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File (rev) Rev. Age Author Last log entry
 Parent Directory        
tests/        
WebApplicationComponents/        
SeedComponents/        
wsdl.cgi  1.1  12 years  redwards  changing the makewsdl script to a live cgi
wiki.cgi  1.1  11 years  parrello  Added to allow for a short URL to get to the wiki.
vert_text.cgi  1.2  13 years  olson  add license words
users.cgi  1.2  13 years  olson  add license words
tyra_sequence.cgi  1.2  12 years  hwang  add modified sequences
tyra_cluster.cgi  1.1  12 years  hwang  given a tyra peg/ it finds the gene neighborhood of that peg
tree_jnlp.cgi  1.2  11 years  disz  Fixed href error in the jnlp
test_basic_functionality.cgi  1.1  12 years  olson  basic func test - for nagios
testGetUniprotKbPrimaryAccessionsForFigIdServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetSubsystemsHavingOrganismServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetSubsystemCollectionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsInSubsystemCellServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsInNeighborhoodServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsForOrganismServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsForEnsemblgeneIDServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsForControlledVocabularyAnnotationServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetOrganismsInSubsystemServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetOrganismCollectionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetGeneForPegServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetFunctionalRolesByUniprotkbPrimaryAccessionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetFigIdsForUniprotKbPrimaryAccessionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetControlledVocabularyAnnotationsForPegServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
targets.cgi  1.8  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
subsys_vectors.cgi  1.13  13 years  overbeek  RAE: removing legacy static urls
subsys_summary.cgi  1.25  13 years  olson  add license words
subsys_hope.cgi  1.2  13 years  olson  add license words
subsys_diagram.cgi  1.8  13 years  parrello  Fixed to work in Sprout.
subsys.cgi  1.214  11 years  overbeek  allow non-numeric variant codes
status_of_model.cgi  1.5  13 years  olson  add license words
start.cgi  1.10  13 years  overbeek  RAE: updated start interface
ssa2.cgi  1.50  13 years  olson  add license words
ssa.cgi  1.32  13 years  olson  add license words
ss_scoreboard.cgi  1.9  13 years  olson  add license words
ss_export.cgi  1.8  13 years  olson  add license words
ss_correlations.cgi  1.4  12 years  overbeek  check sz of rep tree to 40 in insert_prot_into_tree
split_functional_role.cgi  1.2  13 years  overbeek  to make sure
sigs.cgi  1.52  11 years  parrello  Changed to use new NMPDR mode protocol.
show_map.cgi  1.4  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
show_log.cgi  1.3  13 years  overbeek  add ability to log arbitrary correspondences
show_local_map.cgi  1.5  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
show_kegg_map.cgi  1.4  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
show_exp_assertions.cgi  1.9  11 years  overbeek  fix to show_exp_assertions.cgi
set_variants.cgi  1.5  13 years  overbeek  RAE: Adding a link into set variants from subsys.cgi and back
server_check.cgi  1.3  13 years  olson  add license words
select.cgi  1.15  11 years  parrello  Added Etracing support.
seed_running_perl.fragment  1.2  13 years  olson  fixes
seed_ctl.cgi  1.13  12 years  olson  add ability to disable just the control panel.
search_log.cgi  1.3  13 years  hwang   Change absolute path to relative path for getting genome log data
sdk_uniprot_search.cgi  1.7  13 years  mkubal  Gene now Gene Name or Symbol
scopmap_service.cgi  1.4  13 years  olson  add license words
save_to_attributes.cgi  1.6  12 years  hwang  Add in routines that save the attributes to ROLE_FROM_PEG_CURATED_RELEVANT
save_roles_to_attributes.cgi  1.1  12 years  hwang  Added files to display and show precomputed literature for functional roles with...
reset_curator.cgi  1.4  13 years  overbeek  RAE: adding options to reset_curator
region.cgi  1.1  12 years  paczian  initial version
record.cgi  1.4  13 years  olson  add license words
rae.cgi  1.4  13 years  olson  add license words
proteinfamilies.cgi  1.47  13 years  overbeek  RAE: Changes to Protein Families
protein_sets_by_alias.cgi  1.2  13 years  olson  add license words
protein_sets_2.cgi  1.2  13 years  olson  add license words
protein_sets.cgi  1.4  13 years  olson  add license words
protein_new.cgi  1.6  13 years  parrello  Changed to use the new PageBuilder call signature.
protein_info.cgi  1.10  13 years  olson  add license words
protein_by_ss.cgi  1.6  12 years  redwards  undoing horrible mistake
protein.cgi  1.250  11 years  parrello  Changed to redirect search engines to the seed viewer.
