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Index of /FigKernelPackages

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File Rev. Age Author Last log entry
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FF.pm  1.20  12 years  arodri7  updated and corrected sub new
FigFams.pm  1.45  12 years  arodri7  error check on PDB.connections file for older figfam release
FigFam.pm  1.75  12 years  arodri7  updated and corrected sub new
GenomeLists.pm  1.2  12 years  bartels  put in verify_dir so that the directory is produced automatically if you access ...
Scenario.pm  1.5  12 years  dejongh  Added getter/setter for path_info
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
tree_utilities.pm  1.17  12 years  disz  added subsyste display on hover
README  1.1.1.1  16 years  efrank   import
DBKernel.pm  1.52  12 years  gdpusch  Included the name of the failed load-file in the &reload_tables() load failure m...
FIGO.pm  1.33  12 years  gdpusch  Added support for non-installed genome directories. -- /gdp
find_special_proteins.pm  1.9  12 years  gdpusch  Removed duplicate "my" declaration from &find_orf_start(). -- /gdp
NewGenome.pm  1.74  12 years  gdpusch  Final clean-up. -- /gdp
ToCall.pm  1.10  12 years  gdpusch  Clarified error msg for missing PEG FASTA file. -- /gdp
proml.pm  1.8  13 years  golsen  A few updates to proml.pm, but this should be replaced by gjophylip.pm function ...
selenoprotein_ref_seq.pm  1.4  12 years  golsen  Add to the list of reference proteins.
protdist_neighbor.pm  1.1  13 years  golsen  A package for protdist and neighbor PHYLIP trees.
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...
FIGgjo.pm  1.3  13 years  golsen  Improve handling of multidomain query sequences in coloring of sims matches (do ...
ButtonArray.pm  1.1  12 years  golsen  Two subroutines to support a user ordering of items. Created for the compare ge...
pyrrolysylprotein_ref_seq.pm  1.1  12 years  golsen  Add support for pyrrolysyl proteins. Also, major revision and clean-up of the t...
gjoseqlib.pm  1.13  12 years  golsen  Fixed major error in read_fasta() when there is not definition.
gjophylip.pm  1.1  13 years  golsen  The start of a package to provide perl inferfaces into programs in Felsenstein's...
clustaltree.pm  1.1  13 years  golsen  A rudimentary package to make a clustalw tree. The intent is to put the command...
gjolists.pm  1.2  13 years  golsen  Updates for cleaner faster code.
NCBI_genetic_code.pm  1.2  12 years  golsen  Some minor changes and add the FIG header.
gjoalign2html.pm  1.2  13 years  golsen  Major change in the alignment and tree portions of fid_checked. Nicer alignment ...
WebColors.pm  1.6  12 years  jared  Corrected typo -jw
Classes.pm  1.1  14 years  mkubal  added Organism class
GenomeMeta.pm  1.14  12 years  olson  Introduce get_figfam_data().
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.
ChromosomalClusters.pm  1.10  12 years  olson  fix typoe
P2P.pm  1.31  14 years  olson  Added license words.
ContigMD5.pm  1.3  13 years  olson  clone the digest so that checksum() may be called multiple times
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.
KGML.pm  1.4  13 years  olson  Hope college modifications.
Cluster.pm  1.11  14 years  olson  Added license words.
FIGUtilities.pm  1.2  14 years  olson  Added license words.
NRTools.pm  1.3  12 years  olson  Add failed-open-directory check.
FIG.py  1.13  14 years  olson  Added license words.
FIGtree.pm  1.3  14 years  olson  Added license words.
Makefile  1.9  12 years  olson  Rollup of release engineering changes that shoudl make multi-architecture insta...
InterfaceRoutines.pm  1.12  13 years  olson  readonly fixes; seed-run-job update to run from input file
FileLocking.pm  1.2  12 years  olson  add shared locking
COPYING.TXT  1.1  14 years  olson  add license file
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.
