[Bio] / FigKernelPackages Repository:
ViewVC logotype

Index of /FigKernelPackages

Files shown:190 (Show 199 dead files)
Sticky Tag:


File Rev. Age Author Last log entry
 Parent Directory        
Export/        
tests/        
ACH.pm  1.7  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
ACHserver.pm  1.16  10 years  parrello  Removed from the SAS distribution.
ANNO.pm  1.3  10 years  parrello  Fixed an obscure metabolic reconstruction problem.
ANNOserver.pm  1.11  10 years  disz  Fixed doc for assign_using_prot
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  1.9  11 years  parrello  Fixed the pattern for CMR IDs.
AnnoClearinghouse.pm  1.44  11 years  wilke  Modified sql query to ? syntax
Annotation.pm  1.4  12 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  12 years  parrello  Replaced obsolete AddToListMap method.
BasicLocation.pm  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
BinarySearch.pm  1.1  13 years  overbeek  just add a binary search so I do not have to recode it again
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
ButtonArray.pm  1.1  12 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  10 years  parrello  Removed from the SAS distribution.
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
Classes.pm  1.1  14 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  1.13  10 years  parrello  Fixed to produce a less ugly message when there is no response content from a se...
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.
CompareMR.pm  1.8  11 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  13 years  olson  clone the digest so that checksum() may be called multiple times
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
DBKernel.pm  1.63  10 years  parrello  Server database recovery fix.
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
Diagram.pm  1.17  11 years  parrello  Fixed some bad links.
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
ErrorMessage.pm  1.1  10 years  parrello  Error handling restructure.
FBAMODEL.pm  1.3  10 years  chenry  *** empty log message ***
FBAMODELserver.pm  1.2  10 years  parrello  *** empty log message ***
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
FF.pm  1.33  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
FFs.pm  1.46  11 years  paczian  fixed rast figfam display
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
FIG.pm  1.810  10 years  redwards  adding load_dlits to load_all
FIG.py  1.13  14 years  olson  Added license words.
FIG2.py  1.2  14 years  olson  Added license words.
FIGAttributes.pm  1.4  11 years  overbeek  get rid of something
FIGGenDB.pm  1.6  14 years  olson  Added license words.
FIGM.pm  1.17  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIGMODEL.pm  1.42  10 years  chenry  *** empty log message ***
FIGMODELObject.pm  1.3  11 years  chenry  *** empty log message ***
FIGMODELTable.pm  1.12  10 years  chenry  *** empty log message ***
FIGMODELdatabase.pm  1.3  10 years  chenry  *** empty log message ***
FIGMODELmodel.pm  1.4  10 years  chenry  *** empty log message ***
FIGMODELweb.pm  1.1  10 years  chenry  *** empty log message ***
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  1.92  10 years  olson  Support for Seedviewer Subsystems.pm speedups.
FIG_CGI.pm  1.11  12 years  olson  Add annotation support to FIGV. Add FIGM.
FIGgjo.pm  1.3  13 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  1.24  11 years  overbeek  force frameshifts to be of longer chunks
FigFam.pm  1.78  11 years  arodri7  changed to check if is_deleted_fid in sub new
FigFams.pm  1.56  11 years  overbeek  fixes to support Kmer analysis
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FileIOFunctions.pm  1.11  10 years  chenry  *** empty log message ***
FileLocking.pm  1.2  12 years  olson  add shared locking
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  1.22  10 years  golsen  Remove superfluous references to CGI. Add png format as comments.
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
GenomeMeta.pm  1.15  12 years  olson  oops, these need updated.
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
HTML.pm  1.130  11 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  12 years  parrello  Changed POD headers to work better with the new system.
JulianDay.pm  1.1  11 years  chenry  *** empty log message ***
KGML.pm  1.4  13 years  olson  Hope college modifications.
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
Kmers.pm  1.19  10 years  olson  Support constructor that takes friDB/setIDB/table.binary instead of a kmers dir....
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
Makefile  1.12  11 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
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
NRTools.pm  1.4  11 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  11 years  golsen  Modifications to support line-drawing character set in tree printer plots.
