source: branches/3.0-stable/src/core/net/sf/basedb/core @ 5858

Name Size Rev Age Author Last Change
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authentication 5822   10 years Nicklas Nordborg References #1575: Add support for authenticator plug-in in external …
data 5827   10 years Nicklas Nordborg References #1641: Use bcrypt for storing passwords instead of MD5 …
dbengine 5756   10 years Nicklas Nordborg References #1591: Upgrade script for BASE 2.17 --> 3.0 Several …
doc-files 1538   16 years Nicklas Nordborg Implemented delete operation for BioAssaySet?, Transformation and VirtualDb?
dtd 5679   10 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
hibernate 5475   11 years Nicklas Nordborg References #1489: Update to Hibernate 3.6 * Added the 3.6 …
log 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
plugin 5729   10 years Nicklas Nordborg Fixes #1620: Implement a 'Manual derived bioassay creator' plug-in …
query 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
signal 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
snapshot 5740   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data The …
templates 5476   11 years Nicklas Nordborg References #1489: Update to Hibernate 3.6 Changed URL:s to DTD:s used …
xsd 5610   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
AbsoluteProgressReporter.java 1.5 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
AbstractBatcher.java 5.6 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
AbstractEntityQuery.java 8.8 KB 5319   12 years Nicklas Nordborg Merged pre-2.15 changes to the trunk: log:branches/2.15-stable@5251:5317
AbstractHqlQuery.java 11.2 KB 5564   11 years Nicklas Nordborg Fixes #1578: Add support for items as query parameters
AbstractQuery.java 22.7 KB 5564   11 years Nicklas Nordborg Fixes #1578: Add support for items as query parameters
AbstractResultList.java 3.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
AbstractSqlQuery.java 10.8 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
AccessControlled.java 2.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
AccountExpiredException.java 1.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
AlreadyLoggedInException.java 1.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Annotatable.java 2.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
AnnotatableProxy.java 1.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
AnnotatedItem.java 2.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Annotation.java 16.4 KB 5121   12 years Nicklas Nordborg References #1374: Caching of experimental factors This should …
AnnotationBetweenRestriction.java 5.8 KB 5817   10 years Nicklas Nordborg Fixes #1638: Add support for 'between' operator in list pages
AnnotationInRestriction.java 3.5 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
AnnotationRestriction.java 10.0 KB 5429   11 years Nicklas Nordborg References #1512: Add support for datetime annotation types Changed …
AnnotationSet.java 29.2 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
AnnotationSimpleRestriction.java 10.3 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
AnnotationType.java 45.8 KB 5518   11 years Nicklas Nordborg Merged patch release 2.16.1 to the trunk
AnnotationTypeCategory.java 4.3 KB 4696   13 years Nicklas Nordborg Fixes #1166: Store creation date for items
AnyToAny.java 20.4 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
Application.java 36.0 KB 5833   10 years Nicklas Nordborg References #1591: Upgrade script for BASE 2.17 --> 3.0 Check login …
ArrayBatch.java 9.8 KB 5650   10 years Nicklas Nordborg References #1597: Subtypes of items Allow selection of more default …
ArrayDesign.java 24.4 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
ArrayDesignBlock.java 11.0 KB 5220   12 years Nicklas Nordborg References #1364: Update Hibernate when HHH-4065 has been fixed …
ArrayDesignPlate.java 5.2 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ArraySlide.java 9.8 KB 5642   11 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
BaseException.java 2.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
BasicBatcher.java 18.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
BasicChildItem.java 3.2 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
BasicItem.java 16.7 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
BatchedPropertyInfo.java 1.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Batcher.java 2.6 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
BatchUtil.java 16.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
BioAssay.java 12.9 KB 5319   12 years Nicklas Nordborg Merged pre-2.15 changes to the trunk: log:branches/2.15-stable@5251:5317
BioAssaySet.java 51.4 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
BioMaterial.java 5.5 KB 5663   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
BioMaterialEvent.java 31.9 KB 5807   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data Lots …
BioMaterialEventSource.java 4.2 KB 5662   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
BioMaterialList.java 23.1 KB 5014   12 years Martin Svensson Fixes #1328 Remove all or most 'continue' statements from the code. …
BioPlate.java 13.2 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
