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File Rev. Age Author Last log entry
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ACH.pm  1.7  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
ACHserver.pm  1.16  9 years  parrello  Removed from the SAS distribution.
ALITRE.pm  1.4  8 years  parrello  Added get_projections.
ALITREserver.pm  1.1  8 years  parrello  New alignment/tree server stuff.
ANNO.pm  1.11  8 years  olson  Annotation server updates (replace inline code with KmerMgr). Add tests.
ANNOserver.pm  1.24  8 years  olson  if -assignToAll is used, chunk the input into much smaller chunks to reduce per-...
AT.pm  1.6  8 years  fangfang  add blast function
ATserver.pm  1.2  8 years  fangfang  default url set to biobig
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
AliTreeIdConvert.pm  1.1  8 years  golsen  Functions for interconverting MD5 and peg ids of alignments and trees in the SEE...
AliTreeSims.pm  1.8  7 years  fangfang  fixed a variable name
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliasAnalysis.pm  1.12  7 years  olson  add sas comp
AlignTree.pm  1.41  8 years  fangfang  fixed bug with aligning seq ends with clustal
AlignsAndTrees.pm  1.12  7 years  golsen  Some minor changes. These become moot, but ....
AlignsAndTreesServer.pm  1.11  7 years  golsen  Big performance inprovement in finding the roles in a tree.
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  11 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  1.23  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
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
BlankSVP.pm  1.1  7 years  olson  Script & infrastructure for creating easy seedviewer pages.
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...
CGIAlignTreeViewer.pm  1.8  7 years  golsen  Made the target of the fid links _blank.
CO.pm  1.6  9 years  disz  changed doc to say XXserver->new() insetad of XX->new
COPYING.TXT  1.1  13 years  olson  add license file
COserver.pm  1.13  9 years  parrello  Removed from the SAS distribution.
ChromosomalClusters.pm  1.11  8 years  parrello  Added "roles_to_proteins" method.
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  1.29  8 years  olson  add pubseed test URL retry on connection refused, this gets around glitches on t...
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
Cluster.pm  1.11  13 years  olson  Added license words.
ClusterWorker.pm  1.2  13 years  olson  Added license words.
Clustering.pm  1.6  8 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  13 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  1.5  8 years  overbeek  add 20th column - clear_bbhs
Correspondence.pm  1.4  8 years  overbeek  correct the identity check
CorrespondenceCache.pm  1.2  8 years  parrello  Added experiment filter to "fid_experiments". Fixed correspondence cache to work...
DBKernel.pm  1.70  8 years  parrello  Conversion to support Postgres for ERDB.
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
Diagram.pm  1.19  8 years  redwards  fixing jpeg images
Dlits.pm  1.2  8 years  olson  add new dlit / pmid stuff
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.
ExpressionDir.pm  1.12  7 years  olson  add compute_pearson_corr
FBAMODELserver.pm  1.5  8 years  chenry  Moving FBAMODELserver.pm to FigKernelPackages, and changing URL.
FC.pm  1.21  9 years  parrello  Fixed a bug in "co_occurrence_evidence".
FF.pm  1.35  8 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  1.858  7 years  disz  Back out assign log code
FIG.py  1.13  13 years  olson  Added license words.
FIG2.py  1.2  13 years  olson  Added license words.
FIGAttributes.pm  1.4  10 years  overbeek  get rid of something
FIGGenDB.pm  1.6  13 years  olson  Added license words.
FIGM.pm  1.19  8 years  olson  Don't bail on creating a FIGM if one of hte FIGV creations fails.
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
FIGRules.pm  1.56  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGStatisticalModels.pm  1.7  8 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
FIGUtilities.pm  1.2  13 years  olson  Added license words.
FIGV.pm  1.99  8 years  olson  Ick, fix namespace trample.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGgjo.pm  1.5  7 years  golsen  Support for better role coloring and formatting.
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
FIGnet.pm  1.2  13 years  olson  Added license words.
FIGrpc.pm  1.3  13 years  olson  Added license words.
FIGtree.pm  1.3  13 years  olson  Added license words.
FS_RAST.pm  1.37  7 years  overbeek  force scratch to get passed
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
FudgeTransactions.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.
GenoGraphics.pm  1.24  9 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
GenomeIDMap.pm  1.4  13 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  1.135  7 years  golsen  Some new JavaScript buttons for checkboxes (check to first marked).
HTML.py  1.6  13 years  olson  Added license words.
