Activity for VANESA
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VANESA released /vanesa/0.1/VANESA-0.1.9.jar
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Chris committed [r1098]
- I/O for plotColor
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- fixed wrong place/transition counter
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- rungekutta default integrator
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- avoid moving nodes when clicking / selecting. Certain dx or dy of movement is required for new positioning of nodes
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- calculating of token flow for PN arcs connected to discrete transition (after simulation finished)
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- fixed plotColor of PN nodes
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- added missing layouts
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- some more logging while simulation
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- refactored threading of PN simulation / compilation, ability to abort any process
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- refactored usage of progress bar
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- fixed bug in modelica export regarding functions
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- show PN of transformed BN
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- remove clipPaths in generated SVG which might clip longer text
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- fixed import of simulation results if values are missing
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- ommit multiple instances of simulation window for same graph
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- less flickering of toolbar while switching tabs
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- integer result of simulation is now 8 bytes, instead of 4 bytes
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- fixed edge handling in rule editor window
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- Petri net simulation independent of current graph
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- some refactoring
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- vertex and edge dialog remember last selected element type
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- consider logical places during transformation
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- show vertex properties of selected nodes (and corresponding mapped node) in rules GUI
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- faster transformation due to subgraph approach
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- transformation based on permutations
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- generic place and transition for rules
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- removed deprecated Java 9/10 method calls
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- added / fixed png and svg export of graph
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- updated batik lib
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- deleted lib since org.w3c.dom is part of Java 11 now
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- removed freeHEP, incompatible with Java 9+. Graph export as image (svg/png) needs to be reimplemented
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- removed unused libs
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compatibility with java 9+
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- updated jung lib
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- updated snakeyaml
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- deleted and updated libs
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- lots of cleanup of entire code
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- rendering graph is independent of graph in main window
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renamed files
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- window to edit / create a rule
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- read/write yml rules from/to file
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- yml input for rules
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- individual classes for discrete and cont. place
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- first version of rule based transformation BN->PN
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- updated easyRules package
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- removed lower and upper boundary for PNEdges
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- avoiding inhibitory arcs and test arcs connecting Transition->Place
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- JEasyRule libs added
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- fixed copy / clone of pathway
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Jessica Seidel committed [r1049]
Add new Button Icons for Grouping/Ungrouping
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Add missing files
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Add grouping and ungrouping for Nodes
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- fixed PATH variable for simulation process environment
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- removed graph alignment button
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- fixed KEGG query
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- avoid crash for info window if graph is not connected
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- lots of bugs / glitches
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debug commit
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some more lines for transformator
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- fixed node / edge settings for visualization
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- fixed bug (NPE) for generic SBML input
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node name vs. node label safety
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- improved handling of constant places
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- some more checks for referenced nodes
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- transformation: test for multiple edges
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little more stuff for transformation
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- pre-processing for transformation
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- fixed sorted list of nodes: nodes with same name are now also taken into account
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- avoid same names of nodes after split operation
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little stuff
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minor stuff
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some PN transformation code
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improved legend for multiple simulation results
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extracted PNlib constants, easier to adjust if they got renamed in PNlib
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- Petri net functionality enabled (not only for developmental status)
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- fixed naming of stochastic transition due to update of PNlib
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improved parameterized simulation
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- first attempt for parameterized simulation
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- added to kineticsbuilder: activators and relative inhibitors
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- nodes can be continuous / discrete
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- renaming of pathway after saving
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- all nodes may be discrete or continuous
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- change JOptionPane to MyPopUp
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- even more input validations for concentrations, tokens, boundaries
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- improved checking of numbers (tokens / concentrations)
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- improves formula safety
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- fixed exception with multiple views
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- fixed convenience metric for special cases (no substrates or no products)
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- formula is automatically created when formula string changes
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small fixes
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- organized imports
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- update latex rendering of expression after automatic creation of kinetics
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- fixed: highlight of text annotation while dragging
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- annotations are now movable / pickable
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- checking and solving conflicts: priorities and probabilities
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- solve conflict properties: normalizing probabilities