BioPlateEvent.java 13.4 KB 5525   11 years Nicklas Nordborg References #1536: Bioplate events (take 2) Added functions in the gui …
BioPlateEventParticipant.java 8.0 KB 5523   11 years Nicklas Nordborg References #1536: Bioplate events (take 2) Implemented in the core …
BioPlateEventType.java 7.5 KB 5642   11 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
BioPlateType.java 8.9 KB 5709   10 years Nicklas Nordborg References #1597: Subtypes of items Added link to item subtype from …
BioSource.java 6.0 KB 5663   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
BioWell.java 13.4 KB 5566   11 years Nicklas Nordborg Fixes #1573: Display number of free (used) wells on a plate (bioplate …
BlockInfo.java 3.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
BooleanParameterType.java 2.4 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
ChangeHistory.java 13.7 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
ChildItem.java 3.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Client.java 9.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ClientDefaultSetting.java 5.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Coloring.java 5.2 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
CommonItem.java 2.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Config.java 10.2 KB 5595   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
ConfigurationException.java 1.6 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
ConnectionClosedException.java 1.2 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ContextKey.java 2.0 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
Controlled.java 1.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DatabaseException.java 1.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DataCube.java 19.6 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
DataCubeColumn.java 5.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DataCubeExtraValue.java 7.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DataCubeFilter.java 5.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DataCubeLayer.java 5.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DataFileType.java 18.1 KB 5773   10 years Nicklas Nordborg References #1152: Handling short read transcript sequence data * …
DataQuery.java 4.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DataResultIterator.java 3.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DateFormatException.java 1.4 KB 5430   11 years Nicklas Nordborg References #1512: Add support for datetime annotation types The …
DateParameterType.java 2.9 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
DateUtil.java 4.9 KB 5430   11 years Nicklas Nordborg References #1512: Add support for datetime annotation types The …
DbControl.java 36.0 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
DerivedBioAssay.java 17.1 KB 5749   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
DetachedItemException.java 1.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Directory.java 23.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DisallowedValueException.java 1.8 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
DiskConsumable.java 2.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DiskUsage.java 6.7 KB 5011   12 years Nicklas Nordborg Fixes #1341: Implement DiskUsage?.getUsingItems()
DiskUsageStatistics.java 8.5 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
DoubleParameterType.java 4.7 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
DynamicExtraValueQuery.java 2.8 KB 5319   12 years Nicklas Nordborg Merged pre-2.15 changes to the trunk: log:branches/2.15-stable@5251:5317
DynamicJoin.java 7.0 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
DynamicPositionQuery.java 7.3 KB 5711   10 years Nicklas Nordborg References #1618: Improve "Reporter search" performance in experiment …
DynamicPositionQueryJoiners.java 5.9 KB 5711   10 years Nicklas Nordborg References #1618: Improve "Reporter search" performance in experiment …
DynamicQuery.java 3.6 KB 5319   12 years Nicklas Nordborg Merged pre-2.15 changes to the trunk: log:branches/2.15-stable@5251:5317
DynamicRawDataQuery.java 2.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DynamicReporterQuery.java 4.4 KB 5711   10 years Nicklas Nordborg References #1618: Improve "Reporter search" performance in experiment …
DynamicRestriction.java 3.6 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
DynamicResultIterator.java 4.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
DynamicSpotQuery.java 10.5 KB 5711   10 years Nicklas Nordborg References #1618: Improve "Reporter search" performance in experiment …
DynamicSpotQueryJoiners.java 7.1 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
Experiment.java 25.2 KB 5345   12 years Nicklas Nordborg Fixes #1488: Update to Hibernate 3.5.2
ExtendedProperties.java 9.6 KB 5679   10 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
ExtendedProperty.java 8.7 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
ExtendedPropertyAccessor.java 6.1 KB 5220   12 years Nicklas Nordborg References #1364: Update Hibernate when HHH-4065 has been fixed …
ExtendedPropertyLinker.java 2.1 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
