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File Rev. Age Author Last log entry
 Parent Directory        
ERDataBase/        
Shuffler/        
.cvsignore  1.2  5 years  parrello  KBase reorg.
.project  1.1  2 years  parrello  Added replaceAll option for sapling load check.
AAFrequencies.pl  1.1  2 years  parrello  Miscellaneous loader fixes.
AliasCrunch.pl  1.10  6 years  parrello  Inverted some relationships to improve performance.
AlignmentSaplingLoader.pm  1.6  5 years  parrello  Fixed bug in ProjectsOnto load.
AnnotationGroup.pm  1.1  5 years  parrello  Annotation update service module.
AnnotationSproutLoader.pm  1.2  8 years  parrello  ERDB 2.0 support
AttrDBRefresh.pl  1.26  8 years  parrello  ERDB 2.0 support
AttrKeyConvert.pl  1.1  8 years  parrello  New script to convert old-format attribute dumps to the new format.
AttrTime.pl  1.2  9 years  parrello  Removed obsolete use clauses.
AttributeReport.pl  1.5  8 years  parrello  ERDB 2.0 support
AttributeTest.pl  1.5  9 years  parrello  Changed so that it can run on a system without a FIG database.
AttributesDBD.xml  1.11  8 years  parrello  ERDB 2.0 support
BadIdFinder.pl  1.1  8 years  parrello  New program to find bad corresponding IDs in the SEED.
BaseSaplingLoader.pm  1.5  6 years  parrello  Fixed to put back blank fields at the end in LoadFromFiles.
BaseSproutLoader.pm  1.7  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
BioWords.pm  1.4  8 years  parrello  ERDB 2.0 support
Blocks.txt  1.1.1.1  12 years  parrello  no message
CDMIUtilsTest.pl  1.2  5 years  parrello  Fixed CDMI use to new format.
CleanUp.pl  1.2  8 years  parrello  Fixed a comment.
CommonFunctions.pl  1.1  2 years  parrello  Miscellaneous loader fixes.
Contigs.pl  1.1  8 years  parrello  Tutorial examples.
CopyCombinedMaps.pl  1.1  6 years  parrello  Set up directory pointer for expression data. Added CopyCombinedMaps.
CorePegs.pl  1.2  9 years  parrello  Added the "orgs" parameter to enable specifying all, all NMPDR, or only core gen...
CreateLoaderFile.pl  1.1  4 years  parrello  Support for PSEED load and updates.
CustomAttributes.pm  1.48  5 years  parrello  KBase reorg.
CuttingDBD.xml  1.1  8 years  parrello  Tutorial examples.
DBConvert.pl  1.3  9 years  parrello  Removed obsolete use clauses.
DeleteChips.pl  1.1  6 years  parrello  New program to delete Staph from the expression data.
DeleteGenomes.pl  1.7  3 years  parrello  Minor fix to allow blank lines in genome ID file.
DrugClean.pl  1.2  9 years  parrello  Removed obsolete use clauses.
DrugSproutLoader.pm  1.3  8 years  parrello  Put in a hack to get around the non-commutative property of the SQL OR.
DupCheck.pl  1.3  9 years  parrello  Removed obsolete use clauses.
ERDB.js  1.4  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDB.pm  1.169  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBClient.pm  1.2  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBDumper.pl  1.2  5 years  parrello  Added ability to override DB name.
ERDBExtras.pm  1.8  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBFinder.pm  1.2  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBFixRels.pl  1.3  4 years  parrello  Incremental load improvements.
ERDBFixup.pl  1.2  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBGenerate.pm  1.6  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBGenerator.pl  1.11  7 years  parrello  General loader improvements.
ERDBLoad.pm  1.24  8 years  parrello  Changed to skip the sort step if a file is pre-sorted, and to catch errors that ...
ERDBLoadFormat.pl  1.3  2 years  parrello  First pass over SEEDtk database changes.
ERDBLoadGroup.pm  1.9  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBLoadKill.pl  1.1  8 years  parrello  More tweaks to the load technology.
ERDBLoader.pl  1.19  6 years  parrello  Fixed to save the section list in a file.
ERDBObject.pm  1.16  5 years  parrello  First group of KBase API methods.
ERDBPDocPage.pm  1.9  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBQuery.pm  1.13  5 years  parrello  First group of KBase API methods.
ERDBQueryConsole.pm  1.6  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBReloader.pl  1.1  7 years  parrello  New script for reloading individual tables.
ERDBServer.cgi  1.1  8 years  olson  Commit these before I delete them again.
ERDBTune.pl  1.3  4 years  parrello  Fix to previous update.
