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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  1.6  8 years  golsen  Add a new selenoprotein type.
representative_sequences.pm  1.20  8 years  golsen  Minor code reformat.
raelib.pm  1.46  9 years  redwards  adding unzip
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  1.2  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
proml.pm  1.9  10 years  golsen  Minor updates to SEED awareness.
model.pm  1.36  9 years  dejongh  change scenario handling to use path_info.txt
gjostat.pm  1.3  9 years  golsen  Convert die to confess.
gjoseqlib.pm  1.28  8 years  overbeek  add write_fasta as synonym for print_alignment_as_fasta
gjosegmentlib.pm  1.2  9 years  golsen  Forgot the SAS component lines.
gjophylip.pm  1.9  9 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
gjoparseblast.pm  1.8  9 years  golsen  Fix two minor typographical errors in the documentation.
gjonewicklib.pm  1.30  8 years  golsen  Support for embedding links in printer-plot tree.
gjonativecodonlib.pm  1.2  9 years  golsen  Forgot the SAS component lines.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjolib.pm  1.4  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjogff.pm  1.2  9 years  golsen  Changes to fix some bugs in GenBank format reading and writing. Changes to deal ...
gjogenbank.pm  1.10  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjocolorlib.pm  1.7  9 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
gjocodonlib.pm  1.3  9 years  golsen  Many changes and updates in organization of the file. A few new useful function...
gjoalignment.pm  1.40  9 years  fangfang  add option --anysymbol for align_with_mafft
gjoalignandtree.pm  1.19  8 years  fangfang  Remove debugging code
gjoalign2html.pm  1.9  8 years  fangfang  Fixed support for showing literal sequences with spaces and characters that need...
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  1.6  8 years  golsen  Minor modifications to code to improve behavior in rRNA finding (if I remember c...
ffxtree.pm  1.28  8 years  fangfang  add taxonomy color support for trees with organism ID tips
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  1.10  9 years  golsen  Integrate use of SeedAware.pm
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
clustaltree.pm  1.3  11 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
bidir_best_hits.pm  1.1  8 years  golsen  Code for bidirectional best hits in a form used by codon usage analysis software...
align_and_tree_test.pm  1.1  9 years  golsen  Temp code for using DBMS version of alignment and tree access.
__init__.py  1.2  14 years  olson  Added license words.
WriteGenbank.pm  1.2  9 years  gdpusch  Forgot trailing "1;" :(
WriteEMBL.pm  1.1  8 years  gdpusch  Initial checkin --- probably still needs work.
WikiTools.pm  1.8  11 years  parrello  Fixed a glitch in list rendering.
WebColors.pm  1.16  9 years  paczian  re-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.
UpdateServer.pm  1.2  8 years  disz  Remove Sapling stuff`
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  1.134  8 years  olson  windows doesn't have getpwuid
ToCall.pm  1.12  8 years  gdpusch  Modified to allow FIGfam IDs with arbitrarily many digits, and to fail safe if F...
TestUtils.pm  1.12  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TableCell.pm  1.1  8 years  golsen  Support for a new sims table format.
TBLstuff.pm  1.2  11 years  overbeek  minor fixes
SubsystemPrimer2SS.pm  1.2  8 years  overbeek  update index
SubsystemPrimer.pm  1.8  8 years  overbeek  better help
Subsystem.pm  1.154  9 years  olson  forgot the delete on subsystem_nonaux_role
Stats.pm  1.10  8 years  parrello  KBase changes and C-based YAML.
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.
SimsTable.pm  1.4  8 years  golsen  Just a minor change to prevent confusion between old and new versions of a list....
SimFC.pm  1.3  11 years  overbeek  handle deleted FIDs and failure to get translations
Sim2.pm  1.1  9 years  overbeek  tree sims
Sim.pm  1.16  8 years  golsen  Somme new functions for building a sim object from data.
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
ServerThing.pm  1.89  8 years  parrello  Changed a use to a require for performance.
