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Author SHA1 Message Date
halfdan 510170be50 Refactored ABC 
refs #36
 2014-11-23 14:56:42 +01:00
halfdan 08f7b92f86 Fix Artificial Bee Colony by using inverse fitness probability 2014-11-22 19:34:04 +01:00
halfdan 6ae2aa28b9 Finally getting rid of the eva2.optimization.go package 
- Moved GUI related stuff (StandaloneOptimization, MOCCOStandalone, ...) to eva2.gui
- Moved InterfaceOptimizationParameters and implementations up to eva2.optimization
- Moved Processor out of modules
 2014-11-22 11:48:17 +01:00
halfdan 031e5b432a Add Population serializer. 2014-11-18 19:32:19 +01:00
halfdan ad7a5ea86c New CPUPanel to show process load vs. system load. 
Small cleanup.
 2014-11-18 17:15:40 +01:00
halfdan 91549862f1 Removed a few tiptexts from GA 2014-11-18 16:02:35 +01:00
halfdan 0479716f43 Refactor DE and add Rand/2 strategy 2014-11-18 11:34:59 +01:00
halfdan 563c407f0b New --version flag to show current EvA2 version. 2014-11-18 11:34:43 +01:00
halfdan 7f5f3c5cea Show useful info for classes with subtypes. 
closes #35
- Show assignable subtypes
- Rename YamlStatistics to CommandLineStatistics
 2014-11-16 14:47:17 +01:00
halfdan e5c8322d78 Properly format --help output. 
refs #35
 2014-11-16 00:51:00 +01:00
halfdan 35bd5c4a9e Added ParameterGenerator for Command Line interface. 
Added --help parameter to show help for CLI mode.

refs #35
 2014-11-15 12:00:06 +01:00
halfdan 17263cc023 Graceful fallback when .yml files fail to load. 
Only save params once per optimization.
 2014-11-15 07:08:14 +01:00
halfdan 667e069bcc Initialize Look and Feel seperately. 2014-11-15 06:38:10 +01:00
halfdan ca108a5d97 Fix performance issue with CLI execution (SnakeYAML doesn't perform well 
when serializing large objects)
Implement easier access for terminators.
 2014-11-14 17:55:23 +01:00
halfdan 5a80cb781e Processor thread now has a name. 
Fix several html files.
 2014-11-14 15:38:26 +01:00
halfdan b8b44b7644 Code cleanup, comments, javadoc fixes. 2014-11-14 14:33:56 +01:00
halfdan 553002c834 Complete Yaml output for CLI mode. 
Cleanup of AbstractStatistics
 2014-11-14 11:32:05 +01:00
halfdan 2e1f862718 YamlStatistics mostly implemented. 2014-11-13 18:22:14 +01:00
halfdan c3eddfbee4 Removes deprecated method createNextGenerationPerformed from 
InterfaceStatistics. This was only used in EvA2ESModel.
 2014-11-13 17:57:49 +01:00
halfdan ca70b48bd2 Fixed comment fuckup where simple was replaced with eva2.problems.simple 
Implements YamlStatistics in cli.Main
A few fixes in the processor to allow GUI-less optimization
 2014-11-13 17:49:40 +01:00
halfdan 3627d33df5 Cleanup. 2014-11-13 17:23:35 +01:00
halfdan 153b6e3974 Correctly repaint JobList when optimization is done. 2014-11-13 17:13:52 +01:00
halfdan 4326044a1b Organize imports. 
Fix missing data header in F8Problem.
Fix several tip texts.
 2014-11-13 14:50:13 +01:00
halfdan 83194f4d04 Hide stats field and use parameter annotation. 2014-11-13 11:06:32 +01:00
halfdan a2ddf25ce6 Random cleanup and start of CLI log implementation. 2014-11-12 19:23:21 +01:00
halfdan 9ea3f4d464 Fix image references and name changes. 2014-11-12 19:23:03 +01:00
halfdan 014fd85beb Refactor EVAHELP and remove it. 2014-11-12 14:35:58 +01:00
halfdan 40df065a58 Fix the png export by simply using the FunctionArea graphics. 2014-11-11 17:01:31 +01:00
halfdan 837c4fea32 JavaDoc fixes and larger code cleanup. 2014-11-11 16:58:43 +01:00
halfdan 7c896fea8d Test tTestEqSize 
refs #34
 2014-11-11 02:00:58 +01:00
halfdan 1af305ae3d Fix variance implementation and add tests to Math package. 
