November 2006 Commit Log

Number of Commits:
199
Number of Active Developers:
2
andrew 2006-11-30 17:18

indexOf replaces contains

5 lines of code changed in:

andrew 2006-11-30 17:15

char array replaces string for cuts

23 lines of code changed in:

andrew 2006-11-30 15:06

DasRegistry moved again

0 lines of code changed in:

andrew 2006-11-30 14:42

sg might be null if mouse released after coloumns removed

8 lines of code changed in:

andrew 2006-11-30 14:41

Return true or false if file saved

4 lines of code changed in:

andrew 2006-11-30 14:41

Warning message if file was not saved, repaint ids on multiple views

32 lines of code changed in:

jimp 2006-11-30 11:23

fix bad grammar in new alignment title

164 lines of code changed in:

andrew 2006-11-28 18:19

version 2.2

1 lines of code changed in:

andrew 2006-11-28 18:03

Format changes

623 lines of code changed in:

andrew 2006-11-28 17:52

jpg replaces gif

1 lines of code changed in:

andrew 2006-11-28 17:51

replace with jpg

0 lines of code changed in:

andrew 2006-11-28 17:49

Close strong tag

58 lines of code changed in:

andrew 2006-11-28 17:48

lower case file

88 lines of code changed in:

andrew 2006-11-28 17:18

CurrentColour must not be accessed by multiple sequence renderers

14 lines of code changed in:

jimp 2006-11-28 16:52

EBI web service interface update (and SequenceFetcher bugfix)

739 lines of code changed in:

andrew 2006-11-28 16:48

CurrentColour must not be accessed by multiple sequence renderers

23 lines of code changed in:

andrew 2006-11-28 12:39

Dont change ap font from treePanel

9 lines of code changed in:

jimp 2006-11-28 12:18

2.2 documentation

1 lines of code changed in:

andrew 2006-11-28 12:16

Tree title

6 lines of code changed in:

andrew 2006-11-28 12:16

REmove system.out

1 lines of code changed in:

andrew 2006-11-28 12:15

border 1

2 lines of code changed in:

jimp 2006-11-28 11:38

2.2 documentation

9 lines of code changed in:

jimp 2006-11-28 11:32

2.2 documentation

27 lines of code changed in:

jimp 2006-11-28 10:46

2.2 documentation

50 lines of code changed in:

andrew 2006-11-28 10:19

Loads PDB files from jar file, new views can open PDB file

9 lines of code changed in:

andrew 2006-11-28 09:44

No need to create tmpAnnotationPanel every paint

9 lines of code changed in:

andrew 2006-11-28 09:43

Translation should not be adjusted outside annotation loop

2 lines of code changed in:

andrew 2006-11-28 09:43

off by one group consensus calculation

2 lines of code changed in:

jimp 2006-11-27 17:32

2.2 documentation

589 lines of code changed in:

andrew 2006-11-27 16:21

Cant save to a URL loaded Jar file

9 lines of code changed in:

jimp 2006-11-27 14:00

2.2 documentation

973 lines of code changed in:

andrew 2006-11-27 12:05

Allow new window from output sequences

11 lines of code changed in:

jimp 2006-11-27 11:58

2.2 documentation

16 lines of code changed in:

jimp 2006-11-27 11:57

*** keyword substitution change ***

87 lines of code changed in:

jimp 2006-11-27 11:57

2.2 documentation

473 lines of code changed in:

andrew 2006-11-27 11:14

New feature type, new colour set

8 lines of code changed in:

andrew 2006-11-27 11:07

Some reason final radioButtons added to ButtonGroups are reset fixed

8 lines of code changed in:

jimp 2006-11-27 09:34

2.2 documentation

125 lines of code changed in:

jimp 2006-11-26 19:21

2.2 documentation

61 lines of code changed in:

andrew 2006-11-24 16:39

seqColours null

2 lines of code changed in:

andrew 2006-11-24 14:06

Fix load 1 col hidden bug

0 lines of code changed in:

andrew 2006-11-24 10:13

Invert col sel with hidden cols bug fixed

17 lines of code changed in:

jimp 2006-11-24 10:09

new and corrected docs for 2.2 release

895 lines of code changed in:

andrew 2006-11-23 18:27

Dont make groups of hidden sequences

20 lines of code changed in:

andrew 2006-11-23 15:51

If alignment is closed, then undo performed in visible window

26 lines of code changed in:

andrew 2006-11-23 15:29

If alignment is closed, then undo performed in visible window

16 lines of code changed in:

andrew 2006-11-23 15:19

Transparency......