ServerScripts.pm  1.5  10 years  overbeek  add summarize_MG_output
ServSubsysRow.pm  1.11  8 years  overbeek  minor fixes
ServRole.pm  1.5  8 years  overbeek  fixes to make Sapling version work
ServReaction.pm  1.5  8 years  overbeek  fixes
ServOTU.pm  1.8  8 years  overbeek  minor fixes
ServIndex.pm  1.2  8 years  overbeek  starting to work
ServGenome.pm  1.15  8 years  overbeek  pass user
ServFeature.pm  1.24  8 years  overbeek  allow updates
ServFIGfam.pm  1.7  8 years  overbeek  minor changes
ServComplex.pm  1.6  8 years  overbeek  fixes to make Sapling version work
SeedV.pm  1.10  9 years  olson  fix nasty boundary bug
SeedUtils.pm  1.65  8 years  overbeek  make putative hypothetical
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
SeedSearch.pm  1.3  9 years  olson  OK, index rebuilt, we can switch to the new encoding now.
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
SeedEnv.pm  1.4  9 years  olson  Use new path to FBAModelSerer
SeedDas.pm  1.22  13 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedAware.pm  1.8  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
Scenario.pm  1.10  9 years  dejongh  change scenario handling to use path_info.txt
SapCompareRegions.pm  1.5  9 years  olson  Actually commit the bugfix I made.
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  1.3  8 years  parrello  Removed obsolete alignment stuff.
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
SSU_rRNA_reps.pm  1.4  8 years  golsen  Representatives for finding SSU rRNA sequences.
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  1.14  9 years  parrello  Support for local SQLite servers.
SAP.pm  1.186  8 years  olson  bugfix
RoleRuleSubstring.pm  1.1  9 years  parrello  New modules for analyzing protein family functions.
RoleRule.pm  1.1  9 years  parrello  New modules for analyzing protein family functions.
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
ReactionPath.pm  1.1  9 years  parrello  Added new method to compute reaction paths.
README  1.1.1.1  16 years  efrank   import
RC.pm  1.33  8 years  disz  FIxed genome_data call
RASTserver.pm  1.24  8 years  olson  Add kmerDataset selection support.
RAST_submission.pm  1.31  8 years  olson  Fix to change in NCBI web pages.
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
ProtSims.pm  1.20  8 years  gdpusch  Turn off the annoying and confusing "Blat returns 0" diagnostic message unless $...
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  1.36  8 years  olson  Use -FF for blastall runs in pinned regions.
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
Phage.pm  1.3  9 years  redwards  minor correction
PersistentSets.pm  1.3  8 years  disz  filled in all functions
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
ParalogResolution.pm  1.6  8 years  golsen  Add a fraction identity filter of finding paralogs.
PageBuilder.pm  1.15  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
P2Pupdate.pm  1.64  9 years  olson  Fix indexing upon subsystem installation
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  1.83  9 years  redwards  correcting web links
NewGenome.pm  1.82  8 years  gdpusch  Fixed 0 == undef bug on contig IDs.
NRTools.pm  1.4  11 years  olson  update to new metadata standard
NCBI_taxonomy.pm  1.4  9 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
NCBI_genetic_code.pm  1.4  8 years  golsen  Add start codons to genetic code data.
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  1.14  8 years  olson  Annotation server updates (replace inline code with KmerMgr). Add tests.
MSSeedSupport.pm  1.1  8 years  devoid  Adding MSSeedSupport, a SVR package for ModelSEED to support genomes from RAST.
MD5Computer.pm  1.4  8 years  parrello  First pass on new version of MD5 identifiers.
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
ListServerScripts.pm  1.2  9 years  parrello  Fixed to point to PUBSEED server for documentation.
LinksUI.pm  1.20  8 years  overbeek  try to pass user correctly
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
Kmers.pm  1.32  8 years  redwards  adding details to the assign to DNA for kmer calls
KmerMgr.pm  1.4  8 years  olson  fix bug in assignToAll
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  13 years  olson  Hope college modifications.