ERDBType.pm  1.6  3 years  parrello  Added relationship cleaning function. Fixed some comments.
ERDBTypeBoolean.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeChar.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeCountVector.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeCounter.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeDNA.pm  1.5  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeDate.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeFloat.pm  1.6  4 years  parrello  Added support for nullable floats and integers.
ERDBTypeHashString.pm  1.4  2 years  parrello  checkpoint before a big update from GIT
ERDBTypeImage.pm  1.6  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBTypeInteger.pm  1.4  4 years  parrello  Added support for nullable floats and integers.
ERDBTypeLink.pm  1.4  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeLongString.pm  1.4  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeProteinData.pm  1.2  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeRectangle.pm  1.4  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeSemiBoolean.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeShortString.pm  1.1  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
ERDBTypeString.pm  1.3  5 years  parrello  Conversion to support Postgres for ERDB.
ERDBTypeText.pm  1.5  5 years  parrello  Conversion to support Postgres for ERDB.
ErdbChangesTest.pl  1.1  5 years  parrello  KBase reorg.
ErrorDocument.pm  1.2  7 years  parrello  *** empty log message ***
EvCodeRefresh.pl  1.4  9 years  parrello  Converted to new multi-table design concept for attributes.
Exceptions.txt  1.2  8 years  parrello  Added rules for "archael" and "bacterial".
ExportAttributes.pl  1.2  9 years  parrello  Removed obsolete use clauses.
ExpressionSaplingLoader.pm  1.16  6 years  parrello  Changed to use new pearson.tbl file.
FCTester.pl  1.2  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
FCupdate.pl  1.3  4 years  parrello  Updates for new incremental load.
FIGSproutTest.pl  1.3  12 years  olson  Fixes to put XML file in FIGdisk/FIG.
FamilySaplingLoader.pm  1.16  5 years  parrello  Fix for missing FIGfam functions.
FeatureSaplingLoader.pm  1.19  5 years  parrello  Removed MD5 feature IDs.
FeatureSproutLoader.pm  1.10  8 years  parrello  Updated to conform to new loading model.
FidCheck.pm  1.3  9 years  parrello  Changed POD format for better compatability with Wiki.
FigConfigFix.pl  1.5  8 years  parrello  Removed obsolete typing code.
FigTest.pl  1.1  5 years  parrello  KBase reorg.
FindDuplicate.pl  1.1  4 years  parrello  Added support for nullable floats and integers.
FixComplexes.pl  1.1  5 years  parrello  Changes to support complexes.
FixRolesInFile.pl  1.1  5 years  parrello  Changes to support complexes.
FixSubFile.pl  1.1  2 years  parrello  Removed Shrub stuff. Updated ERDB for compatibility with Shrub DBD.
GeneFile.pl  1.4  9 years  parrello  Removed obsolete use clauses.
GenomeSaplingLoader.pm  1.16  4 years  parrello  Updates for new incremental load.
GenomeSproutLoader.pm  1.4  8 years  parrello  Added support for representative genomes and more robust group assignment.
GenomeStats.pl  1.36  8 years  parrello  Made organism stats tables sortable.
Genomes.pl  1.1  8 years  parrello  Tutorial examples.
HyperLink.pm  1.2  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
KBIDUtilsTest.pl  1.1  5 years  parrello  Proposed wrapper for Kbase ID server.
KbaseTest.pl  1.3  5 years  parrello  Updated a CDMI use statement.
LoadComplexData.pl  1.1  5 years  parrello  Changes to support complexes.
LoadExpressionGenome.pl  1.1  6 years  parrello  Created script for loading expression data.
LoadFIGTables.pl  1.2  9 years  parrello  Removed obsolete use clauses.
LoadProjections.pl  1.3  5 years  parrello  Fixed Sapling constructor.
LoadScript.pl  1.4  9 years  parrello  Removed obsolete use clauses.
LoadSproutTables.pl  1.49  8 years  parrello  Fixed some documentation, set the default trace level to 3.
LoadTableTest.pl  1.1  5 years  parrello  Checkpoint before field-name changes.
LoaderUtils.pm  1.3  6 years  parrello  More loader fixes.
Makefile  1.24  8 years  parrello  Removed POD stuff.
MarkUbiquitous.pl  1.1  6 years  parrello  New script to update compounds in the Sapling.
MarkupTest.pl  1.3  9 years  parrello  Removed obsolete use clauses.
ModelSaplingLoader.pm  1.21  5 years  parrello  Added ComplexName table
NeighboringFeatures.pl  1.1  8 years  parrello  Tutorial examples.