Extract.java 9.6 KB 5695   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data Fixes …
ExtraValue.java 16.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ExtraValueExpression.java 3.2 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
ExtraValueJoin.java 6.9 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
ExtraValueType.java 10.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Feature.java 3.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
FeatureBatcher.java 10.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
FeatureCoordinate.java 3.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
FeatureIdentificationMethod.java 5.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
File.java 50.1 KB 5718   10 years Nicklas Nordborg References #1604: Support for multiple files of the same type in a …
FileAttachable.java 1.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
FileParameterType.java 2.2 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
FileServer.java 16.2 KB 5618   11 years Nicklas Nordborg Fixes #1596: Force host and port on file server level for external files
FileSet.java 24.1 KB 5762   10 years Nicklas Nordborg References #1604: Support for multiple files of the same type in a …
FileSetMember.java 7.2 KB 5718   10 years Nicklas Nordborg References #1604: Support for multiple files of the same type in a …
FileStoreEnabled.java 2.5 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
FileStoreUtil.java 12.0 KB 5764   10 years Nicklas Nordborg Fixes #1624: Create array design (feature) importer for GTF files * …
filter-def.hbm.xml 5.4 KB 5476   11 years Nicklas Nordborg References #1489: Update to Hibernate 3.6 Changed URL:s to DTD:s used …
FilterBatcher.java 10.6 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
FloatParameterType.java 4.1 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
Formula.java 24.8 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
GlobalDefaultSetting.java 3.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Group.java 19.7 KB 5403   11 years Martin Svensson Fixes #1507. Burp trying to empty trashcan.
GroupPermissions.java 6.7 KB 5368   11 years Nicklas Nordborg References #1459: Named permissions keys that store predefined …
Hardware.java 11.0 KB 5699   10 years Nicklas Nordborg References #1613: Extend the 'roles' test case with some …
HasAnnotationRestriction.java 3.2 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
Help.java 6.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
HibernateUtil.java 65.8 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
HqlQueryJoiners.java 3.5 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
Identifiable.java 1.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Include.java 2.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Install.java 109.4 KB 5858   10 years Nicklas Nordborg Fixes #1648: Upgrading from BASE 2 to BASE 3 may create duplicate file …
IntegerParameterType.java 4.1 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
IntegerUtil.java 4.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
IntensityFormula.java 2.4 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
IntensityTransform.java 5.1 KB 4916   13 years Nicklas Nordborg References #1120: The dynamic part of BASE should keep track whether …
InternalJobQueue.java 17.2 KB 5406   11 years Nicklas Nordborg References #1509: Job queue order after restarting a job Added a …
InternalStorageController.java 10.1 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
InvalidAnnotationException.java 1.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
InvalidDataException.java 1.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
InvalidPasswordException.java 1.7 KB 5822   10 years Nicklas Nordborg References #1575: Add support for authenticator plug-in in external …
InvalidPathException.java 1.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
InvalidRelationException.java 2.1 KB 5623   11 years Nicklas Nordborg References #1598: Use the extensions system for data file validators …
InvalidUseOfNullException.java 1.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Item.java 26.2 KB 5730   10 years Nicklas Nordborg References #1591: Upgrade script for BASE 2.17 --> 3.0 * Images to …
ItemAlreadyExistsException.java 1.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ItemContext.java 47.5 KB 5817   10 years Nicklas Nordborg Fixes #1638: Add support for 'between' operator in list pages
ItemInUseException.java 2.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ItemKey.java 16.5 KB 5629   11 years Nicklas Nordborg Merged patch release 2.17.1 to the trunk.
ItemModifiedException.java 2.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ItemNotFoundException.java 1.8 KB 5822   10 years Nicklas Nordborg References #1575: Add support for authenticator plug-in in external …
ItemParameterType.java 2.4 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
ItemProxy.java 2.2 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
ItemQuery.java 3.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ItemResultIterator.java 3.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ItemResultList.java 7.1 KB 5218   12 years Jari Häkkinen Removed double 'the the' typos.