KBRpcContext.pm  1.1  8 years  olson  KB context object for RPC support.
JobScheduler.pm  1.10  9 years  olson  Put. The Scheduler. Back.
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  1.135  8 years  golsen  Some new JavaScript buttons for checkboxes (check to first marked).
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: ------------------------------------------------...
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FS_RAST.pm  1.38  8 years  overbeek  fixed frameshift code
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  1.5  8 years  golsen  Support for better role coloring and formatting.
FIG_CGI.pm  1.11  12 years  olson  Add annotation support to FIGV. Add FIGM.
FIGV.pm  1.99  9 years  olson  Ick, fix namespace trample.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGStatisticalModels.pm  1.7  9 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
FIGRules.pm  1.56  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGM.pm  1.19  9 years  olson  Don't bail on creating a FIGM if one of hte FIGV creations fails.
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  1.875  8 years  overbeek  fixes to merge real and estimated subsystems
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
FFs.pm  1.51  8 years  redwards  adding details to the assign to DNA for kmer calls
FFB3.pm  1.1  8 years  olson  figfam build helper module
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  1.5  8 years  chenry  Moving FBAMODELserver.pm to FigKernelPackages, and changing URL.
ExpressionDir.pm  1.12  8 years  olson  add compute_pearson_corr
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.
Dlits.pm  1.5  8 years  parrello  Added some POD comments.
Diagram.pm  1.21  8 years  olson  patch to missing ref
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
DBKernel.pm  1.73  8 years  olson  add new method
Corresponds.pm  1.1  8 years  overbeek  finally debugged
CorrespondenceCache.pm  1.2  9 years  parrello  Added experiment filter to "fid_experiments". Fixed correspondence cache to work...
Correspondence.pm  1.4  9 years  overbeek  correct the identity check
CorrTableEntry.pm  1.5  9 years  overbeek  add 20th column - clear_bbhs
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  1.30  8 years  parrello  KBase changes and C-based YAML.
Clearinghouse.py  1.12  8 years  olson  Use new SS clearinghouse on pubseed.
Clearinghouse.pm  1.6  8 years  olson  Use new SS clearinghouse on pubseed.
Classes.pm  1.1  14 years  mkubal  added Organism class
ChromosomalClusters.pm  1.11  9 years  parrello  Added "roles_to_proteins" method.
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
CGIAlignTreeViewer.pm  1.16  8 years  golsen  Make color by residue default for aligments.
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
BlastInterface.pm  1.2  8 years  overbeek  added a smidge of documentation
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
BlankSVP.pm  1.1  8 years  olson  Script & infrastructure for creating easy seedviewer pages.
BinarySearch.pm  1.1  13 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  1.23  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
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
AlignsAndTreesServer.pm  1.14  8 years  golsen  Change alignment order to match the (aesthetic) tree order.
AlignsAndTrees.pm  1.14  8 years  fangfang  Support for quick retrieval of trees via freeze/thaw.
AlignTree.pm  1.42  8 years  fangfang  update
AliasAnalysis.pm  1.13  8 years  parrello  Added IMG and ERIC.
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTreeSims.pm  1.8  8 years  fangfang  fixed a variable name
AliTreeIdConvert.pm  1.1  9 years  golsen  Functions for interconverting MD5 and peg ids of alignments and trees in the SEE...
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  1.6  9 years  fangfang  add blast function
ANNOserver.pm  1.25  8 years  olson  Add support for YAML::XS.
ANNO.pm  1.11  8 years  olson  Annotation server updates (replace inline code with KmerMgr). Add tests.
ALITREserver.pm  1.1  9 years  parrello  New alignment/tree server stuff.
ALITRE.pm  1.4  8 years  parrello  Added get_projections.
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
5S_rRNA_reps.pm  1.1  8 years  golsen  A set of 5S rRNA sequences.

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