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File Rev. Age Author (rev) Last log entry
 Parent Directory        
Shuffler/        
ERDataBase/        
TargetCriterionCellLocation.pm  1.1  11 years  parrello  Target search support
ERDBTypeImage.pm  1.4  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
BaseSaplingLoader.pm  1.5  9 years  parrello  Fixed to put back blank fields at the end in LoadFromFiles.
ExportAttributes.pl  1.2  12 years  parrello  Removed obsolete use clauses.
SaplingSubsystemLoader.pm  1.6  9 years  parrello  Added tracing to help figure out problems with the PSEED sapling load.
CopyCombinedMaps.pl  1.1  9 years  parrello  Set up directory pointer for expression data. Added CopyCombinedMaps.
NmpdrPage.pm  1.1  13 years  parrello  Moved NMPDRPage to Sprout directory.
ERDBTypeString.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SHTargetSearch.js  1.1  11 years  parrello  Target search support
ERDBTypeChar.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
TargetCriterionKeyword.pm  1.1  11 years  parrello  Target search support
NmpdrSearch.src  1.2  13 years  parrello  Fixed a bad URL.
TargetCriterionGeneric.pm  1.1  11 years  parrello  Target search support
ProteinSaplingLoader.pm  1.5  10 years  parrello  Updates for expression data and ACH loading.
NewSproutDBD.xml  1.3  11 years  parrello  *** empty log message ***
ERDBReloader.pl  1.1  10 years  parrello  New script for reloading individual tables.
ERDBDumper.pl  1.1  11 years  parrello  New script for dumping ERDB databases.
LoadSproutTables.pl  1.49  11 years  parrello  Fixed some documentation, set the default trace level to 3.
ERDBTypeDate.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
LoadScript.pl  1.4  12 years  parrello  Removed obsolete use clauses.
SHDrugSearch.pm  1.12  11 years  parrello  Improved search result support.
ERDBQuery.pm  1.12  10 years  parrello  Server database recovery fix.
CorePegs.pl  1.2  12 years  parrello  Added the "orgs" parameter to enable specifying all, all NMPDR, or only core gen...
ERDBObject.pm  1.15  9 years  parrello  Fixed an error in the retrieval of secondary relation fields.
GenomeStats.pl  1.36  11 years  parrello  Made organism stats tables sortable.
NmpdrSearch.png  1.2  13 years  parrello  Changed to the globe thingy.
SHTargetSearch.pm  1.2  11 years  parrello  Fixed criterion sort.
GeneFile.pl  1.4  12 years  parrello  Removed obsolete use clauses.
DBConvert.pl  1.3  12 years  parrello  Removed obsolete use clauses.
SaplingPerformer.pl  1.1  10 years  parrello  Sapling v08 changes.
SHOpSearch.pm  1.6  11 years  parrello  Converted to new hint system.
fig.htaccess  1.1  11 years  parrello  Blank htaccess file for future use.
NmpdrFix.pl  1.2  11 years  parrello  Improved site maintenance utilities.
CleanUp.pl  1.2  11 years  parrello  Fixed a comment.
ERDBTypeLongString.pm  1.3  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
AttrDBRefresh.pl  1.26  11 years  parrello  ERDB 2.0 support
RHLocations.pm  1.7  11 years  parrello  Converted viewer buttons to feature links.
ERDBLoader.pl  1.19  9 years  parrello  Fixed to save the section list in a file.
BaseSproutLoader.pm  1.7  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeCountVector.pm  1.2  9 years  parrello  Changes for expression vector support.
AliasCrunch.pl  1.10  9 years  parrello  Inverted some relationships to improve performance.
SubsystemSproutLoader.pm  1.4  11 years  parrello  Fixed to clean subsystem objects.
ShowCounts.pl  1.20  11 years  parrello  Changed heading style.
SaplingLoader.pl  1.6  9 years  parrello  Tuned tracing messages a little more.
ERDBPDocPage.pm  1.6  10 years  parrello  Fixed some documentation errors. Added the database notes to the image display f...
