seq_2
selenoprotein_ref_seq.pm  1.5  9 years  golsen  Add some reference sequences and replace ; with @ in functions.
set_utilities.pm  1.3  9 years  overbeek  make SAS components
tree_neighborhood.pm  1.1  12 years  overbeek  add tree_neighbors and latest phylogeny stuff
tree_utilities.pm  1.20  10 years  olson  Add more modules to the SAS toolkit.

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