propose_new_peg.cgi  1.11  13 years  golsen  Fix endpoint error when negative strand region runs off the start of the contig....
pom.cgi  1.22  12 years  overbeek  add check_variants.cgi, a program to automatically validate variant codes
pir.cgi  1.33  13 years  olson  add license words
pchs.cgi  1.4  11 years  olson  put the other batch coupling code in.
pathway.cgi  1.2  13 years  olson  add license words
paint_network.cgi  1.1  13 years  mkubal  for painting ma,flux results, complete genome hybridization exp
p2p_service.cgi  1.2  13 years  olson  add license words
organisms.cgi  1.32  13 years  overbeek  RAE: Updating organisms.cgi for more information per organim
nmpdr_aliases_to_pubmed.cgi  1.4  13 years  hwang  fix grammatical error
myseed.cgi  1.2  13 years  olson  add license words
makewsdl.pl  1.3  12 years  disz  Replaced after Rob delete
ma_to_tf_single.cgi  1.1  13 years  mkubal  new
ma_to_tf_pairs.cgi  1.1  13 years  mkubal  with orpv
ma_to_tf_nr.cgi  1.3  13 years  mkubal  with orpv
ma_to_tf.cgi  1.4  12 years  mkubal  upgrade
ma2sub.cgi  1.6  13 years  olson  add license words
lock_subsys.cgi  1.2  12 years  overbeek  allow selection of all roles/genomes for locking
locate_patterns.cgi  1.1  12 years  overbeek  add ability to filter aux roles on peg_to_subsystems
local_sim_compute.cgi  1.3  13 years  olson  more fixes to sim compute stuff.
list_subsys.cgi  1.1  13 years  olson  fixes
link.cgi  1.6  11 years  parrello  Updated to direct users to the seed viewer.
ligands.cgi  1.2  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
legionella_v4.cgi  1.3  13 years  mkubal  links for nonsubsys reactions
legionella_v1.cgi  1.1  13 years  mkubal  tool for legionella ma analysis
kernel_xmlrpc.cgi  1.11  13 years  efrank   'by_raw_alias' => $wrapper->wrap_array_return("by_raw_alias"), 'fin...
kernel.cgi  1.15  13 years  olson  add license words
install_subsystem_dir.cgi  1.1  12 years  olson  CGI for installing subsystem directory.
index.cgi  1.130  11 years  parrello  Added Etracing support.
hope_tools.cgi  1.3  12 years  dejongh  Hope College updates
homologs_in_clusters.cgi  1.13  11 years  parrello  Changed to use FIG_CGI.
heat_map.cgi  1.20  13 years  overbeek  RAE: minor changes to heat map interface
header  1.1.1.1  15 years  efrank   import
get_map_image.cgi  1.4  13 years  olson  add license words
get_expert_2c.cgi  1.7  11 years  overbeek  minor check for division by 0 in get_expert_2c.cgi
genomebrowser.cgi  1.8  13 years  redwards  minor change to allow proper genome selection
genome_statistics.cgi  1.54  12 years  parrello  Removed the contig display for Sprout.
fusions.cgi  1.2  13 years  olson  add license words
frame.cgi  1.10  13 years  paczian  removed display of proteinpage due to new backend
find_ss_genes.cgi  1.4  13 years  overbeek  added code to show connections between subsystems
find_reaction_paths.cgi  1.1  12 years  olson  Hope College modifications.
find_poss_subsys_instances.cgi  1.2  11 years  overbeek  fixes to find_poss_subsys_instances.cgi
figfam_proto.cgi  1.6  12 years  mkubal  added ss info
fig_scripts_service.cgi  1.10  11 years  redwards  more methods for metagenomes
fid_checked.cgi  1.44  12 years  overbeek  fixes to display on protein page, alternative formats for alignments and trees i...
ff.cgi  1.2  12 years  overbeek  fix test for writable built in FigFam.pm
feature.cgi  1.9  12 years  overbeek  fixes to allow non-peg features in subsystems
extend_subsys.cgi  1.12  13 years  redwards  using is_environmental
eggs.cgi  1.9  13 years  paczian  minor cosmetic changes to layout and text
edit_feature.cgi  1.1  12 years  overbeek  initial, undebugged version of edit_feature.cgi
display_subsys.cgi  1.29  11 years  parrello  Fixed to use new NMPDR mode protocol.