ItemSubtype.java 19.7 KB 5807   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data Lots …
ItemSubtypeFileType.java 5.4 KB 5713   10 years Nicklas Nordborg References #1604: Support for multiple files of the same type in a …
Job.java 62.4 KB 5595   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
JobAgent.java 17.4 KB 5406   11 years Nicklas Nordborg References #1509: Job queue order after restarting a job Added a …
JobAgentSettings.java 10.0 KB 5595   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
Key.java 1.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Keyring.java 27.1 KB 5829   10 years Nicklas Nordborg References #1641: Use bcrypt for storing passwords instead of MD5 …
Location.java 3.7 KB 5325   12 years Nicklas Nordborg References #1485: File items should be able to reference external …
LogControl.java 3.5 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
LoginException.java 1.6 KB 5822   10 years Nicklas Nordborg References #1575: Add support for authenticator plug-in in external …
LogUtil.java 1.7 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
LongParameterType.java 4.0 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
MappingBatcher.java 8.9 KB 4997   12 years Nicklas Nordborg References #1324: Check TODO markers in the BASE code Mapping is only …
MeanRawDataPropertyExpression.java 3.5 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
MeasuredBioMaterial.java 15.6 KB 5663   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
Message.java 11.9 KB 5453   11 years Nicklas Nordborg Fixes #1524: Send messages as emails Added an internal flag …
Metadata.java 23.7 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
MimeType.java 9.7 KB 5630   11 years Nicklas Nordborg References #1597: Subtypes of items Added Subtypable interface and …
MultiPermissions.java 17.7 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
Nameable.java 3.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
NameableUtil.java 2.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
News.java 8.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
NotLoggedInException.java 1.2 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
NumberOutOfRangeException.java 4.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Operator.java 10.0 KB 5817   10 years Nicklas Nordborg Fixes #1638: Add support for 'between' operator in list pages
Ownable.java 2.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
OwnableUtil.java 1.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
OwnedItem.java 3.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
package.html 878 bytes 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ParameterException.java 1.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ParameterInfo.java 2.0 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
ParameterType.java 9.0 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
ParameterValuesImpl.java 6.9 KB 5629   11 years Nicklas Nordborg Merged patch release 2.17.1 to the trunk.
Path.java 8.6 KB 4951   13 years Nicklas Nordborg Merged patch release 2.11.1 to the trunk.
PathParameterType.java 3.2 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
Permission.java 7.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
PermissionDeniedException.java 2.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
PermissionTemplate.java 4.9 KB 5368   11 years Nicklas Nordborg References #1459: Named permissions keys that store predefined …
PhysicalBioAssay.java 13.0 KB 5749   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
Plate.java 15.4 KB 5319   12 years Nicklas Nordborg Merged pre-2.15 changes to the trunk: log:branches/2.15-stable@5251:5317
PlateEvent.java 11.0 KB 5630   11 years Nicklas Nordborg References #1597: Subtypes of items Added Subtypable interface and …
PlateEventType.java 10.0 KB 5630   11 years Nicklas Nordborg References #1597: Subtypes of items Added Subtypable interface and …
PlateGeometry.java 9.5 KB 5339   12 years Nicklas Nordborg References #1442: BioPlate? events Updated isUsed() and …
PlateMapping.java 16.7 KB 5452   11 years Nicklas Nordborg References #1442: BioPlate? events Remove everything that we doen't …
PlateType.java 7.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Platform.java 15.7 KB 5764   10 years Nicklas Nordborg Fixes #1624: Create array design (feature) importer for GTF files * …
PlatformFileType.java 7.6 KB 5713   10 years Nicklas Nordborg References #1604: Support for multiple files of the same type in a …
PlatformVariant.java 13.2 KB 5764   10 years Nicklas Nordborg Fixes #1624: Create array design (feature) importer for GTF files * …
PluginConfiguration.java 26.3 KB 5617   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
PluginConfigurationRequest.java 5.2 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
PluginDefinition.java 45.5 KB 5821   10 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
PluginExecutionRequest.java 5.4 KB 5414   11 years Nicklas Nordborg References #1509: Job queue order after restarting a job Fixes a …
PluginParameter.java 5.0 KB 5218   12 years Jari Häkkinen Removed double 'the the' typos.
