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Index of /FigKernelPackages

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File Rev. Age Author Last log entry (rev)
 Parent Directory        
tests/        
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FigFam.pm  1.75  11 years  arodri7  updated and corrected sub new
Diagram.pm  1.15  11 years  paczian  scaled images will now have better quality scaled images will now always have gr...
AnnoClearinghouse.pm  1.34  11 years  wilke  readonly flag for reading contrib files/indices
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
collect_related_sequences.pm  1.5  12 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
GenomeMeta.pm  1.15  11 years  olson  oops, these need updated.
GenomeMetaDB.pm  1.1  11 years  olson  oops, these need updated.
BinarySearch.pm  1.1  12 years  overbeek  just add a binary search so I do not have to recode it again
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FS_RAST.pm  1.17  11 years  overbeek  fixes to grouping
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
Clearinghouse.pm  1.5  11 years  olson  fix clearinghouse urls.
Assignments.pm  1.16  12 years  overbeek  fix Assignments.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
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
ContigMD5.pm  1.3  12 years  olson  clone the digest so that checksum() may be called multiple times
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
Observation.pm  1.68  11 years  arodri7  allow users to select a non-fig id as an assign_from function
raelib.pm  1.44  12 years  redwards  adding a randomizer function
tree_utilities.pm  1.17  11 years  disz  added subsyste display on hover
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
FFs.pm  1.24  11 years  arodri7  added merge figfams functions
Classes.pm  1.1  14 years  mkubal  added Organism class
PHOB.pm  1.14  12 years  overbeek  add utilities for computing alignments
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
FileLocking.pm  1.2  12 years  olson  add shared locking
representative_sequences.pm  1.9  12 years  overbeek  add make_trimmed_alignment_from_ids
COPYING.TXT  1.1  14 years  olson  add license file
gjocolorlib.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
display_related_genomes.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
FIGO.pm  1.34  11 years  gdpusch  Streamlined FIGV handling, and conditioning of stray debugging statements on $EN...
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
FigGFF.pm  1.22  12 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
DocUtils.pm  1.16  11 years  parrello  Revamped to allow more general processing of log files.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
find_special_proteins.pm  1.9  12 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
SeedDas.pm  1.22  12 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
GenoGraphics.pm  1.18  11 years  parrello  Not sure. The DIFF says there was no change.
P2Pupdate.pm  1.62  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
FIGV.pm  1.60  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
FIG.pm  1.715  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
gjoalign2html.pm  1.2  13 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids
DBKernel.pm  1.52  11 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
TestUtils.pm  1.6  11 years  parrello  Improved display of undefined and empty strings.
FIGgjo.pm  1.3  13 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
KGML.pm  1.4  12 years  olson  Hope college modifications.
KGMLData.pm  1.4  12 years  dejongh  Hope College updates
model.pm  1.18  12 years  dejongh  Fixes for excluding . and .. when reading directories for paths
WikiTools.pm  1.5  11 years  parrello  Fixed table generator to remove line-feeds that would break the table.
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
FIGRules.pm  1.36  11 years  parrello  Fixed for sprout compatability.
NewGenome.pm  1.75  11 years  gdpusch  Fixed bug in ORF::seq(); minor changes in debugging output. -- /gdp
FIGjs.pm  1.14  13 years  parrello  Fixed a missing equal sign in the generated HTML.
PinnedRegions.pm  1.12  11 years  parrello  Fixed a compiler warning.
Tracer.pm  1.107  11 years  parrello  Fixed Warn to leave $@ intact.
FullLocation.pm  1.24  11 years  olson  Fix translation gunk.
Makefile  1.10  11 years  golsen  Fix to path for pod2html
Clearinghouse.py  1.11  11 years  olson  Fix now-broken MCS URLs.
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
FF.pm  1.22  11 years  olson  Fix bug where return of should_be_member is lost.
gjoalignment.pm  1.15  11 years  golsen  Fix FIG dependencies so that it is FIG-aware, but not FIG-dependent.
FigFams.pm  1.46  11 years  arodri7  Figfams update
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
WebColors.pm  1.6  11 years  jared  Corrected typo -jw
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
CompareMR.pm  1.4  11 years  dsouza  Changed sort to make more efficient -- was taking very long.
HTML.pm  1.128  11 years  dsouza  Changed URL for SwissProt, TREMBL and UniProt links.
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
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.
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.
gjoparseblast.pm  1.2  14 years  golsen  Bug fix in parse error message (blast outputs invalid query and database sizes f...
gjonewicklib.pm  1.11  12 years  golsen  Allow matched [ ... ] inside Newick tree comment. This violates the standard, b...
LogReader.pm  1.1  11 years  parrello  Added to facilitate reading the error log.
SFXlate.pm  1.104  11 years  parrello  Added support for to_structured_english.
BasicLocation.pm  1.16  12 years  parrello  Added some new methods for the backfill gaps code in RAST.
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.
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.
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
Stats.pm  1.6  11 years  parrello  Added a method to facilitate periodic tracing.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
selenoprotein_ref_seq.pm  1.4  12 years  golsen  Add to the list of reference proteins.
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
FIG_CGI.pm  1.11  11 years  olson  Add annotation support to FIGV. Add FIGM.
FIGM.pm  1.1  11 years  olson  Add annotation support to FIGV. Add FIGM.
clustaltree.pm  1.1  13 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
proml.pm  1.8  13 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
Subsystem.pm  1.135  11 years  bartels  *** empty log message ***
MetaSubsystem.pm  1.1  11 years  bartels  *** empty log message ***
README  1.1.1.1  16 years  efrank   import

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