[Bio] / FigKernelPackages Repository:
ViewVC logotype

Index of /FigKernelPackages

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


File Rev. Age Author Last log entry
 Parent Directory        
Export/        
tests/        
RAST_submission.pm  1.28  9 years  olson  typofix
FS_RAST.pm  1.33  9 years  gdpusch  Removed duplicate declaration line.
ExpressionDir.pm  1.5  9 years  olson  update
FIG.pm  1.824  9 years  gdpusch  Hack to prevent GC=1 from blowing up.
AliasAnalysis.pm  1.11  9 years  parrello  Updates for single-genome loader.
ServerThing.pm  1.59  9 years  parrello  Fix to reduce Sapling dependence.
NCBI_taxonomy.pm  1.3  9 years  golsen  Change LineageShort to LineageAbbrev, to better match NCBI terminology.
WebColors.pm  1.15  9 years  chenry  Updating ModelSEED scripts with suuport for new PPO DB
find_homologs.pm  1.4  9 years  golsen  use SeedAware Many changes in details of code.
gjophylip.pm  1.9  9 years  golsen  Fix a cosmetic issue in the cleaning of sequences for PHYLIP.
compare_coding.pm  1.10  9 years  golsen  Integrate use of SeedAware.pm
gjogff.pm  1.1  9 years  golsen  Some basic code for reading gff files. Details will almost certainly change.
gjoseqlib.pm  1.24  9 years  golsen  Some minor changes to translation with user codes (saving the ambiguous codon tr...
gjogenbank.pm  1.7  9 years  golsen  Add support for writing GenBank entries. A few bug fixes to reading entries. Cle...
gjoalignandtree.pm  1.14  9 years  fangfang  update options
AlignTree.pm  1.24  9 years  fangfang  update default values
ffxtree.pm  1.13  9 years  fangfang  update
ProtSims.pm  1.19  9 years  overbeek  turn off debugging print
DBKernel.pm  1.65  9 years  olson  Caching / FCGI speedup modifications.
model.pm  1.36  9 years  dejongh  change scenario handling to use path_info.txt
Scenario.pm  1.10  9 years  dejongh  change scenario handling to use path_info.txt
SAPserver.pm  1.14  9 years  parrello  Support for local SQLite servers.
ClientThing.pm  1.18  9 years  parrello  Support for local SQLite servers.
SAP.pm  1.126  9 years  parrello  Added some support for the SQLite stuff.
Kmers.pm  1.28  9 years  olson  fix off-by-one
FIGStatisticalModels.pm  1.7  9 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
Makefile  1.13  9 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
WriteGenbank.pm  1.1  9 years  gdpusch  Initial checkin of module to facilitate writeing GenBank output.
representative_sequences.pm  1.17  9 years  golsen  Many updates to make better use of SeedAware.pm.
gjoalignment.pm  1.36  9 years  golsen  Cleaner handling of external binary programs.
SeedAware.pm  1.6  9 years  golsen  Add a path search function to executable_for(), so that it returns undef if the ...
gjostat.pm  1.3  9 years  golsen  Convert die to confess.
gjocolorlib.pm  1.7  9 years  golsen  Added support for luma (HSY color definitions). Changed all code so that html co...
SeedUtils.pm  1.59  9 years  golsen  Remove the "shebang".
FIGV.pm  1.96  9 years  gdpusch  Modified to gracefully handle Organism directories with no or empty Subsystems/ ...
gjoalign2html.pm  1.5  9 years  fangfang  SAS component
SapCompareRegions.pm  1.2  9 years  parrello  New compare-regions support.
AT.pm  1.5  9 years  fangfang  always return psiblast search history
ANNOserver.pm  1.20  9 years  parrello  Fixed a POD error.
RASTserver.pm  1.23  9 years  gdpusch  Fixed bugs in and added more support for Viral and Euk jobs.
Correspondence.pm  1.4  9 years  overbeek  correct the identity check
CorrTableEntry.pm  1.4  9 years  olson  Add num_matching_functions for column 19
Tracer.pm  1.131  9 years  parrello  Changed a "die" to a "confess".
ATserver.pm  1.2  9 years  fangfang  default url set to biobig
SUP.pm  1.2  9 years  parrello  New methods for alignment data.
Clustering.pm  1.6  9 years  overbeek  added double and triple linkage
FF.pm  1.35  9 years  disz  FigFam 6 digit fix
SampleDir.pm  1.4  9 years  olson  More analysis fixes; user-agent setting.
SUPserver.pm  1.1  9 years  parrello  New Sapling update support.
