May 2005 Commit Log

Number of Commits:
221
Number of Active Developers:
2
jimp 2005-05-31 17:39

Moved comment so it doesn't break jalopy (this is not good!)

3 lines of code changed in:

jimp 2005-05-30 18:02

added the sorting entry to calculations, and corrected the PID
ordering and the redundancy calculation help description.

17 lines of code changed in:

jimp 2005-05-30 17:38

Changed sortByPID to use the gapped PID function.

1 lines of code changed in:

jimp 2005-05-30 17:33

comments

15 lines of code changed in:

jimp 2005-05-30 17:10

Added clustalW 'realignment' (primitive)

54 lines of code changed in:

jimp 2005-05-30 16:47

added default ClustalWS or MuscleWS to remove gaps.

2 lines of code changed in:

jimp 2005-05-30 16:46

propagated use of jalview.util.GapChars for gap removal.

1 lines of code changed in:

jimp 2005-05-30 15:58

more robust parsing for DBset/DBname|id1|id2 type ids

14 lines of code changed in:

jimp 2005-05-30 12:04

modified history for redundancy removal.

16 lines of code changed in:

jimp 2005-05-30 12:03

fixed stacktrace potential for pairwise alignment action.

2 lines of code changed in:

jimp 2005-05-30 12:01

Modified output on stdout for similarity matrix.

34 lines of code changed in:

andrew 2005-05-27 16:52

images moved

62 lines of code changed in:

jimp 2005-05-27 16:46

fixed brain interruption bug.

25 lines of code changed in:

andrew 2005-05-27 16:40

ignores blank lines read in and write out

11 lines of code changed in:

jimp 2005-05-27 16:09

right ordering for RedundancyPanel constructor

1 lines of code changed in:

jimp 2005-05-27 16:07

added proper state check for failedJob flag.

13 lines of code changed in:

jimp 2005-05-27 16:03

Added jobFail state

5 lines of code changed in:

jimp 2005-05-27 16:02

better recognition of MSF files.

3 lines of code changed in:

andrew 2005-05-27 15:43

Added menus

18 lines of code changed in:

andrew 2005-05-27 15:33

edits

21 lines of code changed in:

andrew 2005-05-27 15:31

image moved

3 lines of code changed in:

andrew 2005-05-27 15:30

pref

29 lines of code changed in:

andrew 2005-05-27 15:28

menus

266 lines of code changed in:

andrew 2005-05-27 15:24

Image moved

5 lines of code changed in:

andrew 2005-05-27 15:17

identity changed

1 lines of code changed in:

andrew 2005-05-27 15:16

Cut and paste menus added

75 lines of code changed in:

andrew 2005-05-27 15:14

Cut and paste changes

3 lines of code changed in:

andrew 2005-05-27 15:13

C&P changes

1 lines of code changed in:

andrew 2005-05-27 15:12

Check if colos are null

9 lines of code changed in:

andrew 2005-05-27 15:06

Cut and paste changes

2 lines of code changed in:

andrew 2005-05-27 15:05

Add cut and paste menus

64 lines of code changed in:

andrew 2005-05-27 15:05

CutAndPaste changed

1 lines of code changed in:

jimp 2005-05-27 12:47

Added nicer header formatting for MSFfile output.

31 lines of code changed in:

jimp 2005-05-27 10:55

recovered changes from v 1.84

3 lines of code changed in:

andrew 2005-05-27 10:33

Check if usrCol is null

3 lines of code changed in:

andrew 2005-05-27 10:32

New cut and paste

3 lines of code changed in:

jimp 2005-05-27 10:32

Jpredfile now uses the PileUpfile io class.

1 lines of code changed in:

jimp 2005-05-27 10:32

Addred GapChar string for convenient regex construction

1 lines of code changed in:

jimp 2005-05-27 10:31

Response to bug mantis?id=8187 - some quick hacks to read and write david's MSF file with '~' as a gap character.

19 lines of code changed in:

andrew 2005-05-27 10:30

Remove desc for conserve graph

2 lines of code changed in:

jimp 2005-05-27 10:29

Old MSF Format writer now renamed.

248 lines of code changed in:

jimp 2005-05-26 18:21

fixed use of PID rather than 'Comparison' Alignment percentage id
calculation.

2 lines of code changed in:

jimp 2005-05-26 18:21

fairly pointless catch exception error information added. (attempt to
catch case when a parse() call breaks in an unexpected fashion...)