NewSproutDBD.xml  1.3  8 years  parrello  *** empty log message ***
NewStuffCheck.pl  1.27  8 years  parrello  Improved site maintenance utilities.
NmpdrCheck.pl  1.3  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
NmpdrFix.pl  1.2  8 years  parrello  Improved site maintenance utilities.
NmpdrPage.pm  1.1  11 years  parrello  Moved NMPDRPage to Sprout directory.
NmpdrSearch.png  1.2  11 years  parrello  Changed to the globe thingy.
NmpdrSearch.src  1.2  11 years  parrello  Fixed a bad URL.
NmpdrSetup.pl  1.2  8 years  parrello  ERDB 2.0 support
NmpdrStats.pl  1.4  8 years  parrello  Fixed to use the correct socket for the mirror database check.
NmpdrStatus.pl  1.2  9 years  parrello  Removed obsolete use clauses.
NmpdrSwitch.pl  1.2  9 years  parrello  Removed obsolete use clauses.
Nulltest.pl  1.2  4 years  parrello  Support for PSEED load and updates.
PropertySproutLoader.pm  1.3  8 years  parrello  Removed PFAMs from the attributes to avoid a memory problem.
ProteinSaplingLoader.pm  1.6  4 years  parrello  Fixed to handle missing assigned_functions files without crashing.
RHFeatures.pm  1.13  8 years  parrello  Converted to use new hint support.
RHLigands.pm  1.4  8 years  parrello  Improved search result support.
RHLocations.pm  1.7  8 years  parrello  Converted viewer buttons to feature links.
ReactionNeighborHunt.pl  1.1  5 years  parrello  Changes to support complexes.
ReactionSproutLoader.pm  1.3  8 years  parrello  Fixed to clean subsystem objects.
Rectangle.pm  1.1  8 years  parrello  New data type for rectangular regions.
ResultHelper.pm  1.7  8 years  parrello  Improved search result support.
RoleChangeCheck.pl  1.1  5 years  parrello  Changes to support complexes.
SHBatchSearch.pm  1.4  8 years  parrello  Added an entry field for pasting IDs in addition to uploading them.
SHDrugSearch.pm  1.12  8 years  parrello  Improved search result support.
SHGeneBbhSearch.pm  1.1  8 years  parrello  Improved search result support.
SHGeneSearch.pm  1.4  8 years  parrello  Improved search result support.
SHOpSearch.pm  1.6  8 years  parrello  Converted to new hint system.
SHOrgSumSearch.pm  1.1  8 years  parrello  Improved search result support.
SHPropSearch.pm  1.8  8 years  parrello  Improved search result support.
SHSigGenes.pm  1.22  8 years  parrello  Converted to new hint system.
SHSubSearch.pm  1.10  8 years  parrello  Improved search result support.
SHTargetSearch.js  1.1  8 years  parrello  Target search support
SHTargetSearch.pm  1.2  8 years  parrello  Fixed criterion sort.
SHToolSearch.pm  1.8  8 years  parrello  Changed column ordering in results.
SHWordSearch.pm  1.12  8 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
SapLoaderTest.pl  1.4  2 years  parrello  Miscellaneous loader fixes.
SapLoaderVariantFix.pl  1.1  2 years  parrello  Miscellaneous loader fixes.
SapServerTest.pl  1.4  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
SapServerTest4.pl  1.8  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
Sapling.pm  1.50  4 years  parrello  Updates for new incremental load.
SaplingAssignments.pl  1.1  4 years  parrello  Support for PSEED load and updates.
SaplingConfig.xml  1.1  8 years  parrello  Sapling support.
SaplingDataLoader.pm  1.6  4 years  parrello  Updates for new incremental load.
SaplingExpressionLoader.pm  1.9  4 years  parrello  Changed expression tables to add chip ID to experiment ID.
SaplingFamilyLoader.pm  1.1  4 years  parrello  Incremental load improvements.
SaplingFunctionCheck.pl  1.1  2 years  parrello  New method to fix functional assignments.
SaplingFunctionLoader.pm  1.5  5 years  parrello  Fixed to work if an attempt is made to update a nonexistent feature.
SaplingGenomeLoader.pm  1.20  2 years  parrello  Added replaceAll option for sapling load check.
SaplingLoadCheck.pl  1.8  2 years  parrello  Added replaceAll option for sapling load check.
SaplingLoader.pl  1.8  4 years  parrello  Updates for new incremental load.
SaplingPerformer.pl  1.1  7 years  parrello  Sapling v08 changes.
SaplingSubsys.pm  1.8  7 years  parrello  Fixed to return undefined when the subsystem is not found.
SaplingSubsystemLoader.pm  1.9  2 years  parrello  Miscellaneous loader fixes.