refs #34
 2014-11-10 17:46:34 +01:00
halfdan 6386c03f43 Remove Generic from most editors. They are not generic at all. 2014-11-09 18:57:50 +01:00
halfdan 8f35b0c6d4 Rename StatisticalParameters to remove EvA in name. 2014-11-09 18:50:15 +01:00
halfdan 88ef09db21 Ensure size of population is set when target size is set. 2014-11-07 23:44:34 +01:00
halfdan 7756ceac4e Code cleanup through static analysis. 2014-11-07 23:43:17 +01:00
halfdan 453df310ee Remove crap comments. 2014-11-07 22:58:41 +01:00
halfdan d778dc6e24 Make Population a typed ArrayList 2014-11-07 22:45:06 +01:00
halfdan 1dedb13dc9 Fix bug in humaniseCamelCase. 2014-11-07 21:59:28 +01:00
halfdan 7605dacb8a CLI adjustments 2014-11-06 15:54:57 +01:00
halfdan 3358a469a3 Fix bug in PSO implementation. 2014-11-06 11:27:32 +01:00
halfdan b7749711ca Remove last uses of SelectedTag from core package 
refs #32
 2014-11-06 10:25:51 +01:00
halfdan 93aff6d876 Refactor EnumEditor and actually use it. 
refs #32
 2014-11-05 20:00:00 +01:00
halfdan 62e436274c Removed SelectedTag from ScatterSearch. 
refs #32
 2014-11-05 19:02:39 +01:00
halfdan e18f9e3b38 Replace SelectedTag with useful enum. 
refs #32
 2014-11-05 18:53:47 +01:00
halfdan a91d9fbecc Close dialogs on escape key press. 2014-11-05 18:53:23 +01:00
halfdan a3cf5971fb Remove AlgType Selected in PSO 
refs #32
 2014-11-04 23:20:15 +01:00
halfdan 43768d1f96 Removes SelectedType where unnecessary. 
refs #32
- Replaced SelectedType with an enum in CombinedTerminator
 2014-11-04 22:54:13 +01:00
halfdan cb89110e86 Style adjustments for MacOS 2014-11-04 21:44:24 +01:00
halfdan efe1a1188b Stuff. 2014-11-04 16:33:55 +01:00
halfdan b77cda3046 Cleaner code. 2014-11-04 15:18:26 +01:00
halfdan 049304e9c1 Removed unused classes (dating back to < 2007..) 2014-11-03 18:50:35 +01:00
halfdan a08655a60f Add load/store to configurations. 
refs #31
 2014-11-03 16:26:01 +01:00
halfdan 70dd824d13 Remove globalInfo completely 
closes #9
- Remove all remaining globalInfo methods.
- Remove globalInfo handling.
- WIN.
 2014-11-02 19:04:17 +01:00
halfdan 551b14fe3d Load and store Optimizations as YAML. 
refs #31
- Introduces custom BeanSerializer using SnakeYAML
- Removed previous json package
- Introduces eva2.yaml package
- Hidden properties are not saved
- Reintroduces output in text window
 2014-11-02 17:53:42 +01:00
halfdan 173ebd67c6 Cleanup as well as moving TipText methods to useful @Parameter 
annotations.
 2014-11-02 16:10:57 +01:00
halfdan 6bb4616763 Added enum handling to CLI mode. 2014-11-02 16:10:44 +01:00
halfdan 83ee77f5af Simplify appendArrays method to use generic type. 2014-11-02 15:33:56 +01:00
halfdan ea4b12efab Add snakeyaml dependency 2014-11-02 14:53:40 +01:00
halfdan 8104c9baf7 Rename more init() methods to initialize() 2014-11-02 14:53:27 +01:00
halfdan 97d79612c2 Merge branch '30-dynamic-cli' 2014-11-02 14:03:59 +01:00
halfdan edaa58bd5a Remove apache, gson, cli, reflection dependencies for slimmer EvA2 
package.
 2014-11-02 14:03:23 +01:00
halfdan 89402e0b05 Hide several elements from the UI 2014-11-02 13:40:31 +01:00
halfdan 29a1bb64e3 Performance Optimization in CLI mode 
refs #30
- Abort object building if all params found
 2014-11-02 13:39:58 +01:00
halfdan 2a2162c5da More @Parameters and a fix for empty getters. 2014-11-01 18:59:28 +01:00
halfdan ee73f5dbe5 Renamed init to initialize. 
Added @Parameter annotation to EAIndividual
 2014-11-01 18:32:21 +01:00
halfdan 9efebe8b4b Initial commit of new dynamic CLI mode. 2014-11-01 18:20:58 +01:00
halfdan d0268527b0 Rename InterfaceStatisticsParameter to InterfaceStatisticsParameters for 
consistentcy with OptimizationParameters
 2014-11-01 18:18:58 +01:00
halfdan d676e78f61 Few more @Parameter annotations where useful. 2014-11-01 17:57:56 +01:00
halfdan cb83280a55 Properly show TipTexts again 
refs #29
 2014-11-01 14:53:28 +01:00
halfdan 4909cdd6bc Refactor @Parameter annotation to be applied to setter methods. 
fixes #29
- Change Parameter annotation to exist on methods
- Add default value to name field to make it optional
- Adjust classes that already use the annotation
 2014-11-01 13:27:33 +01:00
halfdan 032a4ce087 Added new convertToUnderscore method. 2014-11-01 13:27:09 +01:00
halfdan 9a8efc403e Move InterfacePopulationChangedEventListener to 
eva2.optimization.population.
