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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
 Parent Directory        
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  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
AnnoClearinghouse.pm  1.30  11 years  paarmann  changed line regexp in clean method
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  1.16  12 years  overbeek  fix Assignments.pm
BadCall.pm  1.4  11 years  parrello  Replaced obsolete AddToListMap method.
BasicLocation.pm  1.16  11 years  parrello  Added some new methods for the backfill gaps code in RAST.
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...
COPYING.TXT  1.1  14 years  olson  add license file
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
Classes.pm  1.1  14 years  mkubal  added Organism class
Clearinghouse.pm  1.4  14 years  olson  Added license words.
Clearinghouse.py  1.10  14 years  olson  Added license words.
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  1.3  12 years  paarmann  fixed compatibility issue with seed viewer
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
CountTransactions.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
DBKernel.pm  1.52  11 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
DBrtns.pm  1.27  13 years  overbeek  Fix extra-args option to go at teh start of the list.
Diagram.pm  1.9  12 years  paczian  inserted option to turn off javascript file inclusion for diagram
DocUtils.pm  1.15  11 years  parrello  Added support for RealCoreGenomes.
FF.pm  1.19  11 years  olson  RAST installation tweaks.
FFs.pm  1.14  11 years  olson  RAST installation tweaks.
FIG.pm  1.683  11 years  olson  Introduce get_figfam_data().
FIG.py  1.13  14 years  olson  Added license words.
FIG2.py  1.2  14 years  olson  Added license words.
FIGAttributes.pm  1.3  14 years  olson  Added license words.
FIGGenDB.pm  1.6  14 years  olson  Added license words.
FIGO.pm  1.32  12 years  parrello  Changed POD format for better compatability with Wiki.
FIGRules.pm  1.29  11 years  parrello  Changed nmpdr_mode to allow use of a cookie for overriding a script's operating ...
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FIGUtilities.pm  1.2  14 years  olson  Added license words.
FIGV.pm  1.52  11 years  olson  Add figv version of get_genome_subsystem_count().
FIG_CGI.pm  1.8  11 years  parrello  Fixed a POD error.
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
FIGjs.pm  1.14  13 years  parrello  Fixed a missing equal sign in the generated HTML.
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  1.12  11 years  overbeek  clean up name conflicts
FigFam.pm  1.74  11 years  olson  Introduce get_figfam_data().
FigFams.pm  1.42  11 years  olson  Introduce get_figfam_data().
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
FigSubsystem.pm  1.2  12 years  parrello  Changed POD format for better compatability with Wiki.
FigSubsystemMaster.pm  1.2  12 years  parrello  Changed POD format for better compatability with Wiki.
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  1.21  11 years  parrello  Added new support for gene boundary methods.
GenoGraphics.pm  1.17  12 years  golsen  A previously uncommited filledRectangle. And fix the Trace message on Ross's Re...
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  1.14  11 years  olson  Introduce get_figfam_data().
HTML.pm  1.122  11 years  paczian  fixed broken cmr link
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.
KGML.pm  1.4  12 years  olson  Hope college modifications.
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
Makefile  1.9  12 years  olson  Rollup of release engineering changes that shoudl make multi-architecture insta...
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.
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
NewGenome.pm  1.74  11 years  gdpusch  Final clean-up. -- /gdp
Observation.pm  1.58  11 years  arodri7  changed the similarities view in the Evidence page
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  1.61  11 years  parrello  Changed POD heading levels.
PHOB.pm  1.14  12 years  overbeek  add utilities for computing alignments
PageBuilder.pm  1.14  12 years  parrello  Changed POD format for better compatability with Wiki.
PinnedRegions.pm  1.10  11 years  olson  Introduce get_figfam_data().
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
RC.pm  1.2  14 years  olson  Added license words.
README  16 years  efrank   import
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
SFXlate.pm  1.102  11 years  parrello  Implemented feature_aliases_bulk, feature_aliasesI_in_tbl, coupled_to_batch, peg...
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
Sim.pm  1.13  11 years  overbeek  implemented new version of dsims based on partitions
SproutFIG.pm  1.10  14 years  olson  Added license words.
SproutSearch.pm  1.11  14 years  olson  Added license words.
Stats.pm  1.4  11 years  parrello  Fixed some major bugs.
Subsystem.pm  1.125  11 years  bartels  added a function for changing just the string of a functional role
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
TestUtils.pm  1.3  11 years  parrello  Revamped to give better displays of more complex structures.
ToCall.pm  1.10  11 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
Tracer.pm  1.96  11 years  gdpusch  Changed useless "warn" to useful "carp" in &Trace(). -- /gdp
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  1.6  11 years  jared  Corrected typo -jw
WikiTools.pm  1.2  11 years  parrello  Fixed Table method to create a header row.
__init__.py  1.2  14 years  olson  Added license words.
clustaltree.pm  1.1  12 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
display_related_genomes.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
fastDNAml.pm  1.2  14 years  olson  Added license words.
find_special_proteins.pm  1.9  11 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
gjoalign2html.pm  1.2  12 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
gjoalignment.pm  1.14  12 years  overbeek  add utilities for computing alignments
gjocolorlib.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
gjolib.pm  1.2  14 years  olson  Added license words.
gjolists.pm  1.2  12 years  golsen  Updates for cleaner faster code.
gjonewicklib.pm  1.11  11 years  golsen  Allow matched [ ... ] inside Newick tree comment. This violates the standard, b...
gjoparseblast.pm  1.2  13 years  golsen  Bug fix in parse error message (blast outputs invalid query and database sizes f...
gjophylip.pm  1.1  12 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
gjoseqlib.pm  1.13  11 years  golsen  Fixed major error in read_fasta() when there is not definition.
model.pm  1.18  11 years  dejongh  Fixes for excluding . and .. when reading directories for paths
proml.pm  1.8  12 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
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  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
selenoprotein_ref_seq.pm  1.4  11 years  golsen  Add to the list of reference proteins.
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  1.17  11 years  disz  added subsyste display on hover

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