ANNO.pm  1.8  9 years  olson  kmer info changes
Phage.pm  1.3  9 years  redwards  minor correction
ScriptThing.pm  1.8  9 years  parrello  Expression vector support methods.
SeedV.pm  1.9  9 years  gdpusch  Changed a debugging line to print to STDERR, not STDOUT; print only if VERBOSE.
gjonewicklib.pm  1.25  9 years  golsen  Change behavior of reroot_tree() to ignore distance if there is only one node.
PinnedRegions.pm  1.34  9 years  olson  fix unlink here too
FFs.pm  1.49  9 years  olson  Clean up errors.
BerkTable.pm  1.2  9 years  olson  fix arg
find_special_proteins.pm  1.12  9 years  olson  typod the declaration
NCBI_genetic_code.pm  1.3  9 years  olson  add SAS header
MinimalTracer.pm  1.1  9 years  olson  More FS_RAST modes & supporting code for SAS use.
Signatures.pm  1.2  9 years  parrello  Various POD fixes.
gjoparseblast.pm  1.8  9 years  golsen  Fix two minor typographical errors in the documentation.
collect_related_sequences.pm  1.6  9 years  golsen  Update to use SeedAware.pm (and do some general clean-up).
display_related_genomes.pm  1.2  9 years  golsen  Minor documentation changes in code.
SSU_rRNA_reps.pm  1.3  9 years  golsen  Adjust end of one reference sequence by padding it slightly.
FileLocking.pm  1.4  9 years  olson  Changes for DesktopRast. CVHnS: ------------------------------------------------...
FIGM.pm  1.18  9 years  olson  Add FIGV and FIGM function_of_bulk
CorrespondenceCache.pm  1.1  9 years  parrello  Updates for new expression-data method.
ListServerScripts.pm  1.1  9 years  parrello  Added to support server script listing.
ServerScripts.pm  1.5  9 years  overbeek  add summarize_MG_output
gd_tree_0.pm  1.5  10 years  golsen  Extensive reworking of color management.
ErrorMessage.pm  1.2  10 years  olson  remove unused use CGI.
Subsystem.pm  1.147  10 years  overbeek  minor fix
set_utilities.pm  1.3  10 years  overbeek  make SAS components
SAPtutorial.pm  1.10  10 years  parrello  Fixed some errors in examples of ID types.
GenomeMeta.pm  1.16  10 years  olson  Add lock retries; probably not needed now that I think I've fixed FileLocking bu...
GenoGraphics.pm  1.24  10 years  golsen  Back pedal on the attempt to diagnose jpeg and png availability in GenoGraphics
proml.pm  1.9  10 years  golsen  Minor updates to SEED awareness.
selenoprotein_ref_seq.pm  1.5  10 years  golsen  Add some reference sequences and replace ; with @ in functions.
SeedHTML.pm  1.3  10 years  olson  More distro fixes.
Sim.pm  1.14  10 years  olson  Distro fixups
SSserver.pm  1.17  10 years  parrello  Removed from the SAS distribution.
FFserver.pm  1.23  10 years  parrello  Removed from the SAS distribution.
ACHserver.pm  1.16  10 years  parrello  Removed from the SAS distribution.
COserver.pm  1.13  10 years  parrello  Removed from the SAS distribution.
SeedEnv.pm  1.3  10 years  parrello  Added ANNOserver. Removed deprecated servers.
KmersOld.pm  1.1  10 years  olson  version of Kmers.pm before the argument changes; made to go with figfam_server_2...
SS.pm  1.13  10 years  parrello  More documentation cleanup.
ACH.pm  1.7  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
CO.pm  1.6  10 years  disz  changed doc to say XXserver->new() insetad of XX->new
TestUtils.pm  1.11  10 years  parrello  Fixed display glitch for pure white space.
FullLocation.pm  1.25  10 years  parrello  Added a method to compute the total location length.
gjolib.pm  1.3  10 years  olson  Add more modules to the SAS toolkit.
tree_utilities.pm  1.20  10 years  olson  Add more modules to the SAS toolkit.
FC.pm  1.21  10 years  parrello  Fixed a bug in "co_occurrence_evidence".
GenomeMetaDatabase.pm  1.1  10 years  jared  *** empty log message ***
MgRastSims.pm  1.1  10 years  redwards  a new package for getting sims for the mg-rast
Observation.pm  1.82  10 years  paczian  fixed hit and query length (cannot be null)
FIGRules.pm  1.54  10 years  olson  Optimize to_structured_english.