HtmlPageParser.pm  1.2  13 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  1.10  8 years  olson  Put. The Scheduler. Back.
KGML.pm  1.4  12 years  olson  Hope college modifications.
KGMLData.pm  1.4  11 years  dejongh  Hope College updates
KmerMgr.pm  1.4  8 years  olson  fix bug in assignToAll
Kmers.pm  1.31  7 years  olson  Turn some fatal errors into empty returns. Fix figfam counts to take into accoun...
KmersOld.pm  1.1  9 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
LinksUI.pm  1.12  7 years  overbeek  new UI
ListServerScripts.pm  1.2  8 years  parrello  Fixed to point to PUBSEED server for documentation.
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
MD5Computer.pm  1.4  8 years  parrello  First pass on new version of MD5 identifiers.
MSSeedSupport.pm  1.1  7 years  devoid  Adding MSSeedSupport, a SVR package for ModelSEED to support genomes from RAST.
Makefile  1.14  8 years  olson  Annotation server updates (replace inline code with KmerMgr). Add tests.
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
Markups.pm  1.2  11 years  parrello  Changed POD format for better compatability with Wiki.
MergeTransactions.pm  1.3  11 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
NCBI_taxonomy.pm  1.4  8 years  golsen  Add more formats in which abbreviated lineages can be returned. Add long form of...
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  1.83  8 years  redwards  correcting web links
OddStarts_ref.pm  1.1  10 years  overbeek  add the ability to find TIF3
Overlap.pm  1.4  11 years  parrello  Changed POD format for better compatability with Wiki.
P2P.pm  1.31  13 years  olson  Added license words.
P2Pupdate.pm  1.64  8 years  olson  Fix indexing upon subsystem installation
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
PageBuilder.pm  1.15  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ParalogResolution.pm  1.6  8 years  golsen  Add a fraction identity filter of finding paralogs.
PartitionSeqs.pm  1.3  10 years  overbeek  return either scalar or list
PersistentSets.pm  1.3  8 years  disz  filled in all functions
Phage.pm  1.3  8 years  redwards  minor correction
PickFeatureSet.pm  1.2  10 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.35  8 years  olson  Add "collapse identical tax-id" option to compared region display.
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  1.20  8 years  gdpusch  Turn off the annoying and confusing "Blat returns 0" diagnostic message unless $...
Quality.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
RAST_submission.pm  1.31  8 years  olson  Fix to change in NCBI web pages.
RASTserver.pm  1.24  8 years  olson  Add kmerDataset selection support.
RC.pm  1.9  7 years  overbeek  UI routines
README  1.1.1.1  15 years  efrank   import
ReactionPath.pm  1.1  8 years  parrello  Added new method to compute reaction paths.
RemoteCustomAttributes.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
RoleRule.pm  1.1  8 years  parrello  New modules for analyzing protein family functions.
RoleRuleSubstring.pm  1.1  8 years  parrello  New modules for analyzing protein family functions.
SAP.pm  1.180  7 years  parrello  Added some new chemistry methods.
SAPserver.pm  1.14  8 years  parrello  Support for local SQLite servers.
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  9 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  1.3  7 years  parrello  Removed obsolete alignment stuff.
SUPserver.pm  1.1  8 years  parrello  New Sapling update support.
SameFunc.pm  1.17  11 years  overbeek  fix to SameFunc.pm
SampleDir.pm  1.4  8 years  olson  More analysis fixes; user-agent setting.
SapCompareRegions.pm  1.5  8 years  olson  Actually commit the bugfix I made.
Scenario.pm  1.10  8 years  dejongh  change scenario handling to use path_info.txt
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
SeedAware.pm  1.8  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedEnv.pm  1.4  8 years  olson  Use new path to FBAModelSerer
SeedHTML.pm  1.3  9 years  olson  More distro fixes.
SeedSearch.pm  1.3  8 years  olson  OK, index rebuilt, we can switch to the new encoding now.
SeedSims.pm  1.1  10 years  overbeek  additions to support partitioning of sims
SeedUtils.pm  1.64  7 years  fangfang  Support large blast database with segmented db.0n.pin files in verify_db().