BinarySearch.pm  1.1  13 years  overbeek  just add a binary search so I do not have to recode it again
AliTree.pm  1.5  12 years  overbeek  FIGfams are now broadened to include PEGs with mismatching functions
InsertIntoTree.pm  1.15  12 years  overbeek  check figfams fixes
Subsystem.pm  1.131  12 years  overbeek  minor fix to Subsystems.pm
tree_neighborhood.pm  1.1  13 years  overbeek  add tree_neighbors and latest phylogeny stuff
gjocolorlib.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
collect_related_sequences.pm  1.5  13 years  overbeek  pack core alignments in make_trimmed_alignment_from_ids
ClosestGenomes.pm  1.2  12 years  overbeek  fix AliTrees.pm to fail gracefully
HTML.pm  1.125  12 years  overbeek  fixes to get_dlits.cgi
FFs.pm  1.18  12 years  overbeek  update to get_dlit.cgi
Sim.pm  1.13  12 years  overbeek  implemented new version of dsims based on partitions
display_related_genomes.pm  1.1  13 years  overbeek  add Gary's compare genome stuff
representative_sequences.pm  1.9  13 years  overbeek  add make_trimmed_alignment_from_ids
SameFunc.pm  1.17  12 years  overbeek  fix to SameFunc.pm
FS_RAST.pm  1.16  12 years  overbeek  fix to computing locations for frameshifts
Blast.pm  1.5  12 years  overbeek  close TMP files in Blast.pm
AliTrees.pm  1.4  12 years  overbeek  fix AliTrees.pm to fail gracefully
PHOB.pm  1.14  13 years  overbeek  add utilities for computing alignments
Assignments.pm  1.16  13 years  overbeek  fix Assignments.pm
DBrtns.pm  1.27  14 years  overbeek  Fix extra-args option to go at teh start of the list.
gjoalignment.pm  1.14  13 years  overbeek  add utilities for computing alignments
CompareMR.pm  1.3  13 years  paarmann  fixed compatibility issue with seed viewer
AnnoClearinghouse.pm  1.30  12 years  paarmann  changed line regexp in clean method
UnvSubsys.pm  1.20  12 years  paczian  added missing "use HTML;"
FIG_CGI.pm  1.10  12 years  parrello  Added a hook to log robot activity.
Diagram.pm  1.10  12 years  parrello  Temporarily changed so that it stores images in a file instead of streaming them...
P2Pupdate.pm  1.61  12 years  parrello  Changed POD heading levels.
DocUtils.pm  1.16  12 years  parrello  Revamped to allow more general processing of log files.
Quality.pm  1.6  12 years  parrello  Changed POD format for better compatability with Wiki.
SFXlate.pm  1.103  12 years  parrello  Added some new FIG methods: next-feature, prev-feature, subsystem-version, and a...
Overlap.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
FullLocation.pm  1.23  12 years  parrello  Changed the name of the Constrain function to avoid a naming conflict. Fixed a c...
Markups.pm  1.2  12 years  parrello  Changed POD format for better compatability with Wiki.
FIG.pm  1.691  12 years  parrello  Changed display_id_and_seq to work in Sprout. Changed boundaries_of to be more t...
BasicLocation.pm  1.16  12 years  parrello  Added some new methods for the backfill gaps code in RAST.
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.
Observation.pm  1.59  12 years  parrello  Fixed some compiler warnings.
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.
LogReader.pm  1.1  12 years  parrello  Added to facilitate reading the error log.
raedraw.pm  1.14  12 years  parrello  Changed POD heading levels.
FudgeTransactions.pm  1.4  12 years  parrello  Changed POD format for better compatability with Wiki.
GenoGraphics.pm  1.18  12 years  parrello  Not sure. The DIFF says there was no change.
BadCall.pm  1.4  12 years  parrello  Replaced obsolete AddToListMap method.
RemoteCustomAttributes.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
Tracer.pm  1.106  12 years  parrello  Fixed the feed so that it is thread-safe and changed it so that it can be used f...
TestUtils.pm  1.5  12 years  parrello  Replaced escapeHTML with the slightly more secure Tracer::Clean.
FIGRules.pm  1.33  12 years  parrello  Added load information to the robot trace.
FIGjs.pm  1.14  13 years  parrello  Fixed a missing equal sign in the generated HTML.
Stats.pm  1.5  12 years  parrello  Added a new method to rank the statistics.
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.
Annotation.pm  1.4  12 years  parrello  Added a TITLE statement for the Wiki.
PinnedRegions.pm  1.12  12 years  parrello  Fixed a compiler warning.
SeedDas.pm  1.22  13 years  parrello  Removed a FIG dependency that was causing duplicate-method warnings.
WikiTools.pm  1.4  12 years  parrello  Added a method that loads a module from the Wiki CPAN stash.
TemplateObject.pm  1.8  12 years  parrello  Changed POD format for better compatability with Wiki.
ComparedRegions.pm  1.6  12 years  parrello  Updated to improve performance.
JobScheduler.pm  1.8  12 years  parrello  Changed POD headers to work better with the new system.
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.
FIGStatisticalModels.pm  1.6  13 years  redwards  fixing log error
FIGV.pm  1.54  12 years  redwards  adding two find functions
raelib.pm  1.44  12 years  redwards  adding a randomizer function
FigGFF.pm  1.22  13 years  redwards  Rewritten gff2tab and updated FigGFF POD/methods
MapIDs.pm  1.1  12 years  wilke  Initial version of functions to map different ids

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