display_role_literature.cgi  1.4  12 years  hwang  Fix bug of 1 literature doesn't show up
diffsF.cgi  1.8  11 years  overbeek  change ::data/FigfamsData to ::FigfamsData
diagram_upload.cgi  1.2  12 years  paarmann  fixed the hrefs
diagram.cgi  1.8  11 years  parrello  Fixed a bug caused by an unspecified action parameter.
das.cgi  1.15  13 years  olson  add license words
cv.cgi  1.16  13 years  olson  add license words
correspondence.cgi  1.2  13 years  olson  add license words
construct.cgi  1.3  13 years  olson  add license words
consistent_sets.cgi  1.3  13 years  olson  add license words
conflicted_pegs.cgi  1.2  13 years  olson  add license words
comp_genomes.cgi  1.10  11 years  parrello  Added tracing support.
comp_MR.cgi  1.4  12 years  overbeek  fixed to comp_MR.cgi and FIGV.pm
cluster_xmlrpc.cgi  1.2  13 years  olson  add license words
cluster_stage.cgi  1.4  13 years  olson  add license words
cluster_service.cgi  1.4  13 years  olson  add license words
clust_ss.cgi  1.5  11 years  overbeek  fixes to the ACH_resolution stuff
close_genome_discrepancies.cgi  1.8  13 years  redwards  minor updates to ev code and default params
chromosomal_clusters_old.cgi  1.2  13 years  parrello  Changed to use the new PageBuilder call signature.
chromosomal_clusters.cgi  1.113  11 years  parrello  Added tracing support.
check_variants.cgi  1.11  11 years  overbeek  allow different format for roles, rules and definitions in check_variants.cgi
check_subsys.cgi  1.26  12 years  overbeek  attempt to fix some of the mistakes introduced into check_subsys.cgi
check_peg_functions.cgi  1.2  11 years  overbeek  add line numbers
check_int_anno.cgi  1.3  13 years  overbeek  $/ fixes
check_fc.cgi  1.1  12 years  overbeek  add check_fc.cgi
check_bad.cgi  1.1  13 years  overbeek  add check_bad.cgi
check_anno.cgi  1.2  13 years  overbeek  fix numbers on chedck_anno.cgi
bbhs.cgi  1.4  12 years  parrello  Changed so that the local datbase is opened if the current HTTP HOST is not a bi...
att2sub.cgi  1.6  13 years  olson  add license words
assignments.cgi  1.16  13 years  overbeek  add potentially_missed_assignments
assign_using_tree.cgi  1.16  11 years  disz  Display subsystems on hover
array2sub.cgi  1.14  13 years  olson  add license words
align_DNA.cgi  1.5  13 years  olson  add license words
aliases_to_pubmed.cgi  1.8  12 years  hwang  Add in routines that save the attributes to ROLE_FROM_PEG_CURATED_RELEVANT
add_links.cgi  1.2  13 years  olson  add license words
WebApplicationComponents.pm  1.3  13 years  paczian  *** empty log message ***
SpanishInquisition.cgi  1.1  11 years  parrello  Created to test the Confess method.
SimPieces.cgi  1.5  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimBlockPattern.cgi  1.8  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimBlockForm.cgi  1.7  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimBlockDisplay.cgi  1.7  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
ShowTableFile.cgi  1.3  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
ShowPage.cgi  1.2  13 years  olson  add license words
SetPassword.cgi  1.11  11 years  parrello  Changed POD format for better compatability with Wiki.
SeedComponents.pm  1.3  13 years  paczian  *** empty log message ***
SearchSkeleton.cgi  1.29  11 years  parrello  Changed to hide the property search from the master list.
README  1.1.1.1  15 years  efrank   import
ProcessTemplate.cgi  1.5  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
Makefile  1.18  12 years  parrello  Converted cp -p to cp to avoid a problem with makefiles.
HOPSS.cgi  1.8  13 years  olson  add license words
FormDisplay.cgi  1.2  13 years  olson  add license words
FigSQL.cgi  1.2  13 years  parrello  Fixed botched attempt to allow multi-table FIG queries.
Emergency.cgi  1.18  11 years  parrello  Made it harder for unauthorized people to invoke the script. The script only wor...
DocDirectory.cgi  1.7  13 years  parrello  Changed to use the new PageBuilder call signature.
COPYING.TXT  1.1  13 years  olson  add license file
Attributes.cgi  1.13  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
AttribXMLRPC.cgi  1.9  12 years  parrello  Added support for the new method to get attribute descriptions by group.
ACH_resolution.cgi  1.13  11 years  olson  Changes for standalone use of this script.

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