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Index of /Sprout

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File Rev. Age Author Last log entry
 Parent Directory        
ERDataBase/        
Shuffler/        
AliasCrunch.pl  1.1  10 years  parrello  New script to process aliases.
AnnotationSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
AttrDBRefresh.pl  1.26  10 years  parrello  ERDB 2.0 support
AttrKeyConvert.pl  1.1  10 years  parrello  New script to convert old-format attribute dumps to the new format.
AttrTime.pl  1.2  11 years  parrello  Removed obsolete use clauses.
AttributeReport.pl  1.5  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.
AttributesDBD.xml  1.11  10 years  parrello  ERDB 2.0 support
BadIdFinder.pl  1.1  10 years  parrello  New program to find bad corresponding IDs in the SEED.
BaseSaplingLoader.pm  1.3  10 years  parrello  Added a utility method for loading from files. Converted subsystem names from MD...
BaseSproutLoader.pm  1.6  10 years  parrello  Added support for loading from an alternate directory. Fixed to avoid loading su...
BioWords.pm  1.4  10 years  parrello  ERDB 2.0 support
Blocks.txt  1.1.1.1  14 years  parrello  no message
CleanUp.pl  1.2  10 years  parrello  Fixed a comment.
ContigDNA.pm  1.3  11 years  parrello  Fixed a POD error.
Contigs.pl  1.1  10 years  parrello  Tutorial examples.
CorePegs.pl  1.2  11 years  parrello  Added the "orgs" parameter to enable specifying all, all NMPDR, or only core gen...
CustomAttributes.pm  1.43  10 years  parrello  Updated to use Bob's protocol for load options.
CuttingDBD.xml  1.1  10 years  parrello  Tutorial examples.
DBConvert.pl  1.3  11 years  parrello  Removed obsolete use clauses.
DeleteGenomes.pl  1.3  11 years  parrello  Removed obsolete use clauses.
DrugClean.pl  1.2  11 years  parrello  Removed obsolete use clauses.
DrugSproutLoader.pm  1.3  10 years  parrello  Put in a hack to get around the non-commutative property of the SQL OR.
DrugTargets.pm  1.2  10 years  parrello  ERDB 2.0 support
DupCheck.pl  1.3  11 years  parrello  Removed obsolete use clauses.
ERDB.js  1.1  10 years  parrello  Target search support.
ERDB.pm  1.119  10 years  parrello  Updated to use Bob's protocol for load options.
ERDBClient.pm  1.1  10 years  olson  Commit these before I delete them again.
ERDBDumper.pl  1.1  10 years  parrello  New script for dumping ERDB databases.
ERDBFinder.pm  1.1  10 years  parrello  Target search support.
ERDBGenerate.pm  1.4  10 years  parrello  Removed the duplicates hash to save memory.
ERDBGenerator.pl  1.7  10 years  parrello  Added memory tracing.
ERDBLoad.pm  1.24  10 years  parrello  Changed to skip the sort step if a file is pre-sorted, and to catch errors that ...
ERDBLoadGroup.pm  1.6  10 years  parrello  Added memory tracing and cleanup support.
ERDBLoadKill.pl  1.1  10 years  parrello  More tweaks to the load technology.
ERDBLoader.pl  1.10  10 years  parrello  Updated to use Bob's protocol for load options.
ERDBObject.pm  1.8  10 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
ERDBPDocPage.pm  1.3  10 years  parrello  Added diagram support.
ERDBQuery.pm  1.5  10 years  parrello  Fixed a comment.
ERDBQueryConsole.pm  1.2  10 years  parrello  Refactored to allow creation oif an ERDB console page in the Seed Viewer.
ERDBServer.cgi  1.1  10 years  olson  Commit these before I delete them again.
ERDBTune.pl  1.1  10 years  parrello  New database utility script.
ERDBType.pm  1.2  10 years  parrello  Added a virtual method that indicates whether or not a type is scalar or complex...
ERDBTypeBoolean.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeChar.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeCounter.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeDNA.pm  1.2  10 years  parrello  Fixed a bad comment.
ERDBTypeDate.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeFloat.pm  1.3  10 years  parrello  Fixed the pattern string for validation.
ERDBTypeHashString.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeImage.pm  1.2  10 years  parrello  Added an override to the ObjectType method that indicates this is a complex data...
ERDBTypeInteger.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeLink.pm  1.2  10 years  parrello  Added an override to the ObjectType method that indicates this is a complex data...
ERDBTypeLongString.pm  1.2  10 years  parrello  Fixed an error in the decoding method.
ERDBTypeRectangle.pm  1.1  10 years  parrello  New data type for rectangular regions.
