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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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README  1.1.1.1  16 years  efrank   import
proml.pm  1.8  13 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
GenoGraphics.pm  1.17  13 years  golsen  A previously uncommited filledRectangle. And fix the Trace message on Ross's Re...
clustaltree.pm  1.1  12 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
FIGV.pm  1.52  12 years  olson  Add figv version of get_genome_subsystem_count().
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
selenoprotein_ref_seq.pm  1.4  12 years  golsen  Add to the list of reference proteins.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
Clearinghouse.py  1.10  14 years  olson  Added license words.
gjolib.pm  1.2  14 years  olson  Added license words.
__init__.py  1.2  14 years  olson  Added license words.
fastDNAml.pm  1.2  14 years  olson  Added license words.
FIGAttributes.pm  1.3  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.
Clearinghouse.pm  1.4  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.
set_utilities.pm  1.2  14 years  olson  Added license words.
FullLocation.pm  1.21  12 years  parrello  Added new support for gene boundary methods.
BasicLocation.pm  1.16  12 years  parrello  Added some new methods for the backfill gaps code in RAST.
DocUtils.pm  1.15  12 years  parrello  Added support for RealCoreGenomes.
gjonewicklib.pm  1.11  12 years  golsen  Allow matched [ ... ] inside Newick tree comment. This violates the standard, b...
gjoparseblast.pm  1.2  14 years  golsen  Bug fix in parse error message (blast outputs invalid query and database sizes f...
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.
AliasAnalysis.pm  1.3  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.
FIGO.pm  1.32  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.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
FigSubsystem.pm  1.2  12 years  parrello  Changed POD format for better compatability with Wiki.
CountTransactions.pm  1.3  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.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
P2Pupdate.pm  1.61  12 years  parrello  Changed POD heading levels.
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
FIGRules.pm  1.29  12 years  parrello  Changed nmpdr_mode to allow use of a cookie for overriding a script's operating ...
Tracer.pm  1.96  11 years  gdpusch  Changed useless "warn" to useful "carp" in &Trace(). -- /gdp
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
WebColors.pm  1.6  11 years  jared  Corrected typo -jw
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
NewGenome.pm  1.74  12 years  gdpusch  Final clean-up. -- /gdp
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
WikiTools.pm  1.2  12 years  parrello  Fixed Table method to create a header row.
FIG_CGI.pm  1.8  12 years  parrello  Fixed a POD error.
FIGjs.pm  1.14  13 years  parrello  Fixed a missing equal sign in the generated HTML.
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
Stats.pm  1.4  12 years  parrello  Fixed some major bugs.
model.pm  1.18  12 years  dejongh  Fixes for excluding . and .. when reading directories for paths
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
KGML.pm  1.4  12 years  olson  Hope college modifications.
SFXlate.pm  1.102  12 years  parrello  Implemented feature_aliases_bulk, feature_aliasesI_in_tbl, coupled_to_batch, peg...
FIGgjo.pm  1.3  12 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
DBKernel.pm  1.52  11 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
GenomeMeta.pm  1.14  11 years  olson  Introduce get_figfam_data().
FIG.pm  1.683  11 years  olson  Introduce get_figfam_data().
PinnedRegions.pm  1.10  11 years  olson  Introduce get_figfam_data().
FigFams.pm  1.42  11 years  olson  Introduce get_figfam_data().
FigFam.pm  1.74  11 years  olson  Introduce get_figfam_data().
gjoalign2html.pm  1.2  12 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
FFs.pm  1.14  11 years  olson  RAST installation tweaks.
FF.pm  1.19  11 years  olson  RAST installation tweaks.
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
find_special_proteins.pm  1.9  12 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
TestUtils.pm  1.3  12 years  parrello  Revamped to give better displays of more complex structures.
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
Makefile  1.9  12 years  olson  Rollup of release engineering changes that shoudl make multi-architecture insta...
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
gjocolorlib.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
display_related_genomes.pm  1.1  12 years  overbeek  add Gary's compare genome stuff
COPYING.TXT  1.1  14 years  olson  add license file
representative_sequences.pm  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
FileLocking.pm  1.2  12 years  olson  add shared locking
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
PHOB.pm  1.14  12 years  overbeek  add utilities for computing alignments
gjoalignment.pm  1.14  12 years  overbeek  add utilities for computing alignments
Classes.pm  1.1  14 years  mkubal  added Organism class
Subsystem.pm  1.125  12 years  bartels  added a function for changing just the string of a functional role
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
tree_utilities.pm  1.17  11 years  disz  added subsyste display on hover
raelib.pm  1.44  12 years  redwards  adding a randomizer function
AnnoClearinghouse.pm  1.30  12 years  paarmann  changed line regexp in clean method
Observation.pm  1.58  11 years  arodri7  changed the similarities view in the Evidence page
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
FS_RAST.pm  1.12  12 years  overbeek  clean up name conflicts
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
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
Assignments.pm  1.16  12 years  overbeek  fix Assignments.pm
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
HTML.pm  1.122  12 years  paczian  fixed broken cmr link
CompareMR.pm  1.3  12 years  paarmann  fixed compatibility issue with seed viewer
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
Diagram.pm  1.9  12 years  paczian  inserted option to turn off javascript file inclusion for diagram
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file

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