10 lines of code changed in:

jimp 2005-05-26 18:19

fixed redundancy Undo and allowed it to work on UNALIGNED SEQUENCES
(ho ho)

68 lines of code changed in:

jimp 2005-05-26 11:21

bug fix in jpred client. TreeViewer display state and gui consistency
improved (treecanvas/Treepanel state exchange functions).

31 lines of code changed in:

jimp 2005-05-26 11:20

partially updated help. Added separate treeviewing item in the root
menu.

109 lines of code changed in:

andrew 2005-05-26 10:54

check for null residues

4 lines of code changed in:

andrew 2005-05-26 10:54

DOnt add Conservation graph to every residue

1 lines of code changed in:

andrew 2005-05-26 10:53

check for null residues

4 lines of code changed in:

andrew 2005-05-26 10:51

toString modified

20 lines of code changed in:

andrew 2005-05-25 18:46

reset colours added

6 lines of code changed in:

andrew 2005-05-25 18:45

more clustalx bugs fixed

48 lines of code changed in:

andrew 2005-05-25 17:44

getHexString added

32 lines of code changed in:

andrew 2005-05-25 17:44

all can threshold

21 lines of code changed in:

andrew 2005-05-25 17:43

output to textbox

18 lines of code changed in:

andrew 2005-05-25 17:43

layout changes

57 lines of code changed in:

andrew 2005-05-25 17:43

capitals

3 lines of code changed in:

andrew 2005-05-25 17:42

format changes

136 lines of code changed in:

andrew 2005-05-25 17:42

remove scrollpane

1 lines of code changed in:

andrew 2005-05-25 17:41

Capitalise

5 lines of code changed in:

andrew 2005-05-25 17:41

c&p changed

2 lines of code changed in:

andrew 2005-05-25 17:40

use getHexString in util

3 lines of code changed in:

andrew 2005-05-25 17:40

usercolours changed

48 lines of code changed in:

andrew 2005-05-25 17:39

output text to textbox

23 lines of code changed in:

andrew 2005-05-25 17:39

all colours can threshold

1 lines of code changed in:

andrew 2005-05-25 17:37

c&p changed

1 lines of code changed in:

andrew 2005-05-25 17:36

selectiongroup could be null

1 lines of code changed in:

andrew 2005-05-25 17:36

saves usercolours

77 lines of code changed in:

andrew 2005-05-25 17:36

usercolours changed

4 lines of code changed in:

andrew 2005-05-25 17:36

c&p changed

1 lines of code changed in:

andrew 2005-05-25 17:35

formatforoutput never used

0 lines of code changed in:

andrew 2005-05-25 17:35

output values to textbox

23 lines of code changed in:

andrew 2005-05-25 17:34

usercolours changed

16 lines of code changed in:

andrew 2005-05-25 17:34

toString method added

10 lines of code changed in:

andrew 2005-05-25 17:33

XML schema changes

1609 lines of code changed in:

andrew 2005-05-25 17:32

usercolourscheme changed

11 lines of code changed in:

andrew 2005-05-25 17:32

formatting changes

158 lines of code changed in:

andrew 2005-05-25 17:27

all colours can threshold

2 lines of code changed in:

andrew 2005-05-25 17:26

usercolours changed

1 lines of code changed in:

andrew 2005-05-25 17:26

remove comment

12 lines of code changed in:

andrew 2005-05-25 17:25

can output details to textbox

15 lines of code changed in:

andrew 2005-05-25 17:24

usercolours added

26 lines of code changed in:

jimp 2005-05-25 17:09

added jalview.browser property so a linux user can choose which browser they want to open swissprot entries with.

11 lines of code changed in:

jimp 2005-05-25 14:59

doh - compile before commit!

1 lines of code changed in:

jimp 2005-05-25 14:35

tidied up system.out messages and moved many to stderr.

69 lines of code changed in:

jimp 2005-05-25 14:00

Improved consistency between JPredWS and MsaWS

41 lines of code changed in:

jimp 2005-05-25 14:00

base class for web service clients.

23 lines of code changed in:

jimp 2005-05-24 18:18

title parameter for single sequence prediction.

2 lines of code changed in:

jimp 2005-05-24 18:18

Added more firePropertyChange calls - mainly for sequence paste events.

