August 2005 Commit Log

Number of Commits:
176
Number of Active Developers:
2
andrew 2005-08-31 17:54

Repaint scale panel after unselect all

1 lines of code changed in:

andrew 2005-08-31 17:53

Must update globalColourScheme with new consensus

3 lines of code changed in:

andrew 2005-08-30 17:30

2.05

47 lines of code changed in:

andrew 2005-08-30 17:07

UserColour gui modified

54 lines of code changed in:

andrew 2005-08-30 16:26

Make 24 colours to be sure

3 lines of code changed in:

andrew 2005-08-30 16:25

Validate buttons and fire on mouse press, not mouse click

4 lines of code changed in:

andrew 2005-08-30 16:24

Set user colours same as global

39 lines of code changed in:

andrew 2005-08-30 15:33

Repaint annotations after edit

10 lines of code changed in:

andrew 2005-08-30 15:11

Wrapped, getWidth > vconsensus

11 lines of code changed in:

andrew 2005-08-30 13:46

Update colours after remove left, cut, paste

9 lines of code changed in:

andrew 2005-08-30 12:35

Keep mouse drag to 1 block when wrapped

20 lines of code changed in:

andrew 2005-08-30 12:24

Dont setSelected on new frames

2 lines of code changed in:

andrew 2005-08-30 12:07

Out of bounds checks

7 lines of code changed in:

andrew 2005-08-30 12:07

Set startSeq 0 if wrap alignment

5 lines of code changed in:

andrew 2005-08-30 11:34

Dont set clip if its not null

6 lines of code changed in:

andrew 2005-08-30 11:33

Bounds checking

2 lines of code changed in:

andrew 2005-08-30 09:59

If Mac, dont use fastpaint

6 lines of code changed in:

andrew 2005-08-30 09:56

Can edit in wrapped view

0 lines of code changed in:

andrew 2005-08-29 18:23

Reset all colour schemes after gaps removed

27 lines of code changed in:

andrew 2005-08-29 18:22

Include None in default colours

4 lines of code changed in:

andrew 2005-08-29 18:21

Reset all colour schemes after gaps removed

29 lines of code changed in:

andrew 2005-08-29 18:20

Default user colour is 23 white colours

5 lines of code changed in:

andrew 2005-08-29 16:51

Keep startRes the same after removing columns

32 lines of code changed in:

andrew 2005-08-29 16:18

Reset ClustalX after removing gaps

56 lines of code changed in:

andrew 2005-08-29 15:00

if seq<0, return

1 lines of code changed in:

andrew 2005-08-29 14:59

load sequenceURLLinks static method

21 lines of code changed in:

andrew 2005-08-29 12:38

Dont call fastPaint if Mac

1 lines of code changed in:

andrew 2005-08-29 11:45

Edit and annotate wrapped alignment

5 lines of code changed in:

andrew 2005-08-29 11:32

Edit and annotate wrapped alignment

106 lines of code changed in:

andrew 2005-08-29 11:18

Edit and annotate wrapped alignment

93 lines of code changed in:

andrew 2005-08-26 16:29

Create new image only on resize, set fontMetrics on new image

29 lines of code changed in:

andrew 2005-08-26 13:48

resizeAgain flag set if user resizes whilst image is being prepared

28 lines of code changed in:

andrew 2005-08-26 13:43

No need to call repaint after font change

1 lines of code changed in:

andrew 2005-08-26 13:42

resizeAgain flag set if user resizes whilst image is being prepared

18 lines of code changed in:

andrew 2005-08-26 13:42

Update overviewImage if font changed

20 lines of code changed in:

andrew 2005-08-26 13:41

When saving, use print instead of println

3 lines of code changed in:

jimp 2005-08-25 15:35

html typo

1 lines of code changed in:

jimp 2005-08-25 15:32

more informative clustal colourscheme doco.

31 lines of code changed in:

andrew 2005-08-24 12:37

Set new group width-1

3 lines of code changed in:

andrew 2005-08-24 12:24

Give extra pixel for graph values

6 lines of code changed in:

andrew 2005-08-24 11:57

Set threshold 0 if conservation

1 lines of code changed in:

andrew 2005-08-24 11:57

Bring trees to front

6 lines of code changed in:

andrew 2005-08-24 11:57

Does edit affect any groups?

