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File (rev) Rev. Age Author Last log entry
 Parent Directory        
Shuffler/        
ERDataBase/        
variation.html  1.1.1.1  15 years  parrello  no message
startconsole.bat  1.1  14 years  parrello  Added this script for starting a FIG console on Windows machines.
robots.txt  1.4  11 years  parrello  Removed some obsolete stuff.
nmpdr.js  1.5  10 years  parrello  Added support for some stuff Leslie is doing.
locations.pl  1.2  13 years  parrello  Fixed default trace level.
indexCGI.pl  1.1  11 years  parrello  DirectoryIndex script for NMPDR.
fig.htaccess  1.1  10 years  parrello  Blank htaccess file for future use.
TargetCriterionSmallTable.pm  1.1  10 years  parrello  Target search support
TargetCriterionRange.pm  1.1  10 years  parrello  Target search support
TargetCriterionQuery.pm  1.1  10 years  parrello  Target search support
TargetCriterionNull.pm  1.1  10 years  parrello  Target search support
TargetCriterionLookup.pm  1.1  10 years  parrello  Failed to add in previous version.
TargetCriterionKeyword.pm  1.1  10 years  parrello  Target search support
TargetCriterionGeneric.pm  1.1  10 years  parrello  Target search support
TargetCriterionGeneId.pm  1.1  10 years  parrello  Target search support
TargetCriterionExternalId.pm  1.1  10 years  parrello  Target search support
TargetCriterionEC.pm  1.1  10 years  parrello  Target search support
TargetCriterionConservedNeighborhood.pm  1.1  10 years  parrello  Target search support
TargetCriterionCodeMatch.pm  1.1  10 years  parrello  Target search support
TargetCriterionCellLocation.pm  1.1  10 years  parrello  Target search support
TargetCriterion.pm  1.1  10 years  parrello  Target search support
SynonymSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
SubsystemSproutLoader.pm  1.4  10 years  parrello  Fixed to clean subsystem objects.
SubsystemSaplingLoader.pm  1.20  8 years  parrello  Even more loader fixes.
StopWords.txt  1.1  11 years  parrello  Changes for v24 database.
SproutSubsys.pm  1.23  10 years  parrello  Fixed a comment.
SproutStats.pl  1.2  13 years  parrello  Fxied obsolete references to the {_erdb} member.
SproutQuery.pm  1.2  13 years  parrello  Fxied obsolete references to the {_erdb} member.
SproutNotes.htm  1.1.1.1  15 years  parrello  no message
SproutLoad.pm  1.97  11 years  parrello  New loader technology.
SproutGFF.pl  1.3  11 years  parrello  Removed obsolete use clauses.
SproutDBD.xml  1.62  10 years  parrello  Added a new relationship for representative genome support.
Sprout.pm  1.128  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
SpanishInquisition.pl  1.2  11 years  parrello  Converted to use StandardSetup.
SourceSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
SmallHarvester.pl  1.1  10 years  parrello  Sapling v08 changes.
SiteMeter.html  1.1  12 years  parrello  Added to make SiteMeter code more generally available.
SingleTableLoad.pl  1.3  11 years  parrello  Removed obsolete use clauses.
SimLoad.pl  1.12  10 years  parrello  ERDB 2.0 support
SimBlocksDBD.xml  1.5  13 years  parrello  Replaced field "end" with "endpoint" to fix reserved word problem.
SimBlocks.pm  1.11  12 years  parrello  Changed POD format for better compatability with Wiki.
ShowCounts.pl  1.20  10 years  parrello  Changed heading style.
SetPermissions.pl  1.8  11 years  parrello  Removed obsolete use clauses.
SetGroup.pl  1.2  11 years  parrello  Removed obsolete use clauses.
SearchSkeleton.pm  1.4  10 years  parrello  Converted to new hint system.
SearchHelper.pm  1.48  10 years  parrello  Added ID parsing logic for the Batch Search.
ScenarioSaplingLoader.pm  1.13  8 years  parrello  *** empty log message ***
SaplingTaxonomyLoader.pm  1.1  8 years  parrello  More loader updates.
SaplingSubsystemLoader.pm  1.5  8 years  parrello  More loader updates.
SaplingSubsys.pm  1.8  10 years  parrello  Fixed to return undefined when the subsystem is not found.
SaplingPerformer.pl  1.1  10 years  parrello  Sapling v08 changes.
SaplingGenomeLoader.pm  1.8  8 years  parrello  Fixed method that computes protein IDs.
SaplingFunctionLoader.pm  1.1  8 years  parrello  More loader updates.
SaplingExpressionLoader.pm  1.5  8 years  parrello  More loader updates.
SaplingDataLoader.pm  1.2  8 years  parrello  More loader updates.
SaplingConfig.xml  1.1  10 years  parrello  Sapling support.
Sapling.pm  1.39  8 years  parrello  More load fixes.
SapServerTest4.pl  1.1  9 years  parrello  Test program for ANNO server find-special-proteins.
