Directory src/dr/app/beauti/mcmcpanel/

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rambaut 2012-08-08 21:31 Rev.: 5110

Porting changes from branch 1.7 r5109

8 lines of code changed in 2 files:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+8 -8)

dong.w.xie 2011-03-14 16:27 Rev.: 3872

Trunk: more work on micro-sat data in BEAUti.

59 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+59 -40)

rambaut 2010-09-07 10:37 Rev.: 3497

Switched all uses of org.virion.jam.* to jam.* (org.virion.jam.* is not being updated or fixed). This has touched alot of files but mainly just in the import statements.

2 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+2 -2)

rambaut 2010-08-20 21:23 Rev.: 3417

Centred components in MCMCPanel for better visual effect.

5 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+5 -1)

rambaut 2010-08-20 21:13 Rev.: 3416

Trying to make BEAUti look less Java-like. Have removed the white background for all the panels that are in scroll panes so that you can't see that they are (in a scrollpane) until the scroll bars activate. Have also turned off the horizontal scrollbars in these cases and checked that all the components are visible when the window is at its smallest size. However, I have not tested this on other platforms so would be interested in how it looks (both normally and when small) on Linux and Windows. If any changes to this are required, they should probably be put in platform specific conditionals (i.e., if (!MacOSX)).

8 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+8 -9)

rambaut 2010-08-19 20:54 Rev.: 3409

Commented out newly added checkbox in MCMCPanel to set the allowOverwrite attribute (sorry Walter). I just don't think this is the place for the user to make this decision. I have left the generation of the attribute in and it will be set to false. If the user wants to override this they can use the BEAST commandline options '-overwrite'. The XML attribute is worth having for test scripts where you probably want to set it to true.

8 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+8 -8)

dong.w.xie 2010-08-19 11:17 Rev.: 3405

Trunk: solve Issue 305: BEAST should warn/halt if log files already exist

11 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+11)

dong.w.xie 2010-08-11 17:32 Rev.: 3381

Trunk: solve Issue 339: GUI within scroll panes is just nasty

5 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+5 -7)

rambaut 2010-08-05 04:13 Rev.: 3364

This is rather a large update as I was making changes in a branch and have merged them back in. This allows any trait name to be created (not just 'Location' and 'Species'). The idea is that the discrete model is not phylogoegraphy specific - you can model any discrete change. Have added a check box to say use *BEAST - at this point you should create a Species trait. Have cleaned up a few othe UI issues. Almost certainly there will be XML generation issues as a result and we should concentrate on testing and fixing these.

1 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+1 -1)

dong.w.xie 2010-01-20 17:47

Trunk: try to fix code breaking caused by IntelliJ.

421 lines of code changed in 2 files:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+30 -29)

dong.w.xie 2010-01-20 17:40 Rev.: 2819

Trunk: try to fix code breaking caused by IntelliJ.

0 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (del)

dong.w.xie 2010-01-20 17:18 Rev.: 2818

Trunk: initial code for project SnAPhyl GUI (using part of BEAUti code).

31 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (new 31)

dong.w.xie 2009-12-10 15:49 Rev.: 2682

Trunk: merge BEAUti from branch 1.5 in

7 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+7 -6)

dong.w.xie 2009-12-10 13:44 Rev.: 2678

Trunk: start merge BEAUti from branch 1.5 in

59 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+59 -13)

bloomquist 2009-11-19 07:39 Rev.: 2551

A few of the classes were using TREE_FILE_NAME string from some of the classes I deleted. I moved this String into STARBEASTOptions and made the appropriate changes. I don't think BEAST will be broken anymore after this.

7 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+7 -6)

dong.w.xie 2009-10-13 14:14 Rev.: 2385

BEAUTi: solve Issue 201: Editing file name stem in MCMC panel causes insertion point to jump to end

25 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+25 -14)

dong.w.xie 2009-10-02 19:15 Rev.: 2340

BEAUTi: solve Issue 185: Guess Trait dialog doesn't offer user defined traits

1 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+1 -1)

dong.w.xie 2009-09-07 12:54 Rev.: 2210

BEAUTi: solve Issue 151: MCMC tab numerical fields resets after GUI events

36 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+36 -33)

dong.w.xie 2009-08-25 10:57 Rev.: 2132

BEAUTi engineering work: big refactorying of *BEAST, and create STARBEASToptions.

2 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+2 -2)

dong.w.xie 2009-08-11 11:17 Rev.: 2053

Add OSType in dr.app.util to detect OS, and replace all old isMacOS into new one.

6 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+6)

dong.w.xie 2009-08-10 17:08 Rev.: 2048

BEAUTi: Resolved issue #103: add addTxt check box in MCMC panel.

21 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+21 -7)

dong.w.xie 2009-08-03 11:06 Rev.: 1998

BEAUTi:
1) remove DisplayTree panel from Tree panel;
2) add making substTreeFileNameField disenabled when the check box is not selected, but it seems not working.

3 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+3 -1)

dong.w.xie 2009-07-21 13:08 Rev.: 1888

Update Big Change of BEAUTi:
1) use List to store treeFileName and subtreeFileName, and update MCMC panel;
2) correct EBSP xml, but still have a problem in VDAnalysis;
3) start to fix *BEAST.

50 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+50 -41)

alexei.drummond 2009-07-15 23:53 Rev.: 1861

intellij tidy

71 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+71 -73)

dong.w.xie 2009-07-01 12:41 Rev.: 1817

Update Big Change of BEAUTi: store the links between PD, PSM, PCM, PTM, PTP in the class using their class references, List<> of them in BeautiOption is not used anymore. And use getPartition...() in BeautiOption to get the current list of PD or PSM or PCM or PTM.

3 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+3 -3)

dong.w.xie 2009-06-19 14:35 Rev.: 1790

BEAUTi: rename partition series classes, and final relation is PartitionData => PartitionSubstitutionModel => PartitionTreeModel => PartitionTreePrior.

4 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+4 -4)

dong.w.xie 2009-06-18 11:03 Rev.: 1786

BEAUti: make Log File and Tree Log File name updated together with File Stem Name.

15 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+15 -5)

dong.w.xie 2009-06-02 10:13 Rev.: 1757

Refactory BEAUTI package structure, add few panel packages and util package.

291 lines of code changed in 1 file:

• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+291)