167 lines of code changed in:

andrew 2005-08-24 11:02

Dont set iframe null

1 lines of code changed in:

andrew 2005-08-23 18:24

Latest version is red

2 lines of code changed in:

andrew 2005-08-23 18:23

End res of selection group corrected

6 lines of code changed in:

andrew 2005-08-23 17:55

Add windowListener in constructor

19 lines of code changed in:

andrew 2005-08-23 17:49

Remove ref in PaintRefresher on close, changeColour updated

47 lines of code changed in:

andrew 2005-08-23 17:10

AddToDesktop is synchronized

19 lines of code changed in:

andrew 2005-08-23 17:10

Sleep for longer

1 lines of code changed in:

andrew 2005-08-23 17:07

Warning no longer red

4 lines of code changed in:

andrew 2005-08-23 17:06

Dont make new frame reference in Buildwebservicemenu

5 lines of code changed in:

andrew 2005-08-23 17:05

Finalize calculate method

2 lines of code changed in:

andrew 2005-08-23 11:40

Finalize formats

2 lines of code changed in:

andrew 2005-08-23 11:35

Regex should not be static in file loader

9 lines of code changed in:

andrew 2005-08-23 11:10

Is fileChooser instanceof Basic

18 lines of code changed in:

andrew 2005-08-23 11:10

Set size and location of frame before visible

35 lines of code changed in:

andrew 2005-08-22 18:10

Check for null colour

23 lines of code changed in:

andrew 2005-08-22 18:06

Dont resize frame if bounds have been set

7 lines of code changed in:

andrew 2005-08-22 18:04

Mosue wheel moved to seqpanel

5 lines of code changed in:

andrew 2005-08-22 18:04

Use mouse wheel press to zoom

40 lines of code changed in:

andrew 2005-08-22 18:03

finalize all these hashtables

28 lines of code changed in:

andrew 2005-08-22 18:02

Checks for null colour in groups

44 lines of code changed in:

jimp 2005-08-22 17:25

jalview-dev doesn't exist.

1 lines of code changed in:

jimp 2005-08-22 17:18

regenerated stubs from wsdl and removed old vamsas object stubs in jalview.ext

167 lines of code changed in:

jimp 2005-08-22 17:03

regenerated from wsdl.

455 lines of code changed in:

jimp 2005-08-22 16:58

Replaced by jpred.java and associated stubs.

0 lines of code changed in:

jimp 2005-08-22 16:53

fixed hanging on job finished bug.

72 lines of code changed in:

jimp 2005-08-22 16:41

tidied client and fixed non-unique msa bug (lead to Hmmer error)

29 lines of code changed in:

jimp 2005-08-22 16:40

fixed uniquify seq[]

8 lines of code changed in:

jimp 2005-08-22 15:22

regenerated Jpred stubs and tidied client thread.

878 lines of code changed in:

jimp 2005-08-22 15:19

comment on WORD_SEP values

2 lines of code changed in:

andrew 2005-08-22 10:15

Conservation colour scheme is no more

415 lines of code changed in:

andrew 2005-08-19 09:56

Reset browser every time

2 lines of code changed in:

andrew 2005-08-19 09:50

remove property user_defined if none left

10 lines of code changed in:

andrew 2005-08-19 09:49

If browser not set, remove property

24 lines of code changed in:

andrew 2005-08-19 09:49

System.out if error setting properties

3 lines of code changed in:

jimp 2005-08-18 19:27

made changes to DEFAULT_BROWSER in user preferences act immediatly (instead of just on restart).

15 lines of code changed in:

jimp 2005-08-18 19:25

changed first clicked to nearest the top of the alignment.

1 lines of code changed in:

jimp 2005-08-18 19:23

typo

1 lines of code changed in:

jimp 2005-08-18 19:20

moved to clustalw.html

0 lines of code changed in:

jimp 2005-08-18 18:58

typo fixes.

9 lines of code changed in:

andrew 2005-08-18 17:04

Add release history to whats new

94 lines of code changed in:

andrew 2005-08-18 16:45

Add name and mouse listener to new user colour menuitems

32 lines of code changed in:

jimp 2005-08-18 16:20

error checking, sanitization and properties support.