SHWordSearch.pm  1.12  10 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
SHToolSearch.pm  1.8  10 years  parrello  Changed column ordering in results.
SHTargetSearch.pm  1.2  10 years  parrello  Fixed criterion sort.
SHTargetSearch.js  1.1  10 years  parrello  Target search support
SHSubSearch.pm  1.10  10 years  parrello  Improved search result support.
SHSigGenes.pm  1.22  10 years  parrello  Converted to new hint system.
SHPropSearch.pm  1.8  10 years  parrello  Improved search result support.
SHOrgSumSearch.pm  1.1  10 years  parrello  Improved search result support.
SHOpSearch.pm  1.6  10 years  parrello  Converted to new hint system.
SHGeneSearch.pm  1.4  10 years  parrello  Improved search result support.
SHGeneBbhSearch.pm  1.1  10 years  parrello  Improved search result support.
SHDrugSearch.pm  1.12  10 years  parrello  Improved search result support.
SHBatchSearch.pm  1.4  10 years  parrello  Added an entry field for pasting IDs in addition to uploading them.
ResultHelper.pm  1.7  10 years  parrello  Improved search result support.
Rectangle.pm  1.1  10 years  parrello  New data type for rectangular regions.
ReactionSproutLoader.pm  1.3  10 years  parrello  Fixed to clean subsystem objects.
RHLocations.pm  1.7  10 years  parrello  Converted viewer buttons to feature links.
RHLigands.pm  1.4  10 years  parrello  Improved search result support.
RHFeatures.pm  1.13  10 years  parrello  Converted to use new hint support.
ProteinSaplingLoader.pm  1.5  9 years  parrello  Updates for expression data and ACH loading.
PropertySproutLoader.pm  1.3  10 years  parrello  Removed PFAMs from the attributes to avoid a memory problem.
NmpdrSwitch.pl  1.2  11 years  parrello  Removed obsolete use clauses.
NmpdrStatus.pl  1.2  11 years  parrello  Removed obsolete use clauses.
NmpdrStats.pl  1.4  10 years  parrello  Fixed to use the correct socket for the mirror database check.
NmpdrSetup.pl  1.2  10 years  parrello  ERDB 2.0 support
NmpdrSearch.src  1.2  13 years  parrello  Fixed a bad URL.
NmpdrSearch.png  1.2  13 years  parrello  Changed to the globe thingy.
NmpdrPage.pm  1.1  13 years  parrello  Moved NMPDRPage to Sprout directory.
NmpdrFix.pl  1.2  10 years  parrello  Improved site maintenance utilities.
NmpdrCheck.pl  1.3  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
NewStuffCheck.pl  1.27  10 years  parrello  Improved site maintenance utilities.
NewSproutDBD.xml  1.3  10 years  parrello  *** empty log message ***
NeighboringFeatures.pl  1.1  10 years  parrello  Tutorial examples.
ModelSaplingLoader.pm  1.16  8 years  parrello  Added more ubiquitous compounds.
ModelLoader.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
MarkupTest.pl  1.3  11 years  parrello  Removed obsolete use clauses.
Makefile  1.24  10 years  parrello  Removed POD stuff.
LoaderUtils.pm  1.3  8 years  parrello  More loader fixes.
LoadSproutTables.pl  1.49  11 years  parrello  Fixed some documentation, set the default trace level to 3.
LoadScript.pl  1.4  11 years  parrello  Removed obsolete use clauses.
LoadFIGTables.pl  1.2  11 years  parrello  Removed obsolete use clauses.
LoadExpressionGenome.pl  1.1  8 years  parrello  Created script for loading expression data.
HyperLink.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
Genomes.pl  1.1  10 years  parrello  Tutorial examples.
GenomeStats.pl  1.36  10 years  parrello  Made organism stats tables sortable.
GenomeSproutLoader.pm  1.4  10 years  parrello  Added support for representative genomes and more robust group assignment.
GenomeSaplingLoader.pm  1.12  9 years  parrello  Changes for expression vector support.
GeneFile.pl  1.4  11 years  parrello  Removed obsolete use clauses.
FigConfigFix.pl  1.5  11 years  parrello  Removed obsolete typing code.
FidCheck.pm  1.3  12 years  parrello  Changed POD format for better compatability with Wiki.
FeatureSproutLoader.pm  1.10  10 years  parrello  Updated to conform to new loading model.
FeatureSaplingLoader.pm  1.13  8 years  parrello  Even more loader fixes.
FamilySaplingLoader.pm  1.14  8 years  parrello  More loader fixes.
FIGSproutTest.pl  1.3  14 years  olson  Fixes to put XML file in FIGdisk/FIG.
FCupdate.pl  1.1  10 years  parrello  New stuff to update functional couplings on the fly.
FCTester.pl  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ExpressionSaplingLoader.pm  1.15  8 years  parrello  Fixed to work even if a coregulation file is invalid.
ExportAttributes.pl  1.2  11 years  parrello  Removed obsolete use clauses.