ERDBTypeSemiBoolean.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeString.pm  1.1  10 years  parrello  ERDB 2.0 support
ERDBTypeText.pm  1.2  10 years  parrello  Increased the size of text fields.
EvCodeRefresh.pl  1.4  11 years  parrello  Converted to new multi-table design concept for attributes.
Exceptions.txt  1.2  10 years  parrello  Added rules for "archael" and "bacterial".
ExportAttributes.pl  1.2  11 years  parrello  Removed obsolete use clauses.
FCTester.pl  1.1  10 years  parrello  Test script for functional coupling updates.
FIGSproutTest.pl  1.3  14 years  olson  Fixes to put XML file in FIGdisk/FIG.
FamilySaplingLoader.pm  1.2  10 years  parrello  Fixed to clean subsystem objects.
FeatureSaplingLoader.pm  1.2  10 years  parrello  Changed the way identifiers are handled.
FeatureSproutLoader.pm  1.9  10 years  parrello  Redid the alias logic. Added memory tracing. Fixed to clear the subsystem cache ...
FidCheck.pm  1.3  11 years  parrello  Changed POD format for better compatability with Wiki.
FigConfigFix.pl  1.5  10 years  parrello  Removed obsolete typing code.
GeneFile.pl  1.4  11 years  parrello  Removed obsolete use clauses.
GenomeSaplingLoader.pm  1.2  10 years  parrello  Converted to use NCBI taxonomy dumps. Added genome sets.
GenomeSproutLoader.pm  1.4  10 years  parrello  Added support for representative genomes and more robust group assignment.
GenomeStats.pl  1.36  10 years  parrello  Made organism stats tables sortable.
Genomes.pl  1.1  10 years  parrello  Tutorial examples.
HyperLink.pm  1.1  10 years  parrello  ERDB 2.0 support
LoadFIGTables.pl  1.2  11 years  parrello  Removed obsolete use clauses.
LoadScript.pl  1.4  11 years  parrello  Removed obsolete use clauses.
LoadSproutTables.pl  1.49  10 years  parrello  Fixed some documentation, set the default trace level to 3.
Makefile  1.22  10 years  parrello  Added javascript support. Removed support for DBD documentation, which is accomp...
MarkupTest.pl  1.3  11 years  parrello  Removed obsolete use clauses.
ModelLoader.pm  1.1  10 years  chenry  *** empty log message ***
ModelSaplingLoader.pm  1.2  10 years  parrello  Fixed to skip models for non-Sapling genomes.
NeighboringFeatures.pl  1.1  10 years  parrello  Tutorial examples.
NewSproutDBD.xml  1.3  10 years  parrello  *** empty log message ***
NewStuffCheck.pl  1.27  10 years  parrello  Improved site maintenance utilities.
NmpdrCheck.pl  1.2  10 years  parrello  Improved site maintenance utilities.
NmpdrFix.pl  1.2  10 years  parrello  Improved site maintenance utilities.
NmpdrPage.pm  1.1  13 years  parrello  Moved NMPDRPage to Sprout directory.
NmpdrSearch.png  1.2  13 years  parrello  Changed to the globe thingy.
NmpdrSearch.src  1.2  13 years  parrello  Fixed a bad URL.
NmpdrSetup.pl  1.2  10 years  parrello  ERDB 2.0 support
NmpdrStats.pl  1.3  10 years  parrello  Added display of subsystem count.
NmpdrStatus.pl  1.2  11 years  parrello  Removed obsolete use clauses.
NmpdrSwitch.pl  1.2  11 years  parrello  Removed obsolete use clauses.
PropertySproutLoader.pm  1.3  10 years  parrello  Removed PFAMs from the attributes to avoid a memory problem.
RHFeatures.pm  1.13  10 years  parrello  Converted to use new hint support.
RHLigands.pm  1.4  10 years  parrello  Improved search result support.
RHLocations.pm  1.7  10 years  parrello  Converted viewer buttons to feature links.
ReactionSproutLoader.pm  1.3  10 years  parrello  Fixed to clean subsystem objects.
Rectangle.pm  1.1  10 years  parrello  New data type for rectangular regions.
ResultHelper.pm  1.7  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.
SHDrugSearch.pm  1.12  10 years  parrello  Improved search result support.
SHGeneBbhSearch.pm  1.1  10 years  parrello  Improved search result support.
SHGeneSearch.pm  1.4  10 years  parrello  Improved search result support.
SHOpSearch.pm  1.6  10 years  parrello  Converted to new hint system.
SHOrgSumSearch.pm  1.1  10 years  parrello  Improved search result support.
SHPropSearch.pm  1.8  10 years  parrello  Improved search result support.
