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File Rev. Age Author Last log entry
 Parent Directory        
ERDataBase/        
Shuffler/        
ModelLoader.pm  1.1  10 years  chenry  *** empty log message ***
ERDBServer.cgi  1.1  10 years  olson  Commit these before I delete them again.
ERDBClient.pm  1.1  10 years  olson  Commit these before I delete them again.
FIGSproutTest.pl  1.3  14 years  olson  Fixes to put XML file in FIGdisk/FIG.
TargetCriterionCellLocation.pm  1.1  10 years  parrello  Target search support
ERDBTypeImage.pm  1.2  10 years  parrello  Added an override to the ObjectType method that indicates this is a complex data...
BaseSaplingLoader.pm  1.3  10 years  parrello  Added a utility method for loading from files. Converted subsystem names from MD...
ExportAttributes.pl  1.2  11 years  parrello  Removed obsolete use clauses.
NmpdrPage.pm  1.1  13 years  parrello  Moved NMPDRPage to Sprout directory.
ERDBTypeString.pm  1.1  10 years  parrello  ERDB 2.0 support
SHTargetSearch.js  1.1  10 years  parrello  Target search support
ERDBTypeChar.pm  1.1  10 years  parrello  ERDB 2.0 support
Sapling.pm  1.7  10 years  parrello  Updated to use Bob's protocol for load options.
TargetCriterionKeyword.pm  1.1  10 years  parrello  Target search support
NmpdrSearch.src  1.2  13 years  parrello  Fixed a bad URL.
TargetCriterionGeneric.pm  1.1  10 years  parrello  Target search support
NewSproutDBD.xml  1.3  10 years  parrello  *** empty log message ***
ERDBDumper.pl  1.1  10 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  1.1  10 years  parrello  ERDB 2.0 support
LoadScript.pl  1.4  11 years  parrello  Removed obsolete use clauses.
SHDrugSearch.pm  1.12  10 years  parrello  Improved search result support.
ERDBQuery.pm  1.5  10 years  parrello  Fixed a comment.
CorePegs.pl  1.2  11 years  parrello  Added the "orgs" parameter to enable specifying all, all NMPDR, or only core gen...
ERDBObject.pm  1.8  10 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
GenomeStats.pl  1.36  10 years  parrello  Made organism stats tables sortable.
NmpdrSearch.png  1.2  13 years  parrello  Changed to the globe thingy.
SHTargetSearch.pm  1.2  10 years  parrello  Fixed criterion sort.
GeneFile.pl  1.4  11 years  parrello  Removed obsolete use clauses.
DBConvert.pl  1.3  11 years  parrello  Removed obsolete use clauses.
SHOpSearch.pm  1.6  10 years  parrello  Converted to new hint system.
fig.htaccess  1.1  10 years  parrello  Blank htaccess file for future use.
NmpdrFix.pl  1.2  10 years  parrello  Improved site maintenance utilities.
CleanUp.pl  1.2  10 years  parrello  Fixed a comment.
ERDBTypeLongString.pm  1.2  10 years  parrello  Fixed an error in the decoding method.
AttrDBRefresh.pl  1.26  10 years  parrello  ERDB 2.0 support
RHLocations.pm  1.7  10 years  parrello  Converted viewer buttons to feature links.
ERDBLoader.pl  1.10  10 years  parrello  Updated to use Bob's protocol for load options.
BaseSproutLoader.pm  1.6  10 years  parrello  Added support for loading from an alternate directory. Fixed to avoid loading su...
AliasCrunch.pl  1.1  10 years  parrello  New script to process aliases.
SubsystemSproutLoader.pm  1.4  10 years  parrello  Fixed to clean subsystem objects.
ShowCounts.pl  1.20  10 years  parrello  Changed heading style.
ERDBPDocPage.pm  1.3  10 years  parrello  Added diagram support.
SHGeneBbhSearch.pm  1.1  10 years  parrello  Improved search result support.
DupCheck.pl  1.3  11 years  parrello  Removed obsolete use clauses.
NmpdrStats.pl  1.3  10 years  parrello  Added display of subsystem count.
ERDBTypeBoolean.pm  1.1  10 years  parrello  ERDB 2.0 support
SproutSubsys.pm  1.22  10 years  parrello  Fixed a bug in genome/role processing.
SimBlocksDBD.xml  1.5  13 years  parrello  Replaced field "end" with "endpoint" to fix reserved word problem.
CustomAttributes.pm  1.43  10 years  parrello  Updated to use Bob's protocol for load options.