17 lines of code changed in:

jimp 2005-05-24 18:17

extended the UpdatePlaceholders to check for any new associations.

17 lines of code changed in:

jimp 2005-05-24 17:37

added PropertyChangeListeners for alignviewport.alignment.sequences
vector. TreeViewer windows now properly reflect deletions to sequence
set.

59 lines of code changed in:

andrew 2005-05-24 14:02

remove .

2 lines of code changed in:

andrew 2005-05-24 12:23

URL getresource adds %20 for spaces. Use user.dir instead

9 lines of code changed in:

andrew 2005-05-24 10:35

filefilter might not be JalviewFileFilter

7 lines of code changed in:

jimp 2005-05-24 10:08

formatting.

14 lines of code changed in:

andrew 2005-05-24 10:04

equalsIgnoreCase

1 lines of code changed in:

andrew 2005-05-24 10:04

setDefaultFileFormat

3 lines of code changed in:

andrew 2005-05-24 10:03

replace get with elementAt

1 lines of code changed in:

andrew 2005-05-24 10:02

setgraphics black

1 lines of code changed in:

jimp 2005-05-24 09:55

slight changes.

8 lines of code changed in:

jimp 2005-05-24 09:51

added sorting alignments documentation.

44 lines of code changed in:

andrew 2005-05-24 09:49

setgraphics black

2 lines of code changed in:

jimp 2005-05-24 09:42

several ordering bug fixes.

43 lines of code changed in:

jimp 2005-05-23 18:55

Added PadGaps and made treeSortMenu dynamic (it gets added when there is a tree ordering added). Alignment orderings are now added to the main sort menu.

45 lines of code changed in:

jimp 2005-05-23 18:49

added some assertions and rangechecks for insert/deleteChar methods.

19 lines of code changed in:

jimp 2005-05-23 18:48

added getSequencesInOrder (part of refactor from AlignPanel menu action for cut'n'paste).

39 lines of code changed in:

jimp 2005-05-23 18:47

editMenuPadGaps and sortByTree/sort items

19 lines of code changed in:

jimp 2005-05-23 18:45

fixed window title names for prediction on MSA or Sequence.

22 lines of code changed in:

andrew 2005-05-23 17:31

colour groups by text colour

1 lines of code changed in:

andrew 2005-05-23 17:31

make sure fonts are not null

16 lines of code changed in:

andrew 2005-05-23 17:30

remove separator

3 lines of code changed in:

andrew 2005-05-23 17:30

new savestate method

57 lines of code changed in:

jimp 2005-05-23 14:27

Ugly but improved recovery of sequence names, starts/ends and other SequenceI properties for an alignment returned from a webservice.

68 lines of code changed in:

jimp 2005-05-23 14:26

bug fix for wierdness retrieving QUERY sequence index.

1 lines of code changed in:

andrew 2005-05-23 12:23

boxes, colour text, show text added to groups

169 lines of code changed in:

andrew 2005-05-23 10:26

historyitem added

428 lines of code changed in:

jimp 2005-05-22 19:18

include MsaWS ordering but not perfect (undo destroys ordering efficacy).

1 lines of code changed in:

jimp 2005-05-22 18:57

marginal improvements - still no automated client constructor.

14 lines of code changed in:

jimp 2005-05-22 18:56

Added alignment ordering option to 'Sort by' and implemented generic
MsaWS client.

1528 lines of code changed in:

jimp 2005-05-22 18:12

later version of client-side WSDL2Java generated simple Alignment
container.

2 lines of code changed in:

jimp 2005-05-20 17:43

Semiworking generic MSA client

271 lines of code changed in:

jimp 2005-05-20 16:18

added placeholder indicators and menu item

31 lines of code changed in:

jimp 2005-05-20 16:17

Various sort methods added and bugs fixed (coping with associated trees and alignment orders from web services)

88 lines of code changed in:

andrew 2005-05-20 15:57

DEFAULT_FILE_FORMAT added

5 lines of code changed in:

jimp 2005-05-20 15:54

sequence place holder reveal menu item.

24 lines of code changed in:

jimp 2005-05-20 15:52

added tree node property for sequence placeholders.