SeedV.pm  1.10  8 years  olson  fix nasty boundary bug
ServComplex.pm  1.3  7 years  disz  Fix links
ServFIGfam.pm  1.4  7 years  disz  Fix links
ServFeature.pm  1.12  7 years  overbeek  UI routines
ServGenome.pm  1.7  7 years  disz  Added find gene in organism link
ServOTU.pm  1.4  7 years  overbeek  mods
ServReaction.pm  1.2  7 years  disz  NewInterface Stuff
ServRole.pm  1.3  7 years  disz  Fix links
ServSubsysRow.pm  1.8  7 years  disz  Fix links
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
ServerThing.pm  1.84  8 years  olson  Add vhost, fast/slow queue support
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
Sim.pm  1.16  7 years  golsen  Somme new functions for building a sim object from data.
Sim2.pm  1.1  8 years  overbeek  tree sims
SimFC.pm  1.3  10 years  overbeek  handle deleted FIDs and failure to get translations
SimsTable.pm  1.1  7 years  golsen  Support for a new sims table format.
SproutFIG.pm  1.10  13 years  olson  Added license words.
SproutSearch.pm  1.11  13 years  olson  Added license words.
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
Stats.pm  1.9  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
Subsystem.pm  1.154  8 years  olson  forgot the delete on subsystem_nonaux_role
SubsystemPrimer.pm  1.8  8 years  overbeek  better help
SubsystemPrimer2SS.pm  1.1  8 years  overbeek  convert requests to subsystems
TBLstuff.pm  1.2  10 years  overbeek  minor fixes
TableCell.pm  1.1  7 years  golsen  Support for a new sims table format.
TemplateObject.pm  1.8  11 years  parrello  Changed POD format for better compatability with Wiki.
TestUtils.pm  1.12  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ToCall.pm  1.12  8 years  gdpusch  Modified to allow FIGfam IDs with arbitrarily many digits, and to fail safe if F...
Tracer.pm  1.134  7 years  olson  windows doesn't have getpwuid
TransactionProcessor.pm  1.6  11 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  13 years  olson  Added license words.
UserData.pm  1.6  11 years  parrello  Changed POD format for better compatability with Wiki.
WebColors.pm  1.16  8 years  paczian  re-added circle color scheme
WikiTools.pm  1.8  10 years  parrello  Fixed a glitch in list rendering.
WriteEMBL.pm  1.1  8 years  gdpusch  Initial checkin --- probably still needs work.
WriteGenbank.pm  1.2  8 years  gdpusch  Forgot trailing "1;" :(
__init__.py  1.2  13 years  olson  Added license words.
align_and_tree_test.pm  1.1  8 years  golsen  Temp code for using DBMS version of alignment and tree access.
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  1.10  8 years  golsen  Integrate use of SeedAware.pm
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
fastDNAml.pm  1.2  13 years  olson  Added license words.
ffxtree.pm  1.28  7 years  fangfang  add taxonomy color support for trees with organism ID tips
find_homologs.pm  1.4  8 years  golsen  use SeedAware Many changes in details of code.
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  1.7  8 years  golsen  Change − to −
gjoalignandtree.pm  1.19  7 years  fangfang  Remove debugging code
gjoalignment.pm  1.40  8 years  fangfang  add option --anysymbol for align_with_mafft
gjocodonlib.pm  1.3  8 years  golsen  Many changes and updates in organization of the file. A few new useful function...
gjocolorlib.pm  1.7  8 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
gjogenbank.pm  1.10  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjogff.pm  1.2  8 years  golsen  Changes to fix some bugs in GenBank format reading and writing. Changes to deal ...
gjolib.pm  1.4  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
gjonativecodonlib.pm  1.2  8 years  golsen  Forgot the SAS component lines.
gjonewicklib.pm  1.29  8 years  golsen  Add support for a scale bar in printer plot trees. Add -s (scale bar) and -S (sc...
gjoparseblast.pm  1.8  9 years  golsen  Fix two minor typographical errors in the documentation.
gjophylip.pm  1.9  8 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
gjosegmentlib.pm  1.2  8 years  golsen  Forgot the SAS component lines.
gjoseqlib.pm  1.27  7 years  golsen  Improve error handling in read_fasta.
gjostat.pm  1.3  8 years  golsen  Convert die to confess.
model.pm  1.36  8 years  dejongh  change scenario handling to use path_info.txt
proml.pm  1.9  9 years  golsen  Minor updates to SEED awareness.
protdist_neighbor.pm  1.2  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
pyrrolysylprotein_ref_seq.pm  1.1  11 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  1.46  8 years  redwards  adding unzip
representative_sequences.pm  1.19  8 years  golsen  Make $_ local so that it does not clobber the global value when changed.
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  9 years  olson  Add more modules to the SAS toolkit.

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