SHGeneBbhSearch.pm  1.1  11 years  parrello  Improved search result support.
DupCheck.pl  1.3  12 years  parrello  Removed obsolete use clauses.
NmpdrStats.pl  1.4  11 years  parrello  Fixed to use the correct socket for the mirror database check.
ERDBTypeBoolean.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SproutSubsys.pm  1.23  11 years  parrello  Fixed a comment.
SimBlocksDBD.xml  1.5  14 years  parrello  Replaced field "end" with "endpoint" to fix reserved word problem.
SmallHarvester.pl  1.1  10 years  parrello  Sapling v08 changes.
CustomAttributes.pm  1.46  10 years  parrello  Fixed an error in the handling of generic key queries.
SiteMeter.html  1.1  12 years  parrello  Added to make SiteMeter code more generally available.
AttrKeyConvert.pl  1.1  11 years  parrello  New script to convert old-format attribute dumps to the new format.
FeatureSproutLoader.pm  1.10  11 years  parrello  Updated to conform to new loading model.
GenomeSproutLoader.pm  1.4  11 years  parrello  Added support for representative genomes and more robust group assignment.
ScenarioSaplingLoader.pm  1.13  9 years  parrello  *** empty log message ***
DrugSproutLoader.pm  1.3  11 years  parrello  Put in a hack to get around the non-commutative property of the SQL OR.
Contigs.pl  1.1  11 years  parrello  Tutorial examples.
NmpdrCheck.pl  1.3  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
MarkUbiquitous.pl  1.1  9 years  parrello  New script to update compounds in the Sapling.
NmpdrSwitch.pl  1.2  12 years  parrello  Removed obsolete use clauses.
ResultHelper.pm  1.7  11 years  parrello  Improved search result support.
ERDBLoadGroup.pm  1.8  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SaplingSubsys.pm  1.8  10 years  parrello  Fixed to return undefined when the subsystem is not found.
TargetCriterionNull.pm  1.1  11 years  parrello  Target search support
indexCGI.pl  1.1  11 years  parrello  DirectoryIndex script for NMPDR.
ERDBLoadKill.pl  1.1  11 years  parrello  More tweaks to the load technology.
SproutDBD.xml  1.62  11 years  parrello  Added a new relationship for representative genome support.
SproutQuery.pm  1.2  14 years  parrello  Fxied obsolete references to the {_erdb} member.
SHToolSearch.pm  1.8  11 years  parrello  Changed column ordering in results.
NewStuffCheck.pl  1.27  11 years  parrello  Improved site maintenance utilities.
CuttingDBD.xml  1.1  11 years  parrello  Tutorial examples.
LoadExpressionGenome.pl  1.1  9 years  parrello  Created script for loading expression data.
AnnotationSproutLoader.pm  1.2  11 years  parrello  ERDB 2.0 support
DeleteGenomes.pl  1.3  12 years  parrello  Removed obsolete use clauses.
Blocks.txt  1.1.1.1  15 years  parrello  no message
NmpdrSetup.pl  1.2  11 years  parrello  ERDB 2.0 support
BioWords.pm  1.4  11 years  parrello  ERDB 2.0 support
LoadFIGTables.pl  1.2  12 years  parrello  Removed obsolete use clauses.
SHSigGenes.pm  1.22  11 years  parrello  Converted to new hint system.
FamilySaplingLoader.pm  1.14  9 years  parrello  More loader fixes.
Exceptions.txt  1.2  11 years  parrello  Added rules for "archael" and "bacterial".
ERDBQueryConsole.pm  1.6  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
AttributeReport.pl  1.5  11 years  parrello  ERDB 2.0 support
SynonymSproutLoader.pm  1.2  11 years  parrello  ERDB 2.0 support
SproutNotes.htm  1.1.1.1  15 years  parrello  no message
robots.txt  1.4  11 years  parrello  Removed some obsolete stuff.
startconsole.bat  1.1  14 years  parrello  Added this script for starting a FIG console on Windows machines.