322 lines of code changed in:

andrew 2005-05-20 14:40

if fullid shown, resize fonts

1 lines of code changed in:

andrew 2005-05-20 14:30

startup file added

41 lines of code changed in:

andrew 2005-05-20 14:29

a flauss changes

15 lines of code changed in:

andrew 2005-05-20 14:29

scroller is now a panel

3 lines of code changed in:

andrew 2005-05-20 14:28

startup file added

38 lines of code changed in:

andrew 2005-05-20 14:28

look for startup file

18 lines of code changed in:

andrew 2005-05-20 14:27

scroller is now a panel, removes border

1 lines of code changed in:

andrew 2005-05-20 12:01

change ActionListeners to ItemListeners

17 lines of code changed in:

andrew 2005-05-20 11:48

not centered

2 lines of code changed in:

andrew 2005-05-20 11:47

removed

0 lines of code changed in:

andrew 2005-05-20 11:46

apostrophes

3 lines of code changed in:

andrew 2005-05-20 10:26

copy order maintained

49 lines of code changed in:

jimp 2005-05-20 10:18

xml-apis from the same place as xercesImpl.jar
This was needed to make the axis.jar happy using my (jims)
Jbuilder2005 buid environment.

0 lines of code changed in:

jimp 2005-05-20 10:04

This is the xercesImpl.jar from xerces-2_6_2

0 lines of code changed in:

andrew 2005-05-20 10:01

deleted

0 lines of code changed in:

andrew 2005-05-20 09:55

Updated

11488 lines of code changed in:

jimp 2005-05-20 09:26

Fixing the broken cvs.

15495 lines of code changed in:

andrew 2005-05-20 09:19

updated

0 lines of code changed in:

andrew 2005-05-20 09:16

xml schemas

209 lines of code changed in:

andrew 2005-05-20 09:14

castor lib

0 lines of code changed in:

andrew 2005-05-20 08:54

Fasta FASTA

10 lines of code changed in:

andrew 2005-05-19 19:01

image changes

0 lines of code changed in:

andrew 2005-05-19 19:01

new libraries for XML binding

15486 lines of code changed in:

andrew 2005-05-19 19:00

returns name if given colourscheme

33 lines of code changed in:

andrew 2005-05-19 18:59

A Flauss reccommends

224 lines of code changed in:

andrew 2005-05-19 18:59

A Flauss recommends

1 lines of code changed in:

andrew 2005-05-19 18:58

A flauss recommendations

6 lines of code changed in:

andrew 2005-05-19 18:57

filechooser has multiple filters

58 lines of code changed in:

andrew 2005-05-19 18:57

loading/saving changes

58 lines of code changed in:

andrew 2005-05-19 18:56

changes to jalviewfilechooser

10 lines of code changed in:

andrew 2005-05-19 18:56

% identity is consensus

1 lines of code changed in:

andrew 2005-05-19 18:55

no need for right mouse click

1 lines of code changed in:

andrew 2005-05-19 18:55

Load and Save State added

67 lines of code changed in:

andrew 2005-05-19 18:54

dont show redundant menuitems

30 lines of code changed in:

andrew 2005-05-19 18:54

load in gap symbol

4 lines of code changed in:

andrew 2005-05-19 18:53

block edit bug fixed

50 lines of code changed in:

andrew 2005-05-19 18:53

maintain original threshold value

9 lines of code changed in:

andrew 2005-05-19 18:51

changes to JalviewFileChooser

27 lines of code changed in:

andrew 2005-05-19 18:51

new class

466 lines of code changed in:

andrew 2005-05-19 18:50

calculate max and min for graph

15 lines of code changed in:

andrew 2005-05-19 18:49

release version

2 lines of code changed in:

andrew 2005-05-19 18:49

Copied sequences title altered

8 lines of code changed in:

andrew 2005-05-19 18:48

remove redundant menuitems

30 lines of code changed in:

andrew 2005-05-19 18:48

remove actionevents

7 lines of code changed in:

andrew 2005-05-19 18:47

group editing bug fixed

82 lines of code changed in:

andrew 2005-05-19 18:47

toString () method added

5 lines of code changed in:

andrew 2005-05-19 18:46

Created by Castor

5653 lines of code changed in:

jimp 2005-05-19 15:08

The archetypal Multiple Sequence Alignment Web Service

21 lines of code changed in:

andrew 2005-05-12 10:09

conservation removed

0 lines of code changed in:

andrew 2005-05-12 10:09

separator added

2 lines of code changed in:

andrew 2005-05-12 10:07

corrections for find when edit takes place

111 lines of code changed in:

andrew 2005-05-11 11:44

JalviewApplet jbuilder project

78 lines of code changed in:

andrew 2005-05-11 11:42

output newick to textbox

17 lines of code changed in:

andrew 2005-05-11 11:40

reads in treeFile from applet parameter

75 lines of code changed in:

andrew 2005-05-09 12:02

paintComponent. not paint

2 lines of code changed in:

andrew 2005-05-09 12:00

correct conservation errors after edit

19 lines of code changed in:

andrew 2005-05-09 12:00

if imgWidth <0

1 lines of code changed in:

andrew 2005-05-06 18:06

wrap align correction for last row

6 lines of code changed in:

andrew 2005-05-06 13:35

add 1 to fastPaint, in case seqs of different length

1 lines of code changed in:

andrew 2005-05-06 13:34

if clustal + edit, make new clustal

13 lines of code changed in:

andrew 2005-05-06 13:34

add 1 to fastPaint, in case seqs of different length

1 lines of code changed in:

andrew 2005-05-05 14:25

pdb end seq and startseq determined here

50 lines of code changed in:

andrew 2005-05-05 14:25

colour by sequence just about works

36 lines of code changed in:

andrew 2005-05-05 14:24

Accelerator on menu takes care of actionkey

1 lines of code changed in:

jimp 2005-05-05 14:16

Added cancel interface for JPred Client and fixed some messages.

304 lines of code changed in:

jimp 2005-05-05 14:15

Moved tree leafname to alignment set matching into SequenceIdMatcher class for
use in other contexts.

150 lines of code changed in:

jimp 2005-05-05 12:40

<No Comment Entered>

0 lines of code changed in:

andrew 2005-05-05 12:21

saveAs .....

166 lines of code changed in:

andrew 2005-05-05 12:21

saveAsNewick

7 lines of code changed in:

andrew 2005-05-05 11:36

moved to jalview.io

0 lines of code changed in:

andrew 2005-05-05 11:35

new place for sequencefeaturefetcher

315 lines of code changed in:

andrew 2005-05-05 11:35

send rotCanvas sequence and viewport

2 lines of code changed in:

andrew 2005-05-05 11:34

pdbfile details not essential to sequence

6 lines of code changed in:

andrew 2005-05-05 09:54

addelement replaces add

1 lines of code changed in:

andrew 2005-05-04 17:00

added remark about right mouse in awt

2 lines of code changed in:

andrew 2005-05-04 16:59

validate and repaint after changing panels

3 lines of code changed in:

andrew 2005-05-04 16:59

mouse listeners added

100 lines of code changed in:

andrew 2005-05-04 16:22

renderer removed

0 lines of code changed in:

andrew 2005-05-04 16:22

no need to send pid, seqnum

2 lines of code changed in:

andrew 2005-05-04 16:21

SequenceRenderer changes

7 lines of code changed in:

andrew 2005-05-04 16:20

no need to send vector pid or seqnum

2 lines of code changed in:

andrew 2005-05-04 16:20

No need for this interface

0 lines of code changed in:

andrew 2005-05-04 16:08

Applet files

9447 lines of code changed in:

jimp 2005-05-03 14:20

Better treatment of error states and cancellability in wsclient.

26 lines of code changed in:

andrew 2005-05-03 13:49

formatAdapter.formatSequences and maintain annotation after undo

7 lines of code changed in:

andrew 2005-05-03 13:48

formatAdapter.formats

2 lines of code changed in:

andrew 2005-05-03 13:48

formatAdapter.readFile

4 lines of code changed in:

andrew 2005-05-03 13:47

change Container to Component

10 lines of code changed in:

andrew 2005-05-03 13:46

formatAdapter.formats, remove redundant code

61 lines of code changed in:

andrew 2005-05-03 13:44

formatAdapter.formats

3 lines of code changed in:

andrew 2005-05-03 13:43

1.1 compatible, formatting changes

188 lines of code changed in:

andrew 2005-05-03 13:42

FormatAdapter readFile

5 lines of code changed in:

andrew 2005-05-03 13:39

1.1 compatible

40 lines of code changed in:

andrew 2005-05-03 13:39

findKmers and fetchSequenceFeatures removed

0 lines of code changed in:

andrew 2005-05-03 13:38

Removed as obfuscation of classes wiill change class names

0 lines of code changed in:

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