TODO check correlation store in arraylist with one element (???)
TODO check specificity?
TODO finish custom network impl


v1.1.3

Changes:
- new method to parse CSV/TSV files with custom quotes

Fixes:
- the custom network is now working
- Fix the network creation, the Jlist selected index was use to get the file in a other empty list

v1.1.2

Changes:

- Add keyListener to search nodes name in the result tables (result panel)
- remove networkTask (was doing HTTPtask + GRNTask)
- rename "ignore horizontal edge" to "include horizontal edges" and change variable name
- reshape the network panel (remove "use a local file" buttons) and add the custom network (still not working)

Fixes:
- Free memory directly after each random network generated using .clear()
- discretization table with ignore sign active
- correlation Class type the Engine
- sign of discretization "Non-responsive" in network panel > to >= etc.

v1.1.1

Changes:

- Zscore of specificity has been replaced by p-value

Fixes:

- Fix rule of First differentially expressed TP (v 1.0.9)
  Its only apply on start nodes
- Fix FinalNodeSelectionPanel1:
  previously there was no filter on the list of final node, only on the 
  Time point selection by the user, consequently, all final node where visible
  is the table displayed in the FinalNodeSelectionPanel2.
  Now on final nodes First DF at the selected time points are use to construct the table
  displayed in the FinalNodeSelectionPanel2.
- Add the key "randomize network count" in the config file saved

v.1.1

Changes:

- change name of the plugin from SST to TETRAMER
- Change Yield Zscore to pvalue
- Sorting one on this results tables [Node, Node (Selected), Node (random)]
  It Will sort the other tables in the list identically according to the rank column
- Add panel to reduce the list of final node base on their change in regulation per selected TP
- "Merge selected results into a single network" Jbutton is now working

Fixes:

- Fix rule of First differentially expressed TP (v 1.0.9)
- Popups are now displayed after the task ended (using task Observer)
- Randomization + propagation - no self loop and duplicate edges
- Fix calcul of Zscore (divide by 0)
- Zscore specificity (meanY instead of meanS)
- Fix calcul of Yield (divide by 0)


v.1.0.10

Changes:

- add regulatoryCircuit network (local file)
- add No data correlation in the "check correlation" table
- edges with all correlation values = 0 are now discard before the randomization and the propagation

Fixes:

- Correlation "with ignore sign" are 4 not 8

v.1.0.9

Changes:

- First differentially expressed TP is UP regulated only or,
  if never UP regulated, its when first time no differentially expressed (0)

Fixes:

- Network construction and correlation Class type

v.1.0.8

Changes:

- Manage multiple correlation columns (configuration file have change!)
- New correlation panel
- Check if the network is disconnected
- Check if network contains no-directed edges
- Added JDialog to construct network
- Remove "save result directory"

Fixes:

- Randomization - no self loop and duplicate edges

v.1.0.7

Fixes:

- Randomization - no self loop and duplicate edges

v.1.0.6

Changes:

- Add view signal propagation for KO nodes / groups
- Construct relation net view and propagation net view are now done in a task
- Change the SST style

Fixes:

- Expression LVL of start node is 1 for propagation 
- KO group expression LVL was not restored correctly
- fix view signal propagation and relationship for groups

v.1.0.5

Changes:

- Add combination for KO node (Iter one by one)
- Memory optimization
- Lists are automatically updated when tables columns are modified 

Fixes:

- Saved configuration contains now all options
- Combination node are now all tested
- UI improvement
- Fix context menu options
- Option "include horizontal edge" is now affecting network produced by the tool 


v.1.0.4

Fixes:

- Get correct index of selected rows (after sorting) in results tables (SST results tab)
- Correlation limits are used
- Construction of propagation network now display correctly all edges

v.1.0.3

Changes:

- Remove button check discretization
- Add button "save result tables"
  identical function like "save result directory"

Fixes:

- Get correct index of selected rows (after sorting) in results tables (SST results tab)
- Correlation is now correctly interpreted


v1.0.2

Changes:

- Add randomization (randomize network edge and edge corr values)
  the new network has the same number of source node
  and the same number of edge. The correlation values
  are the same be attributed to random edge

- Change SST style node color continuous mapping (up to 14TP)

- Results tables are reorgenized. "No (random)" and "Node (TP)" tabs added
  
Fixes

- Fix SST style edge color


v1.0.1

Changes:

- "save config", "load config" and "save result directory" are now working
  "save result directory" button, automatically save the result tables at the end on the compute

- add button to visualize signal transduction / relationship network of selected start node rows
  A new visual style is created "SST style"