Exceptions.txt  1.2  11 years  parrello  Added rules for "archael" and "bacterial".
EvCodeRefresh.pl  1.4  11 years  parrello  Converted to new multi-table design concept for attributes.
ErrorDocument.pm  1.2  9 years  parrello  *** empty log message ***
ERDBTypeText.pm  1.4  10 years  parrello  Fixed an error in the documentation.
ERDBTypeString.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeSemiBoolean.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeRectangle.pm  1.3  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeProteinData.pm  1.1  9 years  parrello  Protein-data type.
ERDBTypeLongString.pm  1.3  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeLink.pm  1.3  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeInteger.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeImage.pm  1.4  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeHashString.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeFloat.pm  1.4  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeDate.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeDNA.pm  1.4  10 years  parrello  Fixed the DecodeField bug.
ERDBTypeCounter.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeCountVector.pm  1.2  9 years  parrello  Changes for expression vector support.
ERDBTypeChar.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTypeBoolean.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBType.pm  1.3  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBTune.pl  1.1  11 years  parrello  New database utility script.
ERDBServer.cgi  1.1  10 years  olson  Commit these before I delete them again.
ERDBReloader.pl  1.1  10 years  parrello  New script for reloading individual tables.
ERDBQueryConsole.pm  1.6  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBQuery.pm  1.12  10 years  parrello  Server database recovery fix.
ERDBPDocPage.pm  1.6  10 years  parrello  Fixed some documentation errors. Added the database notes to the image display f...
ERDBObject.pm  1.15  9 years  parrello  Fixed an error in the retrieval of secondary relation fields.
ERDBLoader.pl  1.18  8 years  parrello  Latest load-process fixes.
ERDBLoadKill.pl  1.1  11 years  parrello  More tweaks to the load technology.
ERDBLoadGroup.pm  1.8  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBLoad.pm  1.24  11 years  parrello  Changed to skip the sort step if a file is pre-sorted, and to catch errors that ...
ERDBGenerator.pl  1.11  9 years  parrello  General loader improvements.
ERDBGenerate.pm  1.6  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBFinder.pm  1.2  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
ERDBExtras.pm  1.6  9 years  parrello  Updates for proteindata type.
ERDBDumper.pl  1.1  10 years  parrello  New script for dumping ERDB databases.
ERDBClient.pm  1.1  10 years  olson  Commit these before I delete them again.
ERDB.pm  1.133  8 years  parrello  Updates for single-genome loader.
ERDB.js  1.4  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
DupCheck.pl  1.3  11 years  parrello  Removed obsolete use clauses.
DrugTargets.pm  1.2  10 years  parrello  ERDB 2.0 support
DrugSproutLoader.pm  1.3  10 years  parrello  Put in a hack to get around the non-commutative property of the SQL OR.
DrugClean.pl  1.2  11 years  parrello  Removed obsolete use clauses.
DeleteGenomes.pl  1.3  11 years  parrello  Removed obsolete use clauses.
DeleteChips.pl  1.1  9 years  parrello  New program to delete Staph from the expression data.
DBConvert.pl  1.3  11 years  parrello  Removed obsolete use clauses.
CuttingDBD.xml  1.1  10 years  parrello  Tutorial examples.
CustomAttributes.pm  1.46  10 years  parrello  Fixed an error in the handling of generic key queries.
CorePegs.pl  1.2  11 years  parrello  Added the "orgs" parameter to enable specifying all, all NMPDR, or only core gen...
CopyCombinedMaps.pl  1.1  8 years  parrello  Set up directory pointer for expression data. Added CopyCombinedMaps.
Contigs.pl  1.1  10 years  parrello  Tutorial examples.
ContigDNA.pm  1.3  11 years  parrello  Fixed a POD error.
CleanUp.pl  1.2  10 years  parrello  Fixed a comment.
Blocks.txt  1.1.1.1  15 years  parrello  no message
BioWords.pm  1.4  10 years  parrello  ERDB 2.0 support
BaseSproutLoader.pm  1.7  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
BaseSaplingLoader.pm  1.4  10 years  parrello  Fixed documentation for more compatibility with non-NMPDR environment.
BadIdFinder.pl  1.1  10 years  parrello  New program to find bad corresponding IDs in the SEED.
AttributesDBD.xml  1.11  10 years  parrello  ERDB 2.0 support
AttributeTest.pl  1.5  11 years  parrello  Changed so that it can run on a system without a FIG database.
AttributeReport.pl  1.5  10 years  parrello  ERDB 2.0 support
AttrTime.pl  1.2  11 years  parrello  Removed obsolete use clauses.
AttrKeyConvert.pl  1.1  11 years  parrello  New script to convert old-format attribute dumps to the new format.
AttrDBRefresh.pl  1.26  10 years  parrello  ERDB 2.0 support
AnnotationSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
AlignmentSaplingLoader.pm  1.1  9 years  parrello  More loader updates.
AliasCrunch.pl  1.10  8 years  parrello  Inverted some relationships to improve performance.
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