SHSigGenes.pm  1.22  10 years  parrello  Converted to new hint system.
SHSubSearch.pm  1.10  10 years  parrello  Improved search result support.
SHTargetSearch.js  1.1  10 years  parrello  Target search support
SHTargetSearch.pm  1.2  10 years  parrello  Fixed criterion sort.
SHToolSearch.pm  1.8  10 years  parrello  Changed column ordering in results.
SHWordSearch.pm  1.12  10 years  parrello  Cleaned up some error messages. Fixed some bugs in search.
Sapling.pm  1.7  10 years  parrello  Updated to use Bob's protocol for load options.
SaplingConfig.xml  1.1  10 years  parrello  Sapling support.
ScenarioSaplingLoader.pm  1.2  10 years  parrello  Fixed to clean subsystem objects.
SearchHelper.pm  1.48  10 years  parrello  Added ID parsing logic for the Batch Search.
SearchSkeleton.pm  1.4  10 years  parrello  Converted to new hint system.
SetGroup.pl  1.2  11 years  parrello  Removed obsolete use clauses.
SetPermissions.pl  1.8  11 years  parrello  Removed obsolete use clauses.
ShowCounts.pl  1.20  10 years  parrello  Changed heading style.
SimBlocks.pm  1.11  11 years  parrello  Changed POD format for better compatability with Wiki.
SimBlocksDBD.xml  1.5  13 years  parrello  Replaced field "end" with "endpoint" to fix reserved word problem.
SimLoad.pl  1.12  10 years  parrello  ERDB 2.0 support
SingleTableLoad.pl  1.3  11 years  parrello  Removed obsolete use clauses.
SiteMeter.html  1.1  11 years  parrello  Added to make SiteMeter code more generally available.
SourceSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
SpanishInquisition.pl  1.2  11 years  parrello  Converted to use StandardSetup.
Sprout.pm  1.127  10 years  parrello  Updated to use Bob's protocol for load options.
SproutDBD.xml  1.62  10 years  parrello  Added a new relationship for representative genome support.
SproutGFF.pl  1.3  11 years  parrello  Removed obsolete use clauses.
SproutLoad.pm  1.97  10 years  parrello  New loader technology.
SproutNotes.htm  1.1.1.1  14 years  parrello  no message
SproutQuery.pm  1.2  13 years  parrello  Fxied obsolete references to the {_erdb} member.
SproutStats.pl  1.2  13 years  parrello  Fxied obsolete references to the {_erdb} member.
SproutSubsys.pm  1.22  10 years  parrello  Fixed a bug in genome/role processing.
StopWords.txt  1.1  10 years  parrello  Changes for v24 database.
SubsystemSaplingLoader.pm  1.4  10 years  parrello  Fixed to clean subsystem objects.
SubsystemSproutLoader.pm  1.4  10 years  parrello  Fixed to clean subsystem objects.
SynonymSproutLoader.pm  1.2  10 years  parrello  ERDB 2.0 support
TargetCriterion.pm  1.1  10 years  parrello  Target search support
TargetCriterionCellLocation.pm  1.1  10 years  parrello  Target search support
TargetCriterionCodeMatch.pm  1.1  10 years  parrello  Target search support
TargetCriterionConservedNeighborhood.pm  1.1  10 years  parrello  Target search support
TargetCriterionEC.pm  1.1  10 years  parrello  Target search support
TargetCriterionExternalId.pm  1.1  10 years  parrello  Target search support
TargetCriterionGeneId.pm  1.1  10 years  parrello  Target search support
TargetCriterionGeneric.pm  1.1  10 years  parrello  Target search support
TargetCriterionKeyword.pm  1.1  10 years  parrello  Target search support
TargetCriterionLookup.pm  1.1  10 years  parrello  Failed to add in previous version.
TargetCriterionNull.pm  1.1  10 years  parrello  Target search support
TargetCriterionQuery.pm  1.1  10 years  parrello  Target search support
TargetCriterionRange.pm  1.1  10 years  parrello  Target search support
TargetCriterionSmallTable.pm  1.1  10 years  parrello  Target search support
fig.htaccess  1.1  10 years  parrello  Blank htaccess file for future use.
indexCGI.pl  1.1  10 years  parrello  DirectoryIndex script for NMPDR.
locations.pl  1.2  12 years  parrello  Fixed default trace level.
nmpdr.js  1.5  10 years  parrello  Added support for some stuff Leslie is doing.
robots.txt  1.4  10 years  parrello  Removed some obsolete stuff.
startconsole.bat  1.1  14 years  parrello  Added this script for starting a FIG console on Windows machines.
variation.html  1.1.1.1  14 years  parrello  no message

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