SaplingTaxonomyLoader.pm  1.4  2 years  parrello  Miscellaneous loader fixes.
SaplingTest.pl  1.6  3 years  parrello  Added optional mode to UpdateEntity.
SaplingXLoader.pl  1.1  4 years  parrello  New script for updating expression data.
ScenarioSaplingLoader.pm  1.13  6 years  parrello  *** empty log message ***
SearchHelper.pm  1.48  8 years  parrello  Added ID parsing logic for the Batch Search.
ServerMethodCounts.pl  1.1  5 years  parrello  Changes to support complexes.
SetGroup.pl  1.2  9 years  parrello  Removed obsolete use clauses.
SetPermissions.pl  1.8  9 years  parrello  Removed obsolete use clauses.
ShowCounts.pl  1.20  8 years  parrello  Changed heading style.
SimBlocksDBD.xml  1.5  11 years  parrello  Replaced field "end" with "endpoint" to fix reserved word problem.
SimpleTest.pl  1.1  5 years  parrello  Conversion to support Postgres for ERDB.
SiteMeter.html  1.1  9 years  parrello  Added to make SiteMeter code more generally available.
SmallHarvester.pl  1.1  7 years  parrello  Sapling v08 changes.
SourceSproutLoader.pm  1.2  8 years  parrello  ERDB 2.0 support
SpanishInquisition.pl  1.2  9 years  parrello  Converted to use StandardSetup.
Sprout.pm  1.128  8 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SproutDBD.xml  1.62  8 years  parrello  Added a new relationship for representative genome support.
SproutGFF.pl  1.3  9 years  parrello  Removed obsolete use clauses.
SproutLoad.pm  1.97  8 years  parrello  New loader technology.
SproutNotes.htm  1.1.1.1  12 years  parrello  no message
SproutQuery.pm  1.2  11 years  parrello  Fxied obsolete references to the {_erdb} member.
SproutStats.pl  1.2  11 years  parrello  Fxied obsolete references to the {_erdb} member.
SproutSubsys.pm  1.23  8 years  parrello  Fixed a comment.
StopWords.txt  1.1  8 years  parrello  Changes for v24 database.
SubsysRowsTest.pl  1.1  5 years  parrello  KBase reorg.
SubsystemSaplingLoader.pm  1.21  4 years  parrello  Updates for new incremental load.
SubsystemSproutLoader.pm  1.4  8 years  parrello  Fixed to clean subsystem objects.
SynonymSproutLoader.pm  1.2  8 years  parrello  ERDB 2.0 support
TargetCriterion.pm  1.1  8 years  parrello  Target search support
TargetCriterionCellLocation.pm  1.1  8 years  parrello  Target search support
TargetCriterionCodeMatch.pm  1.1  8 years  parrello  Target search support
TargetCriterionConservedNeighborhood.pm  1.1  8 years  parrello  Target search support
TargetCriterionEC.pm  1.1  8 years  parrello  Target search support
TargetCriterionExternalId.pm  1.1  8 years  parrello  Target search support
TargetCriterionGeneId.pm  1.1  8 years  parrello  Target search support
TargetCriterionGeneric.pm  1.1  8 years  parrello  Target search support
TargetCriterionKeyword.pm  1.1  8 years  parrello  Target search support
TargetCriterionLookup.pm  1.1  8 years  parrello  Failed to add in previous version.
TargetCriterionNull.pm  1.1  8 years  parrello  Target search support
TargetCriterionQuery.pm  1.1  8 years  parrello  Target search support
TargetCriterionRange.pm  1.1  8 years  parrello  Target search support
TargetCriterionSmallTable.pm  1.1  8 years  parrello  Target search support
UpdateSaplingAnnotations.pl  1.3  5 years  parrello  Changes to support complexes.
UpdateSaplingDbd.pl  1.1  5 years  parrello  Changes to support complexes.
fig.htaccess  1.1  8 years  parrello  Blank htaccess file for future use.
indexCGI.pl  1.1  8 years  parrello  DirectoryIndex script for NMPDR.
km_test.pl  1.1  2 years  parrello  Miscellaneous loader fixes.
locations.pl  1.2  10 years  parrello  Fixed default trace level.
nmpdr.js  1.5  8 years  parrello  Added support for some stuff Leslie is doing.
rebuild_dlit_titles.pl  1.1  5 years  parrello  More KBase reorg.
robots.txt  1.4  8 years  parrello  Removed some obsolete stuff.
startconsole.bat  1.1  12 years  parrello  Added this script for starting a FIG console on Windows machines.
variation.html  1.1.1.1  12 years  parrello  no message

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