ParseDate.pm  1.1  11 years  chenry  *** empty log message ***
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
PinnedRegions.pm  1.28  10 years  paczian  added location for artificial features
ProtFamLite.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
ProtFamsLite.pm  1.2  11 years  arodri7  added functions and made functions work
ProtSims.pm  1.10  10 years  olson  Distro fixups
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
RAST_submission.pm  1.20  10 years  olson  bugfix
RASTserver.pm  1.16  10 years  disz  Submit doc
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  1.62  10 years  parrello  Added ids_to_annotations method.
SAPserver.pm  1.11  10 years  parrello  Changed to use the default URL if an empty string is specified, for compatibilit...
SAPtutorial.pm  1.9  10 years  parrello  More documentation cleanup.
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  1.2  10 years  golsen  Update to the variable names (for more universal application).
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
Scenario.pm  1.9  10 years  dejongh  new methods
ScriptThing.pm  1.3  10 years  parrello  Added a column parameter to GetBatch.
SeedDas.pm  1.22  13 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
SeedEnv.pm  1.3  10 years  parrello  Added ANNOserver. Removed deprecated servers.
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
SeedUtils.pm  1.29  10 years  dejongh  Removed extraneous curly bracket causing compilation error
SeedV.pm  1.2  10 years  olson  remove Tracer ref
ServerScripts.pm  1.2  10 years  parrello  Final server updates.
ServerThing.pm  1.34  10 years  parrello  Fixed so that the ETracing parameter overrides the environment variable.
Sim.pm  1.14  10 years  olson  Distro fixups
SimFC.pm  1.3  11 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  11 years  parrello  Added a method to extract saved messages.
Subsystem.pm  1.145  10 years  redwards  moving error messages from STDOUT to STDERR
TBLstuff.pm  1.2  11 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  11 years  chenry  *** empty log message ***
ToCall.pm  1.11  11 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
Tracer.pm  1.129  10 years  parrello  Fixed race condition while checking the emergency tracing file.
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
UnvSubsys.pm  1.20  12 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  1.12  10 years  dejongh  add many_except_gray and rgb_to_hex
WikiTools.pm  1.8  11 years  parrello  Fixed a glitch in list rendering.
__init__.py  1.2  14 years  olson  Added license words.
clustaltree.pm  1.3  11 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
collect_related_sequences.pm  1.5  13 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
compare_coding.pm  1.9  11 years  overbeek  gene calling stuff
display_related_genomes.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
fastDNAml.pm  1.2  14 years  olson  Added license words.
find_homologs.pm  1.3  11 years  overbeek  update from Gary
find_special_proteins.pm  1.10  11 years  overbeek  add the ability to find TIF3
gd_tree_0.pm  1.2  11 years  golsen  Add PNG format trees to fid_checked.cgi. Add support elsewhere. Some code clea...
gjoalign2html.pm  1.4  10 years  golsen  Fix problem with line wrap in the alignment. Change all #abc colors to #aabbcc f...
gjoalignment.pm  1.28  10 years  overbeek  mark as SAS component
gjocolorlib.pm  1.3  11 years  golsen  Added more named colors from X11, but these are almost certainly based on a diff...
gjolib.pm  1.3  10 years  olson  Add more modules to the SAS toolkit.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjonewicklib.pm  1.17  10 years  olson  Add more modules to the SAS toolkit.
gjoparseblast.pm  1.7  10 years  overbeek  add as SAS components
gjophylip.pm  1.2  10 years  golsen  Add and/or update routines to support bootstrapping and bootstrap consensus tree...
gjoseqlib.pm  1.17  10 years  golsen  Add new function for assessing similarity of aligned sequences. Fix a bug in pri...
gjostat.pm  1.1  10 years  golsen  Adding a library of useful statistical functions.
model.pm  1.34  10 years  dejongh  fix reference
proml.pm  1.9  10 years  golsen  Minor updates to SEED awareness.
protdist_neighbor.pm  1.1  13 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  12 years  parrello  Changed POD heading levels.
raelib.pm  1.44  12 years  redwards  adding a randomizer function
representative_sequences.pm  1.11  10 years  golsen  Minor changes in style.
selenoprotein_ref_seq.pm  1.5  10 years  golsen  Add some reference sequences and replace ; with @ in functions.
set_utilities.pm  1.2  14 years  olson  Added license words.
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
tree_utilities.pm  1.20  10 years  olson  Add more modules to the SAS toolkit.

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3