SiteMeter.html  1.1  11 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  1.9  10 years  parrello  Redid the alias logic. Added memory tracing. Fixed to clear the subsystem cache ...
GenomeSproutLoader.pm  1.4  10 years  parrello  Added support for representative genomes and more robust group assignment.
ScenarioSaplingLoader.pm  1.2  10 years  parrello  Fixed to clean subsystem objects.
DrugSproutLoader.pm  1.3  10 years  parrello  Put in a hack to get around the non-commutative property of the SQL OR.
Contigs.pl  1.1  10 years  parrello  Tutorial examples.
NmpdrCheck.pl  1.2  10 years  parrello  Improved site maintenance utilities.
NmpdrSwitch.pl  1.2  11 years  parrello  Removed obsolete use clauses.
ResultHelper.pm  1.7  10 years  parrello  Improved search result support.
ERDBLoadGroup.pm  1.6  10 years  parrello  Added memory tracing and cleanup support.
TargetCriterionNull.pm  1.1  10 years  parrello  Target search support
indexCGI.pl  1.1  11 years  parrello  DirectoryIndex script for NMPDR.
ERDBLoadKill.pl  1.1  10 years  parrello  More tweaks to the load technology.
SproutDBD.xml  1.62  10 years  parrello  Added a new relationship for representative genome support.
SproutQuery.pm  1.2  13 years  parrello  Fxied obsolete references to the {_erdb} member.
SHToolSearch.pm  1.8  10 years  parrello  Changed column ordering in results.
NewStuffCheck.pl  1.27  10 years  parrello  Improved site maintenance utilities.
CuttingDBD.xml  1.1  10 years  parrello  Tutorial examples.
AnnotationSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
DeleteGenomes.pl  1.3  11 years  parrello  Removed obsolete use clauses.
Blocks.txt  1.1.1.1  14 years  parrello  no message
NmpdrSetup.pl  1.2  10 years  parrello  ERDB 2.0 support
BioWords.pm  1.4  10 years  parrello  ERDB 2.0 support
LoadFIGTables.pl  1.2  11 years  parrello  Removed obsolete use clauses.
SHSigGenes.pm  1.22  10 years  parrello  Converted to new hint system.
ERDB.pm  1.119  10 years  parrello  Updated to use Bob's protocol for load options.
FamilySaplingLoader.pm  1.2  10 years  parrello  Fixed to clean subsystem objects.
Exceptions.txt  1.2  10 years  parrello  Added rules for "archael" and "bacterial".
ERDBQueryConsole.pm  1.2  10 years  parrello  Refactored to allow creation oif an ERDB console page in the Seed Viewer.
AttributeReport.pl  1.5  10 years  parrello  ERDB 2.0 support
SynonymSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
SproutNotes.htm  1.1.1.1  14 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  1.3  10 years  parrello  Fixed the pattern string for validation.
EvCodeRefresh.pl  1.4  11 years  parrello  Converted to new multi-table design concept for attributes.
ReactionSproutLoader.pm  1.3  10 years  parrello  Fixed to clean subsystem objects.
SetGroup.pl  1.2  11 years  parrello  Removed obsolete use clauses.
SHWordSearch.pm  1.12  10 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
ERDBTypeCounter.pm  1.1  10 years  parrello  ERDB 2.0 support
TargetCriterionCodeMatch.pm  1.1  10 years  parrello  Target search support
SpanishInquisition.pl  1.2  11 years  parrello  Converted to use StandardSetup.
NeighboringFeatures.pl  1.1  10 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  1.1  10 years  parrello  New data type for rectangular regions.
FeatureSaplingLoader.pm  1.2  10 years  parrello  Changed the way identifiers are handled.
TargetCriterionLookup.pm  1.1  10 years  parrello  Failed to add in previous version.
ERDBFinder.pm  1.1  10 years  parrello  Target search support.
SHBatchSearch.pm  1.4  10 years  parrello  Added an entry field for pasting IDs in addition to uploading them.
SproutLoad.pm  1.97  10 years  parrello  New loader technology.
ERDBTypeInteger.pm  1.1  10 years  parrello  ERDB 2.0 support
PropertySproutLoader.pm  1.3  10 years  parrello  Removed PFAMs from the attributes to avoid a memory problem.
ERDBTypeText.pm  1.2  10 years  parrello  Increased the size of text fields.
NmpdrStatus.pl  1.2  11 years  parrello  Removed obsolete use clauses.
SourceSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
variation.html  1.1.1.1  14 years  parrello  no message
TargetCriterionConservedNeighborhood.pm  1.1  10 years  parrello  Target search support
Makefile  1.22  10 years  parrello  Added javascript support. Removed support for DBD documentation, which is accomp...