 2014-10-31 19:05:38 +01:00
halfdan c8de290e4c Random refactoring to make EvA2Problems work again. 2014-10-31 18:36:15 +01:00
halfdan 3ac628e85f Rename init method to initialize and fix a bug for SBMLsimulator interop 2014-10-31 15:21:13 +01:00
halfdan ba814ec492 Remove hostname from Main 2014-10-31 10:54:51 +01:00
halfdan 0b35a9e880 Fixes sidebar issue with content disappearing. 
fixes #6
- Use the correct LayoutManager for the CellRenderer/Editor
- Fixed Button style
 2014-10-30 18:42:16 +01:00
halfdan b9e43e1174 Fix GUI hidden properties (setProblem) in Optimizers 2014-10-30 16:27:35 +01:00
halfdan 6465afb3e9 New MaximumTimeTerminator 
closes #28
- Implements new MaximumTimeTerminator
- Bit of cleanup + making some classes final where useful
 2014-10-29 23:10:47 +01:00
halfdan 0202692844 Various bugfixes. 
- Properly handle loading/searching of classes with EvA prefix
- Properly open Main window and set Logger when invoked from within JVM
- New F22Problem
 2014-10-29 17:44:34 +01:00
halfdan 668dcb6974 New @Hidden annotation to permanently hide properties from the UI. 
refs #13
 2014-10-28 20:35:35 +01:00
halfdan 24597ad01b Hide properties from Population. 
refs #13
 2014-10-28 19:04:57 +01:00
halfdan 3a3ebc502b Cleanup. 2014-10-28 18:53:52 +01:00
halfdan 90f006a239 Hide problem in optimizers 
refs #13
 2014-10-28 18:17:10 +01:00
halfdan f752f2bcc6 Update pom.xml 
no ref
- Remove jchart2d until we can move to it
- Update SCM connector paths
 2014-10-27 20:39:11 +01:00
halfdan d170727f8e Small bugfix for setting the problemDimension. 
refs #26
 2014-10-27 20:36:23 +01:00
halfdan f43e575b18 Abstract getProblemDimension into InterfaceOptimizationProblem 
closes #26
- Clean up problems that implemented getProblemDimension
- Move getProblemDimension to Interface and implement it in AbstractOptimizationProblem
- Output the problem dimension in the Processor (e.g. when running an optimization)
 2014-10-27 15:54:16 +01:00
halfdan 5799e6bdd2 Rename method in EvAStatisticalEvaluation to what it actually does. 2014-10-27 15:16:52 +01:00
halfdan adc5f58133 Some corrections to ABC. 
More cleanup.
 2014-10-27 09:46:59 +01:00
halfdan 3a02431d25 Remove ANT files. 
refs #22
 2014-10-26 20:24:17 +01:00
halfdan adc0d74bf7 Rename AbstractEAIndividualComparator to EAIndividualComparator as it is not abstract. 2014-10-26 19:40:55 +01:00
halfdan a8320cad76 Implements ABC algorithm 
fixes #24
 2014-10-26 17:08:37 +01:00
halfdan 5bd11e4624 Small cleanup and better documentation. 2014-10-26 17:08:01 +01:00
halfdan ca30e6c705 Start of implementation for AdaptiveDE 2014-10-25 17:34:04 +02:00
halfdan 2ae2a17cfe Introduce new AbstractOptimizer 
closes #21
- Remove methods implemented in AbstractOptimizer from optimizers whenever possible.
 2014-10-25 17:03:44 +02:00
halfdan a42bbf685a Remove setIdentifier/getIdentifier from InterfaceOptimizer as it was not used. 
refs #2
 2014-10-25 01:27:18 +02:00
halfdan 6b05a71a86 Documenation update in statistics package. 
refs #2
 2014-10-24 20:49:03 +02:00
halfdan 3987cd11e2 Minor fixes. 
refs #2
 2014-10-24 16:01:31 +02:00
halfdan 3cdb25b393 Show modal when attempting to close EvA with CMD+Q or via menu. 2014-10-24 11:03:23 +02:00
halfdan cb5bedd263 Clean up statistics code 
fixes #20
- Move enums from .stat to .enums
- rename .stat package to .statistics
- make strings in StringSelectionEditor human readable
 2014-10-24 10:58:44 +02:00
halfdan 15e5efb2a0 Fix ToolTip not appearing on front sheet panel. 
We now traverse the superclass hierarchy and search for a field with the
matching annotation.
 2014-10-23 19:35:11 +02:00