ERDBTypeFloat.pm  1.4  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
EvCodeRefresh.pl  1.4  11 years  parrello  Converted to new multi-table design concept for attributes.
ReactionSproutLoader.pm  1.3  11 years  parrello  Fixed to clean subsystem objects.
SetGroup.pl  1.2  12 years  parrello  Removed obsolete use clauses.
SHWordSearch.pm  1.12  11 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
ERDBTypeCounter.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
TargetCriterionCodeMatch.pm  1.1  11 years  parrello  Target search support
SpanishInquisition.pl  1.2  12 years  parrello  Converted to use StandardSetup.
NeighboringFeatures.pl  1.1  11 years  parrello  Tutorial examples.
StopWords.txt  1.1  11 years  parrello  Changes for v24 database.
ERDBLoad.pm  1.24  11 years  parrello  Changed to skip the sort step if a file is pre-sorted, and to catch errors that ...
ERDBTypeRectangle.pm  1.3  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
FeatureSaplingLoader.pm  1.17  9 years  parrello  Added more information to the MD5 computation error message.
TargetCriterionLookup.pm  1.1  11 years  parrello  Failed to add in previous version.
ERDBFinder.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SHBatchSearch.pm  1.4  11 years  parrello  Added an entry field for pasting IDs in addition to uploading them.
SproutLoad.pm  1.97  11 years  parrello  New loader technology.
ERDBTypeInteger.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
PropertySproutLoader.pm  1.3  11 years  parrello  Removed PFAMs from the attributes to avoid a memory problem.
ERDBTypeText.pm  1.4  10 years  parrello  Fixed an error in the documentation.
NmpdrStatus.pl  1.2  12 years  parrello  Removed obsolete use clauses.
SourceSproutLoader.pm  1.2  11 years  parrello  ERDB 2.0 support
variation.html  1.1.1.1  15 years  parrello  no message
TargetCriterionConservedNeighborhood.pm  1.1  11 years  parrello  Target search support
Makefile  1.24  11 years  parrello  Removed POD stuff.
ExpressionSaplingLoader.pm  1.16  8 years  parrello  Changed to use new pearson.tbl file.
SetPermissions.pl  1.8  12 years  parrello  Removed obsolete use clauses.
ERDBTypeHashString.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
FCupdate.pl  1.2  9 years  parrello  Changes to facilitate loading in the new environment.
ERDBGenerate.pm  1.6  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
Genomes.pl  1.1  11 years  parrello  Tutorial examples.
SaplingTaxonomyLoader.pm  1.3  9 years  parrello  Added tracing to help figure out problems with the PSEED sapling load.
SproutStats.pl  1.2  14 years  parrello  Fxied obsolete references to the {_erdb} member.
TargetCriterionQuery.pm  1.1  11 years  parrello  Target search support
nmpdr.js  1.5  11 years  parrello  Added support for some stuff Leslie is doing.
BadIdFinder.pl  1.1  11 years  parrello  New program to find bad corresponding IDs in the SEED.
AlignmentSaplingLoader.pm  1.3  9 years  parrello  Added support for loading alignment data after a pre-load dump.
ERDBTypeProteinData.pm  1.1  9 years  parrello  Protein-data type.
SHPropSearch.pm  1.8  11 years  parrello  Improved search result support.
DrugClean.pl  1.2  12 years  parrello  Removed obsolete use clauses.
ERDBGenerator.pl  1.11  10 years  parrello  General loader improvements.
FCTester.pl  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ModelSaplingLoader.pm  1.17  9 years  parrello  Fixed field order in ModelGenome file.
TargetCriterionSmallTable.pm  1.1  11 years  parrello  Target search support
SaplingFunctionLoader.pm  1.2  9 years  parrello  Latest re-shuffling of the incremental load stuff.
SaplingExpressionLoader.pm  1.7  9 years  parrello  Added tracing to help figure out problems with the PSEED sapling load.
HyperLink.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SaplingConfig.xml  1.1  11 years  parrello  Sapling support.