GenomeMetaDB.pm  1.5  10 years  jared  added update_path
DocUtils.pm  1.18  10 years  parrello  Added documentation functions to the Sapling server.
BasicLocation.pm  1.19  10 years  parrello  Updated to Sapling Server for Berkeley.
PHOB.pm  1.15  10 years  overbeek  switch from clustalw to muscle
SFXlate.pm  1.119  10 years  parrello  Added "families_containing_peg".
NewGenome.pm  1.80  10 years  parrello  Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.
NRTools.pm  1.4  10 years  olson  update to new metadata standard
ToCall.pm  1.11  10 years  gdpusch  Major rewrite to prevent already-found PEGs from being re-called by every stage ...
ParalogResolution.pm  1.5  10 years  golsen  Modifications to support line-drawing character set in tree printer plots.
clustaltree.pm  1.3  10 years  golsen  New super duper ala Peter T. Hooper paralog resolution interface.
PartitionSeqs.pm  1.3  11 years  overbeek  return either scalar or list
TBLstuff.pm  1.2  11 years  overbeek  minor fixes
Stats.pm  1.8  11 years  parrello  Added a method to extract saved messages.
Diagram.pm  1.17  11 years  parrello  Fixed some bad links.
AnnoClearinghouse.pm  1.44  11 years  wilke  Modified sql query to ? syntax
PickFeatureSet.pm  1.2  11 years  overbeek  add .html to HTML files
HTML.pm  1.130  11 years  arodri7  added links to set_prot_links
WikiTools.pm  1.8  11 years  parrello  Fixed a glitch in list rendering.
SimFC.pm  1.3  11 years  overbeek  handle deleted FIDs and failure to get translations
FIGAttributes.pm  1.4  11 years  overbeek  get rid of something
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
ProtFamsLite.pm  1.2  11 years  arodri7  added functions and made functions work
Contigs.pm  1.1  11 years  overbeek  new Contigs.pm and compare_coding.pm
CompareMR.pm  1.8  11 years  paczian  cutting comments off of functional roles
SeedSims.pm  1.1  11 years  overbeek  additions to support partitioning of sims
OddStarts_ref.pm  1.1  11 years  overbeek  add the ability to find TIF3
StandaloneSims.pm  1.1  11 years  olson  FIGM/FIGV changes for sims between RAST orgs.
MetaSubsystem.pm  1.4  11 years  bartels  added functions for genome manipulation
Assignments.pm  1.17  11 years  overbeek  remove impact of our annotations on making assignments using auto_assign
FIGjs.pm  1.15  11 years  parrello  Fixed URL references.
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
raelib.pm  1.44  12 years  redwards  adding a randomizer function
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
Overlap.pm  1.4  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.
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
TransactionProcessor.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
UserData.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
RemoteCustomAttributes.pm  1.8  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.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
ApplyTransactions.pm  1.7  12 years  parrello  Changed POD format for better compatability with Wiki.
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
KGML.pm  1.4  13 years  olson  Hope college modifications.
ContigMD5.pm  1.3  13 years  olson  clone the digest so that checksum() may be called multiple times
FIGgjo.pm  1.3  13 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
Classes.pm  1.1  14 years  mkubal  added Organism class
COPYING.TXT  1.1  14 years  olson  add license file
__init__.py  1.2  14 years  olson  Added license words.
fastDNAml.pm  1.2  14 years  olson  Added license words.
GenomeIDMap.pm  1.4  14 years  olson  Added license words.
FIGrpc.pm  1.3  14 years  olson  Added license words.
P2P.pm  1.31  14 years  olson  Added license words.
FIGGenDB.pm  1.6  14 years  olson  Added license words.
SproutSearch.pm  1.11  14 years  olson  Added license words.
ClusterWorker.pm  1.2  14 years  olson  Added license words.
RC.pm  1.2  14 years  olson  Added license words.
Construct.pm  1.2  14 years  olson  Added license words.
UserDB.pm  1.2  14 years  olson  Added license words.
FIGnet.pm  1.2  14 years  olson  Added license words.
HtmlPageParser.pm  1.2  14 years  olson  Added license words.
Cluster.pm  1.11  14 years  olson  Added license words.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIG.py  1.13  14 years  olson  Added license words.
FIGtree.pm  1.3  14 years  olson  Added license words.
FIG2.py  1.2  14 years  olson  Added license words.
HTML.py  1.6  14 years  olson  Added license words.
SproutFIG.pm  1.10  14 years  olson  Added license words.
README  1.1.1.1  16 years  efrank   import

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3