PluginPermission.java 1.0 KB 4669   13 years Nicklas Nordborg Merged 2.9-stable@4643:4666 to trunk.
PluginRequest.java 9.7 KB 5038   12 years Nicklas Nordborg References #108: Logging the change history of an item This enables …
PluginResponse.java 9.2 KB 5480   11 years Nicklas Nordborg References #1542: Plug-ins should be able to suggest a better job name …
PluginSessionControl.java 2.8 KB 5827   10 years Nicklas Nordborg References #1641: Use bcrypt for storing passwords instead of MD5 …
PluginType.java 10.2 KB 5613   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
PositionBatcher.java 8.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
PositionExtraValueBatcher.java 12.0 KB 5218   12 years Jari Häkkinen Removed double 'the the' typos.
PredefinedQuery.java 4.8 KB 5054   12 years Nicklas Nordborg References #108: Logging the change history of an item * Added …
Presets.java 7.9 KB 5616   11 years Nicklas Nordborg References #1592: Unified installation procedure for plug-ins, …
ProgressReporter.java 1.4 KB 5325   12 years Nicklas Nordborg References #1485: File items should be able to reference external …
Project.java 34.6 KB 5814   10 years Nicklas Nordborg References #1597: Subtypes of items Validation rules for "project …
ProjectKey.java 11.7 KB 5629   11 years Nicklas Nordborg Merged patch release 2.17.1 to the trunk.
ProjectPermissions.java 7.5 KB 5368   11 years Nicklas Nordborg References #1459: Named permissions keys that store predefined …
PropertyFilter.java 25.2 KB 5817   10 years Nicklas Nordborg Fixes #1638: Add support for 'between' operator in list pages
Protocol.java 17.2 KB 5699   10 years Nicklas Nordborg References #1613: Extend the 'roles' test case with some …
Quantity.java 16.0 KB 4888   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 All *.java, *.jsp and …
QueryExecutor.java 9.5 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
QueryRuntimeFilter.java 2.5 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
QueryRuntimeFilterFactory.java 15.8 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
QueryRuntimeFilterManager.java 2.5 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
Quota.java 12.9 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
QuotaException.java 2.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
QuotaType.java 5.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
RawBioAssay.java 41.3 KB 5807   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data Lots …
RawDataBatcher.java 20.0 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
RawDataProperty.java 1.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
RawDataPropertyExpression.java 5.1 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
RawDataType.java 9.8 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
RawDataTypes.java 17.0 KB 5679   10 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
RawDataUtil.java 2.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
RealJoin.java 5.4 KB 5320   12 years Nicklas Nordborg Fixes #1471: Implement equals() and hashCode() in all QueryElement?
RealTable.java 2.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Registered.java 1.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Removable.java 2.3 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Reporter.java 7.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ReporterBatcher.java 8.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ReporterList.java 22.0 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ReporterListJoin.java 6.7 KB 5711   10 years Nicklas Nordborg References #1618: Improve "Reporter search" performance in experiment …
ReporterPropertyExpression.java 4.1 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
ReporterScore.java 2.2 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
ReporterScoreQuery.java 2.4 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
ReporterScoreResultIterator.java 2.9 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
ReporterType.java 6.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
RequestInformation.java 4.9 KB 4962   12 years Nicklas Nordborg Fixes #1329: A plug-in should be able to use a JSP page from an …
Role.java 11.3 KB 5818   10 years Nicklas Nordborg References #1590: Documentation cleanup Some more sections in the …
RoleKey.java 7.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Sample.java 8.6 KB 5688   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data Fixes …
ScrollIterator.java 2.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
SecondaryStorageController.java 3.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Session.java 5.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
SessionControl.java 65.5 KB 5829   10 years Nicklas Nordborg References #1641: Use bcrypt for storing passwords instead of MD5 …
Setting.java 4.5 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Shareable.java 3.6 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
ShareableUtil.java 9.9 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
SharedItem.java 3.9 KB 5368   11 years Nicklas Nordborg References #1459: Named permissions keys that store predefined …
SimpleAbsoluteProgressReporter.java 2.6 KB 5374   11 years Nicklas Nordborg References #1479: Create BASEfile importer for the external program …
SimpleProgressReporter.java 2.2 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
Software.java 8.2 KB 5685   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
SpecialQuery.java 2.5 KB 5662   10 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
SpotBatcher.java 11.3 KB 4992   12 years Nicklas Nordborg References #1324: Check TODO markers in the BASE code We have made it …
SpotExtraValueBatcher.java 11.7 KB 5218   12 years Jari Häkkinen Removed double 'the the' typos.