AttrTime.pl  1.2  12 years  parrello  Removed obsolete use clauses.
AttributesDBD.xml  1.11  11 years  parrello  ERDB 2.0 support
MarkupTest.pl  1.3  12 years  parrello  Removed obsolete use clauses.
TargetCriterionExternalId.pm  1.1  11 years  parrello  Target search support
TargetCriterion.pm  1.1  11 years  parrello  Target search support
SearchHelper.pm  1.48  11 years  parrello  Added ID parsing logic for the Batch Search.
ERDBType.pm  1.3  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
Rectangle.pm  1.1  11 years  parrello  New data type for rectangular regions.
locations.pl  1.2  13 years  parrello  Fixed default trace level.
AttributeTest.pl  1.5  12 years  parrello  Changed so that it can run on a system without a FIG database.
SHOrgSumSearch.pm  1.1  11 years  parrello  Improved search result support.
ERDB.js  1.4  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
LoaderUtils.pm  1.3  9 years  parrello  More loader fixes.
ERDBTypeLink.pm  1.3  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
RHFeatures.pm  1.13  11 years  parrello  Converted to use new hint support.
SapServerTest4.pl  1.1  10 years  parrello  Test program for ANNO server find-special-proteins.
TargetCriterionRange.pm  1.1  11 years  parrello  Target search support
SHGeneSearch.pm  1.4  11 years  parrello  Improved search result support.
ErrorDocument.pm  1.2  10 years  parrello  *** empty log message ***
TargetCriterionGeneId.pm  1.1  11 years  parrello  Target search support
ERDBTypeSemiBoolean.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SapServerTest.pl  1.1  9 years  parrello  Changes to facilitate loading in the new environment.
SubsystemSaplingLoader.pm  1.20  9 years  parrello  Even more loader fixes.
SHSubSearch.pm  1.10  11 years  parrello  Improved search result support.
FigConfigFix.pl  1.5  11 years  parrello  Removed obsolete typing code.
ERDBTypeDNA.pm  1.4  10 years  parrello  Fixed the DecodeField bug.
SaplingDataLoader.pm  1.4  9 years  parrello  Added tracing to help figure out problems with the PSEED sapling load.
TargetCriterionEC.pm  1.1  11 years  parrello  Target search support
DeleteChips.pl  1.1  9 years  parrello  New program to delete Staph from the expression data.
FidCheck.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
SproutGFF.pl  1.3  12 years  parrello  Removed obsolete use clauses.
Sprout.pm  1.128  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
RHLigands.pm  1.4  11 years  parrello  Improved search result support.
GenomeSaplingLoader.pm  1.14  9 years  parrello  Hacked to point the taxonomy load to a directory I can update.
ERDBTune.pl  1.1  11 years  parrello  New database utility script.
SimLoad.pl  1.12  11 years  parrello  ERDB 2.0 support
SearchSkeleton.pm  1.4  11 years  parrello  Converted to new hint system.
ModelLoader.pm  1.2  11 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
DrugTargets.pm  1.2  11 years  parrello  ERDB 2.0 support
SimBlocks.pm  1.11  12 years  parrello  Changed POD format for better compatability with Wiki.
ContigDNA.pm  1.3  12 years  parrello  Fixed a POD error.
SingleTableLoad.pl  1.3  12 years  parrello  Removed obsolete use clauses.
Sapling.pm  1.44  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ERDBServer.cgi  1.1  11 years  olson  Commit these before I delete them again.
SaplingGenomeLoader.pm  1.13  8 years  olson  Fix infinite loop when an annotation file is missing the final //
ERDBClient.pm  1.1  11 years  olson  Commit these before I delete them again.
ERDB.pm  1.139  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
ERDBExtras.pm  1.7  8 years  olson  Add a bunch of modules to the SAS release for myRAST. Make use of FIG_Config opt...
FIGSproutTest.pl  1.3  15 years  olson  Fixes to put XML file in FIGdisk/FIG.

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