44 lines of code changed in:

andrew 2005-08-18 16:20

Blosum62 PID and conservation bug fixed

4 lines of code changed in:

jimp 2005-08-18 16:13

GUI typo

2 lines of code changed in:

andrew 2005-08-18 15:26

Return if UNIPROT_CACHE is null

7 lines of code changed in:

andrew 2005-08-18 15:09

Add idwidth.gif in applet jar

2 lines of code changed in:

andrew 2005-08-18 14:41

Character methods don't exist in java 1.1

7 lines of code changed in:

jimp 2005-08-18 11:41

typo - Muscle->JNet

2 lines of code changed in:

jimp 2005-08-18 11:41

Jpred to JNet

1 lines of code changed in:

andrew 2005-08-18 11:38

2_03 build project

19 lines of code changed in:

andrew 2005-08-18 10:47

Proceed with upperCase residue

18 lines of code changed in:

jimp 2005-08-18 10:33

various case sensitivity bugs fixed in residue comparison functions.

12 lines of code changed in:

andrew 2005-08-18 10:20

Use aa index for aboveThreshold as well as colour index

5 lines of code changed in:

jimp 2005-08-17 17:31

Client threads for discovered web services.

455 lines of code changed in:

jimp 2005-08-17 17:30

GUI modifications for service discovery.

5 lines of code changed in:

jimp 2005-08-17 17:30

Gui Modifications for Service Discovery.

2552 lines of code changed in:

jimp 2005-08-17 17:24

<No Comment Entered>

14 lines of code changed in:

andrew 2005-08-17 17:09

Has version, Groups are optional, trees added to schema

26 lines of code changed in:

andrew 2005-08-17 17:08

Add attribute schemeName

1 lines of code changed in:

andrew 2005-08-17 17:08

Add buildPropertiesFile to applet jar

4 lines of code changed in:

andrew 2005-08-17 17:07

Read in version from build details file in applet jar

34 lines of code changed in:

andrew 2005-08-17 16:40

Web Services moved from Calculate

648 lines of code changed in:

andrew 2005-08-17 16:36

Capitalise menus

3 lines of code changed in:

jimp 2005-08-17 16:31

Maintain list of webservices and query any Service Discovery services.

14 lines of code changed in:

jimp 2005-08-17 16:23

Simple Registry Service stubs

680 lines of code changed in:

jimp 2005-08-17 16:20

Fixed basic name to sequence ID matching (bug http://dragonfly.compbio.dundee.ac.uk/mantis/view.php?id=9227)
and improved code robustness when dealing with badly formed IDs (null strings).

22 lines of code changed in:

andrew 2005-08-17 15:11

No basicDirectoryModel on the Mac

0 lines of code changed in:

andrew 2005-08-17 15:11

Set size for mac users

2 lines of code changed in:

andrew 2005-08-17 14:43

Error reply is kept separate from file type

5 lines of code changed in:

andrew 2005-08-17 14:05

Add names to schemes

16 lines of code changed in:

andrew 2005-08-17 14:04

New image

0 lines of code changed in:

andrew 2005-08-17 14:03

Check default colour is not null

48 lines of code changed in:

andrew 2005-08-17 14:02

Remove user colour menu item

29 lines of code changed in:

andrew 2005-08-17 12:01

Check default >0, not <1

3 lines of code changed in:

andrew 2005-08-17 11:27

Conservation group colour saved

5 lines of code changed in:

andrew 2005-08-17 10:59

Add SRS as default

4 lines of code changed in:

andrew 2005-08-17 10:31

Return white userColourScheme, not null colourscheme

8 lines of code changed in:

andrew 2005-08-17 10:30

Use getDefault for exampleFile

13 lines of code changed in:

andrew 2005-08-17 10:13

Advice on proxy servers

28 lines of code changed in:

andrew 2005-08-17 10:12

Rebuilt with new schema

4901 lines of code changed in:

andrew 2005-08-17 10:11

Put basic file chooser test in try catch loop

22 lines of code changed in:

andrew 2005-08-17 10:10

Scheme name added

11 lines of code changed in:

andrew 2005-08-17 10:10

User colours have scheme name

213 lines of code changed in:

andrew 2005-08-17 10:09

User colours

76 lines of code changed in:

andrew 2005-08-17 10:08

No score colour scheme, group colours saved if conservation applied

23 lines of code changed in:

andrew 2005-08-17 10:08

Calculation - consensus

2 lines of code changed in:

andrew 2005-08-17 10:06

updateUserColourMenu

44 lines of code changed in:

andrew 2005-08-17 10:06

Discover user colours

4 lines of code changed in:

andrew 2005-08-17 10:05

Calculation - consensus

1 lines of code changed in:

andrew 2005-08-16 09:51

Remove redundant imports

0 lines of code changed in:

andrew 2005-08-15 15:08

Jalview Version:

2 lines of code changed in:

andrew 2005-08-15 15:08

Output java version, os version on startup

7 lines of code changed in:

andrew 2005-08-15 15:07

Remove null check

1 lines of code changed in:

andrew 2005-08-15 14:58

Sparc for Solaris

85 lines of code changed in:

andrew 2005-08-15 13:14

Use default fileChooser for now

41 lines of code changed in:

andrew 2005-08-15 13:13

super.setconsensus

2 lines of code changed in:

andrew 2005-08-15 13:13

Percentage precalculated in aafrequency

21 lines of code changed in:

andrew 2005-08-15 13:13

isGap slightly more efficient

2 lines of code changed in:

andrew 2005-08-15 13:12

Percentage precalculated in aafrequency

23 lines of code changed in:

andrew 2005-08-15 13:10

Add taylor to default colour check

74 lines of code changed in:

andrew 2005-08-15 13:09

Hashtable now in array, not vector

1 lines of code changed in:

andrew 2005-08-15 13:08

IgnoreGapsConsensus

2 lines of code changed in:

andrew 2005-08-15 13:08

Dont color Checking... red

3 lines of code changed in:

andrew 2005-08-15 13:05

IgnoreGapsConsensus

90 lines of code changed in:

andrew 2005-08-15 13:04

Declare variables outside loops

66 lines of code changed in:

andrew 2005-08-15 13:04

IgnoreGapsConsensus

68 lines of code changed in:

andrew 2005-08-15 13:02

Calculate gap and nogap ratio here

32 lines of code changed in:

jimp 2005-08-12 15:26

fixed leafMapping bug for Id's like SequenceX (where X=14 matches all X=1,10,11,12,13).
Fixes Mantis 0009227

27 lines of code changed in:

andrew 2005-08-09 18:07

Add notes on proxy settings

10 lines of code changed in:

andrew 2005-08-09 18:06

InstallAnywhere readme

24 lines of code changed in:

andrew 2005-08-09 17:55

New classes

4 lines of code changed in:

andrew 2005-08-09 17:53

Cache.getDefault

1 lines of code changed in:

andrew 2005-08-09 17:53

Proxy server, default browser, multiple links added

228 lines of code changed in:

andrew 2005-08-09 17:53

cache.getDefault

2 lines of code changed in:

andrew 2005-08-09 17:52

Try/catch loading default icons

4 lines of code changed in:

andrew 2005-08-09 17:52

Splash screen is repainted when checking latest version

15 lines of code changed in:

andrew 2005-08-09 17:51

Proxy server, default browser, multiple links added

214 lines of code changed in:

andrew 2005-08-09 17:50

Handle multiple url links

85 lines of code changed in:

andrew 2005-08-09 17:48

Cache.getDefault

5 lines of code changed in:

andrew 2005-08-09 17:47

Can give a name to new browser window

11 lines of code changed in:

andrew 2005-08-09 17:47

Properties file is used in preference to viewport/cache/preferences replicating defaults

135 lines of code changed in:

andrew 2005-08-09 17:46

Edit/add/delete a sequence link

132 lines of code changed in:

andrew 2005-08-09 17:45

Applet handles multiple sequence links

71 lines of code changed in:

andrew 2005-08-04 09:16

Add docs in build

72 lines of code changed in:

andrew 2005-08-03 16:07

Fix for user entering number in search window

6 lines of code changed in:

andrew 2005-08-03 14:13

Version 2.02

1 lines of code changed in:

andrew 2005-08-03 14:10

1 & -1

3 lines of code changed in:

andrew 2005-08-03 14:09

Trees aren't save in headless state in this version

31 lines of code changed in:

andrew 2005-08-03 14:08

Loading thread moved to io.FileLoader

18 lines of code changed in:

andrew 2005-08-03 14:08

Use Container to get fontMetrics

9 lines of code changed in:

andrew 2005-08-03 14:07

FileLoading removed from desktop

99 lines of code changed in:

andrew 2005-08-03 14:07

Can run headless=true

133 lines of code changed in:

andrew 2005-08-02 10:23

Use font.getName, not font.getFontName

2 lines of code changed in:

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