SetPermissions.pl  1.8  11 years  parrello  Removed obsolete use clauses.
ERDBTypeHashString.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBGenerate.pm  1.4  10 years  parrello  Removed the duplicates hash to save memory.
Genomes.pl  1.1  10 years  parrello  Tutorial examples.
SproutStats.pl  1.2  13 years  parrello  Fxied obsolete references to the {_erdb} member.
TargetCriterionQuery.pm  1.1  10 years  parrello  Target search support
nmpdr.js  1.5  10 years  parrello  Added support for some stuff Leslie is doing.
BadIdFinder.pl  1.1  10 years  parrello  New program to find bad corresponding IDs in the SEED.
SHPropSearch.pm  1.8  10 years  parrello  Improved search result support.
DrugClean.pl  1.2  11 years  parrello  Removed obsolete use clauses.
ERDBGenerator.pl  1.7  10 years  parrello  Added memory tracing.
FCTester.pl  1.1  10 years  parrello  Test script for functional coupling updates.
ModelSaplingLoader.pm  1.2  10 years  parrello  Fixed to skip models for non-Sapling genomes.
TargetCriterionSmallTable.pm  1.1  10 years  parrello  Target search support
HyperLink.pm  1.1  10 years  parrello  ERDB 2.0 support
SaplingConfig.xml  1.1  10 years  parrello  Sapling support.
AttrTime.pl  1.2  11 years  parrello  Removed obsolete use clauses.
AttributesDBD.xml  1.11  10 years  parrello  ERDB 2.0 support
MarkupTest.pl  1.3  11 years  parrello  Removed obsolete use clauses.
TargetCriterionExternalId.pm  1.1  10 years  parrello  Target search support
TargetCriterion.pm  1.1  10 years  parrello  Target search support
SearchHelper.pm  1.48  10 years  parrello  Added ID parsing logic for the Batch Search.
ERDBType.pm  1.2  10 years  parrello  Added a virtual method that indicates whether or not a type is scalar or complex...
Rectangle.pm  1.1  10 years  parrello  New data type for rectangular regions.
locations.pl  1.2  12 years  parrello  Fixed default trace level.
AttributeTest.pl  1.5  11 years  parrello  Changed so that it can run on a system without a FIG database.
SHOrgSumSearch.pm  1.1  10 years  parrello  Improved search result support.
ERDB.js  1.1  10 years  parrello  Target search support.
ERDBTypeLink.pm  1.2  10 years  parrello  Added an override to the ObjectType method that indicates this is a complex data...
RHFeatures.pm  1.13  10 years  parrello  Converted to use new hint support.
TargetCriterionRange.pm  1.1  10 years  parrello  Target search support
SHGeneSearch.pm  1.4  10 years  parrello  Improved search result support.
TargetCriterionGeneId.pm  1.1  10 years  parrello  Target search support
ERDBTypeSemiBoolean.pm  1.1  10 years  parrello  ERDB 2.0 support
SubsystemSaplingLoader.pm  1.4  10 years  parrello  Fixed to clean subsystem objects.
SHSubSearch.pm  1.10  10 years  parrello  Improved search result support.
FigConfigFix.pl  1.5  10 years  parrello  Removed obsolete typing code.
ERDBTypeDNA.pm  1.2  10 years  parrello  Fixed a bad comment.
TargetCriterionEC.pm  1.1  10 years  parrello  Target search support
FidCheck.pm  1.3  11 years  parrello  Changed POD format for better compatability with Wiki.
SproutGFF.pl  1.3  11 years  parrello  Removed obsolete use clauses.
Sprout.pm  1.127  10 years  parrello  Updated to use Bob's protocol for load options.
RHLigands.pm  1.4  10 years  parrello  Improved search result support.
GenomeSaplingLoader.pm  1.2  10 years  parrello  Converted to use NCBI taxonomy dumps. Added genome sets.
ERDBTune.pl  1.1  10 years  parrello  New database utility script.
SimLoad.pl  1.12  10 years  parrello  ERDB 2.0 support
SearchSkeleton.pm  1.4  10 years  parrello  Converted to new hint system.
DrugTargets.pm  1.2  10 years  parrello  ERDB 2.0 support
SimBlocks.pm  1.11  11 years  parrello  Changed POD format for better compatability with Wiki.
ContigDNA.pm  1.3  11 years  parrello  Fixed a POD error.
SingleTableLoad.pl  1.3  11 years  parrello  Removed obsolete use clauses.

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