5 lines of code changed in:

andrew 2006-11-23 15:18

If alignment is closed, then undo performed in visible window

34 lines of code changed in:

andrew 2006-11-23 13:35

defaultConnectTimeout and NO REPONSE message

0 lines of code changed in:

andrew 2006-11-23 12:04

Settooltips null

5 lines of code changed in:

andrew 2006-11-23 11:57

Associate PCA with multiple views

130 lines of code changed in:

andrew 2006-11-23 11:19

REmove component when frame is closed

4 lines of code changed in:

andrew 2006-11-23 11:03

set icon false if raising windows

14 lines of code changed in:

andrew 2006-11-23 11:03

Register TreePanel with paintrefresher

6 lines of code changed in:

andrew 2006-11-22 17:41

TreePanel added to PaintRefresher, not TreeCanvas

37 lines of code changed in:

andrew 2006-11-22 17:41

Dynamically build tree sort menu when sort menu is selected

40 lines of code changed in:

andrew 2006-11-22 17:40

sort menuListener

21 lines of code changed in:

andrew 2006-11-22 17:39

menus renamed

37 lines of code changed in:

andrew 2006-11-22 15:59

Associate trees with views

778 lines of code changed in:

andrew 2006-11-22 14:58

Renaming viewNames

29 lines of code changed in:

andrew 2006-11-22 14:58

View name

24 lines of code changed in:

andrew 2006-11-22 14:58

frameListener must call close if AlignFrame

5 lines of code changed in:

andrew 2006-11-22 12:29

applet has multiple views

89 lines of code changed in:

andrew 2006-11-21 17:55

Seq may be null if hide has occurred

3 lines of code changed in:

jimp 2006-11-21 17:50

corrected subtree colour dialogbox title

881 lines of code changed in:

andrew 2006-11-21 17:45

Copy to this implemented

7 lines of code changed in:

andrew 2006-11-21 17:25

Get alignPanel from treeCanvas

2 lines of code changed in:

andrew 2006-11-21 17:15

remove unnesccessary lines

1 lines of code changed in:

andrew 2006-11-21 17:15

Set start seq and end seq correctly

4 lines of code changed in:

andrew 2006-11-21 17:14

Add more keys

66 lines of code changed in:

andrew 2006-11-21 17:14

Change case new implementation

66 lines of code changed in:

jimp 2006-11-21 16:31

fix unselectable tree leaf nodes when node mapping changes after aligmment update (and some null object exceptions from property update)

18 lines of code changed in:

andrew 2006-11-21 16:25

Transparency available again

5 lines of code changed in:

andrew 2006-11-21 16:25

Right align print and images

20 lines of code changed in:

andrew 2006-11-21 16:02

Undo cut from end of alignment, padding on

12 lines of code changed in:

andrew 2006-11-21 15:40

preferredSize for spinners

5 lines of code changed in:

andrew 2006-11-21 15:29

rightAlignIds

3 lines of code changed in:

andrew 2006-11-21 15:28

Colour may have been updated in another view

7 lines of code changed in:

andrew 2006-11-21 15:28

Checks on features displayed

2 lines of code changed in:

andrew 2006-11-21 15:27

Close associated windows

21 lines of code changed in:

andrew 2006-11-21 15:27

RightAlign ids from prefs

4 lines of code changed in:

andrew 2006-11-21 15:27

expanded views, j2xml use setinitialtabvisible, close all frames from jar file

38 lines of code changed in:

andrew 2006-11-21 14:06

F1 accelerator

4 lines of code changed in:

andrew 2006-11-21 14:05

Align boxes

3 lines of code changed in:

andrew 2006-11-21 14:05

Memory check on loading file

9 lines of code changed in:

andrew 2006-11-21 14:05

Set fsettings in constuctor

0 lines of code changed in:

andrew 2006-11-21 12:48

Highlight feature to edit

19 lines of code changed in:

andrew 2006-11-21 12:22

JOptionPanes launched in new thread

0 lines of code changed in:

andrew 2006-11-21 12:18

Panels replace colour buttons

20 lines of code changed in:

andrew 2006-11-21 12:18

Use textColourChooser

6 lines of code changed in:

andrew 2006-11-21 12:17

New file, as its used in popup and alignframe previuously

208 lines of code changed in:

andrew 2006-11-21 11:20

Colour is a panel, not button

10 lines of code changed in:

andrew 2006-11-21 10:35

foreground changes

22 lines of code changed in:

andrew 2006-11-20 18:17

Cancel DAS fetching

31 lines of code changed in:

andrew 2006-11-20 18:17

Reset DAS registry

0 lines of code changed in:

andrew 2006-11-20 18:16

Look for pairwiseAlignpanel

7 lines of code changed in:

andrew 2006-11-20 18:16

works on focused viewport

24 lines of code changed in:

andrew 2006-11-20 18:16

expand and gather

44 lines of code changed in:

andrew 2006-11-20 18:10

Right align as pref

3 lines of code changed in:

andrew 2006-11-20 18:10

Mouse wheel to zoom

20 lines of code changed in:

andrew 2006-11-20 18:10

Expand and gather added

32 lines of code changed in:

andrew 2006-11-20 18:09

Right align as pref

20 lines of code changed in:

andrew 2006-11-20 18:09

Cancel added

0 lines of code changed in:

andrew 2006-11-20 18:09

warning message changed

2 lines of code changed in:

andrew 2006-11-20 18:08

currentAlignFrame is public

2 lines of code changed in:

andrew 2006-11-20 18:08

check cursor is visible for hidden cols

42 lines of code changed in:

andrew 2006-11-20 18:07

look for current alignframe to search

7 lines of code changed in:

andrew 2006-11-20 18:07

embeddedMenus

3 lines of code changed in:

andrew 2006-11-20 17:58

Memory check on PDB file

69 lines of code changed in:

andrew 2006-11-20 11:25

use Shift for paste to new window

6 lines of code changed in:

andrew 2006-11-20 11:24

Must copy old dbrefs

2 lines of code changed in:

andrew 2006-11-15 16:43

Must be able to find originating alignment modified

5 lines of code changed in:

andrew 2006-11-15 16:43

dont adjust aligments if they're the same size

10 lines of code changed in:

andrew 2006-11-15 16:41

Add remove seq from multiple views, must fire alignmentChange from originating source

78 lines of code changed in:

andrew 2006-11-15 15:47

Check if groupWidth is greater than sequence width

6 lines of code changed in:

andrew 2006-11-15 15:46

IdMask must be Max seq end, not seq width

24 lines of code changed in:

andrew 2006-11-15 15:46

right align ids

43 lines of code changed in:

andrew 2006-11-15 15:44

RIght align seq ids

17 lines of code changed in:

andrew 2006-11-14 18:05

minimize and raise associated windows

83 lines of code changed in:

andrew 2006-11-14 15:54

Close all added

32 lines of code changed in:

andrew 2006-11-14 15:26

select menu

10 lines of code changed in:

andrew 2006-11-14 15:26

Paintrefresh alignpanel

3 lines of code changed in:

andrew 2006-11-14 15:26

set seqColours null

2 lines of code changed in:

andrew 2006-11-14 15:26

recalc cons for group size change

3 lines of code changed in:

andrew 2006-11-14 15:25

Commands, history, consensus, refresh updated

1036 lines of code changed in:

andrew 2006-11-14 12:22

Paste uses alt rather than shift

1 lines of code changed in:

andrew 2006-11-14 12:21

Single seq Blc file detection

13 lines of code changed in:

andrew 2006-11-14 12:21

we already have c defined

3 lines of code changed in:

andrew 2006-11-13 17:46

REload from URL

4 lines of code changed in:

andrew 2006-11-13 16:16

Enable lower case colours

1 lines of code changed in:

andrew 2006-11-13 16:12

Dont readd identical DBRef

11 lines of code changed in:

andrew 2006-11-13 16:11

Use j not i

0 lines of code changed in:

andrew 2006-11-13 16:11

Fasta files with * read not identified as BLC

8 lines of code changed in:

andrew 2006-11-13 14:20

Querystring made from line tokenized seq name, seq refs held with what was sent to uniprot

0 lines of code changed in:

andrew 2006-11-13 11:14

Colours in viewport

1105 lines of code changed in:

andrew 2006-11-13 11:13

Text colour adapter

117 lines of code changed in:

andrew 2006-11-13 11:13

sequence colours and text colours added

27 lines of code changed in:

andrew 2006-11-13 11:12

colours in viewport

12 lines of code changed in:

andrew 2006-11-13 11:11

Save text colours

41 lines of code changed in:

andrew 2006-11-13 11:11

Group Menu level changed

108 lines of code changed in:

andrew 2006-11-13 11:10

Colour text

48 lines of code changed in:

andrew 2006-11-13 11:10

Sequence colour in viewport

8 lines of code changed in:

andrew 2006-11-13 11:09

Format menu item

35 lines of code changed in:

andrew 2006-11-13 11:09

text colour saved

0 lines of code changed in:

andrew 2006-11-13 11:08

Sequence colour moved to viewport

1 lines of code changed in:

andrew 2006-11-13 11:08

Text colour for group

5 lines of code changed in:

andrew 2006-11-13 11:07

Sequence colour moved to viewport

1 lines of code changed in:

andrew 2006-11-13 10:48

Save text colours

6 lines of code changed in:

andrew 2006-11-09 18:31

remove system.out

1 lines of code changed in:

andrew 2006-11-09 18:31

tooltip

2 lines of code changed in:

andrew 2006-11-09 18:17

Shortcuts

9 lines of code changed in:

andrew 2006-11-09 18:15

smooth font gone, setFileName and close open alignPanel

85 lines of code changed in:

andrew 2006-11-09 18:14

close frame true

3 lines of code changed in:

andrew 2006-11-09 18:13

smooth fonts moved here

16 lines of code changed in:

andrew 2006-11-09 18:13

cut and paste input output

2 lines of code changed in:

andrew 2006-11-09 18:13

close menu item true

3 lines of code changed in:

andrew 2006-11-09 18:12

New window

4 lines of code changed in:

andrew 2006-11-09 18:12

Smooth fonts

53 lines of code changed in:

andrew 2006-11-09 18:12

Shortcuts

90 lines of code changed in:

andrew 2006-11-09 18:11

Check conensus is not null

9 lines of code changed in:

andrew 2006-11-09 18:11

alignFrame.setFileName

4 lines of code changed in:

andrew 2006-11-09 18:10

Cutandpaste used for input/output

2 lines of code changed in:

andrew 2006-11-09 18:10

1.1 compatible

1 lines of code changed in:

andrew 2006-11-08 17:38

Reload alignment

25 lines of code changed in:

andrew 2006-11-08 17:38

Set description

3 lines of code changed in:

andrew 2006-11-08 17:37

currentSeq and set description in dataset

10 lines of code changed in:

andrew 2006-11-08 17:36

Text by default

2 lines of code changed in:

andrew 2006-11-08 17:36

Use sequence description

3 lines of code changed in:

andrew 2006-11-08 17:35

Dont set the dataset name and description

5 lines of code changed in:

andrew 2006-11-08 17:35

Tooltip on mouseover

16 lines of code changed in:

andrew 2006-11-08 17:34

Apple friendly

2 lines of code changed in:

andrew 2006-11-08 17:34

Remove unnecessary imports

1 lines of code changed in:

andrew 2006-11-08 17:33

Apple friendly

33 lines of code changed in:

andrew 2006-11-07 16:14

warning note added to consequence

4 lines of code changed in:

andrew 2006-11-07 16:13

Dont load trees if copying Viewport

7 lines of code changed in:

andrew 2006-11-07 16:13

Check features.length>0

2 lines of code changed in:

andrew 2006-11-07 16:13

Color updated for new seq, OK is default option

8 lines of code changed in:

andrew 2006-11-07 11:52

Tidy up group size after alignmentChanged

17 lines of code changed in:

andrew 2006-11-07 11:51

hidden seqs and setOrder bug fixed

13 lines of code changed in:

andrew 2006-11-07 09:25

Add keylistener to InternalFrame, not canvas

5 lines of code changed in:

andrew 2006-11-06 17:12

Only recalc consensus for start to end of group

25 lines of code changed in:

andrew 2006-11-06 17:12

Only calculate consenus from start to end

3 lines of code changed in:

andrew 2006-11-06 17:11

If start is not zero, we need to put -- at the start

5 lines of code changed in:

andrew 2006-11-06 14:02

example links

3 lines of code changed in:

andrew 2006-11-06 14:00

Remember fileName in alignFrame

7 lines of code changed in:

andrew 2006-11-06 14:00

dont limit menu size

2 lines of code changed in:

andrew 2006-11-06 13:59

accelerators, save menu item

387 lines of code changed in:

andrew 2006-11-03 15:20

Alignpanel is not new if copied from j2xml

2 lines of code changed in:

andrew 2006-11-03 15:19

Consensus may already have been removed

3 lines of code changed in:

andrew 2006-11-03 14:27

Remove unnecessary refresh

1 lines of code changed in:

andrew 2006-11-03 14:26

Use Jalview2XML to copy AlignmentPanel

87 lines of code changed in:

andrew 2006-11-02 15:13

return if image is null

5 lines of code changed in:

andrew 2006-11-02 15:13

Update editMenuBar after alignment changed

5 lines of code changed in:

andrew 2006-11-02 15:12

Set menu state in alignFrame

39 lines of code changed in:

andrew 2006-11-02 15:12

Fire align change for case change

6 lines of code changed in:

andrew 2006-11-02 15:11

History is per viewport

9 lines of code changed in:

andrew 2006-11-02 15:11

selected states set in updateMenusFromViewport

54 lines of code changed in:

andrew 2006-11-02 15:10

Use system path separator char

2 lines of code changed in:

andrew 2006-11-02 15:10

dasregistry is now dasregistry.org

0 lines of code changed in:

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