SpotImage.java 1.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
SpotImages.java 31.1 KB 5630   11 years Nicklas Nordborg References #1597: Subtypes of items Added Subtypable interface and …
StringParameterType.java 4.1 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
StringTooLongException.java 1.8 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
StringUtil.java 8.2 KB 5534   11 years Nicklas Nordborg Fixes #1565: Command line options for the external program executor …
Subtypable.java 1.3 KB 5631   11 years Nicklas Nordborg References #1597: Subtypes of items Added support for subtypes with …
SubtypableRelatedItems.java 1.5 KB 5823   10 years Nicklas Nordborg References #1590: Documentation cleanup Fixed javadoc warnings.
SystemItem.java 2.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
SystemItems.java 4.7 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Tag.java 4.9 KB 5641   11 years Nicklas Nordborg References #1153: Handling short read transcript sequence data …
TimestampParameterType.java 2.8 KB 5437   11 years Nicklas Nordborg Fixes #1519: Add TimestampParameterType? to plug-in api and provide …
Transactional.java 2.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Transformation.java 15.9 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
Trashcan.java 9.6 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
Type.java 15.3 KB 5776   10 years Nicklas Nordborg Fixes #1633: NumberFormatException? when parsing NaN values
Unit.java 17.7 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
UnmodifiableResultList.java 3.3 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
UnsavedItemException.java 2.0 KB 4517   13 years Jari Häkkinen Addresses #1106. Missed to change reference wherefrom retrive GPLv3 …
UnsupportedFileFormatException.java 2.0 KB 4594   13 years Nicklas Nordborg Fixes #1145: Make the generic raw data importer support batch import
Update.java 67.5 KB 5858   10 years Nicklas Nordborg Fixes #1648: Upgrading from BASE 2 to BASE 3 may create duplicate file …
UsableDataFileType.java 1.4 KB 5713   10 years Nicklas Nordborg References #1604: Support for multiple files of the same type in a …
User.java 40.2 KB 5829   10 years Nicklas Nordborg References #1641: Use bcrypt for storing passwords instead of MD5 …
UserClientSetting.java 8.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
UserDefaultSetting.java 6.1 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
UserPermissions.java 6.7 KB 5368   11 years Nicklas Nordborg References #1459: Named permissions keys that store predefined …
Validatable.java 1.4 KB 4889   13 years Nicklas Nordborg References #1290: Change source files to UTF-8 Changed 'Hakkinen' to …
Values.java 4.1 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
Version.java 4.7 KB 5607   11 years Nicklas Nordborg References #1593: Extension system for the core API References #1592: …
VirtualColumn.java 9.7 KB 5590   11 years Nicklas Nordborg References #1589: Delete deprecated classes and methods Removed …
VirtualDb.java 12.3 KB 5689   10 years Nicklas Nordborg Fixes #1612: Remove commented out code that is no longer in use Added …
VirtualTable.java 9.1 KB 5384   11 years Nicklas Nordborg References #1498: Investigate and fix issues found by FindBugs? Fixes …
Well.java 10.4 KB 5319   12 years Nicklas Nordborg Merged pre-2.15 changes to the trunk: log:branches/2.15-stable@5251:5317
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