May 2007 Commit Log

Number of Commits:
133
Number of Active Developers:
4
jprocter 2007-05-28 12:15

prototype DBRef and Feature Type semantics (for annotating coding regions and distinguishing between DNA and peptide sequence databases)

6 lines of code changed in:

jprocter 2007-05-28 12:13

moved castor-mapping.xsd to schemas

0 lines of code changed in:

jprocter 2007-05-28 12:12

jalview source development documentation

0 lines of code changed in:

jprocter 2007-05-28 11:02

fix compact annotation array routine

14 lines of code changed in:

jprocter 2007-05-28 10:57

castor mapping file schema (for mappings in resources dir) - this is put in for development documentation purposes.

0 lines of code changed in:

jprocter 2007-05-28 10:53

mapping file change for castor-1.1 upgrade

0 lines of code changed in:

jprocter 2007-05-28 10:53

castor mapping unmarshalling logging

3 lines of code changed in:

jprocter 2007-05-28 10:51

loglevel property constants and castor validation logger config

26 lines of code changed in:

jprocter 2007-05-24 16:20

castor-1.1 classes (descriptors moved to subpackage)

0 lines of code changed in:

jprocter 2007-05-24 16:19

castor-1.1 compatible classes from ant task

0 lines of code changed in:

jprocter 2007-05-24 16:16

jalview 2.0 XML schema versions for backwards compatibility in future castor upgrades

9687 lines of code changed in:

www-jalview 2007-05-24 10:08

New file for /homes/www-jalview

362 lines of code changed in:

jprocter 2007-05-22 22:17

fixed jalview 2.3 bug where gapped aligned codons were always translated as inserted residues rather than aligned with eachother

0 lines of code changed in:

jprocter 2007-05-22 17:35

1.4 version of vamsas-client

0 lines of code changed in:

jprocter 2007-05-22 16:54

refactored document objects and bugfix on jvdataset-vamsasdataset binding

51 lines of code changed in:

amwaterhouse 2007-05-22 15:25

DONT SET PICKING LABEL

0 lines of code changed in:

jprocter 2007-05-21 14:55

vamsas svn 14.55 May 21

0 lines of code changed in:

jprocter 2007-05-18 16:45

fixed getObject(VorbaId) lookup in vamsas-client

10 lines of code changed in:

amwaterhouse 2007-05-18 14:59

2.3

77 lines of code changed in:

jprocter 2007-05-18 12:03

update to and from document (and remove deprecated classes)

16 lines of code changed in:

jprocter 2007-05-18 11:43

removed uneccessary vamsasLoad commented out.

1 lines of code changed in:

jprocter 2007-05-17 19:03

refining - still debugging.

39 lines of code changed in:

jprocter 2007-05-17 18:09

updated source generator properties for castor-1.1

0 lines of code changed in:

jprocter 2007-05-17 18:07

use of proper vamsas client API by Jalview

2254 lines of code changed in:

jprocter 2007-05-17 18:06

modified castor-1.1 library and refactored uk.ac.vamsas

396 lines of code changed in:

andrew 2007-05-16 10:16

visible

1 lines of code changed in:

andrew 2007-05-15 16:35

SequenceListener highlights SearchResults, not just a single sequence

18 lines of code changed in:

andrew 2007-05-14 15:56

Invert mouse drag controls

1 lines of code changed in:

jprocter 2007-05-10 14:59

apparent bug in JpredFile parser where annotation was not being removed from alignment profile when reading in a concise file as an alignment.

4 lines of code changed in:

amwaterhouse 2007-05-10 10:00

Airbrush out Uniprot

0 lines of code changed in:

jprocter 2007-05-10 09:42

ensure that only annotation referenced in given alignment is duplicated on returned sequence selection set

18 lines of code changed in:

jprocter 2007-05-10 09:41

documentation

5 lines of code changed in:

jprocter 2007-05-10 09:40

bugfix on copy only referenced annotation in copy constructor

13 lines of code changed in:

jprocter 2007-05-10 09:39

fixed array index out of bounds when not removing alignment annotation

2 lines of code changed in:

andrew 2007-05-10 09:10

visibility setting

7 lines of code changed in:

andrew 2007-05-10 09:08

Keep record of last tooltip

7 lines of code changed in:

andrew 2007-05-10 08:14

Visible state of annotation

17 lines of code changed in:

andrew 2007-05-10 08:13

Add show all hidden menu

7 lines of code changed in:

andrew 2007-05-10 08:13

Dont duplicate annotations in multiple views

12 lines of code changed in:

andrew 2007-05-10 08:12

save visible state of annotation

0 lines of code changed in:

jprocter 2007-05-09 16:51

main method for running from command line and better binary file/archive detection

47 lines of code changed in:

jprocter 2007-05-09 14:48

reword jmol state storage

0 lines of code changed in:

jprocter 2007-05-09 14:20

image size

1 lines of code changed in:

andrew 2007-05-09 14:12

minor formatting of tooltip

7 lines of code changed in:

jprocter 2007-05-09 14:08

new binary image

0 lines of code changed in:

andrew 2007-05-09 13:59

9th may

14 lines of code changed in:

jprocter 2007-05-08 18:19

removed cdna coding region 'new feature'

0 lines of code changed in:

jprocter 2007-05-08 18:18

embl mapping and das feature retrieval

0 lines of code changed in:

jprocter 2007-05-08 18:18

optimise order

46 lines of code changed in:

jprocter 2007-05-08 18:18

multiple view pdb view association

58 lines of code changed in:

jprocter 2007-05-08 17:53

formatting and wording

54 lines of code changed in:

jprocter 2007-05-08 17:52

grammar, clarity and typos

130 lines of code changed in:

jprocter 2007-05-08 17:52

typo

42 lines of code changed in:

jprocter 2007-05-08 17:51

formatting

55 lines of code changed in:

jprocter 2007-05-08 17:51

page setup entry

3 lines of code changed in:

jprocter 2007-05-08 17:51

dialog box menu item naming

2 lines of code changed in:

jprocter 2007-05-08 17:50

correct menu entry names and typos

4 lines of code changed in:

jprocter 2007-05-08 17:50

PID distance measure and finishing sentence.

66 lines of code changed in:

jprocter 2007-05-08 17:49

sort by score

8 lines of code changed in:

jprocter 2007-05-08 17:49

dialog box menu item naming

1 lines of code changed in:

jprocter 2007-05-08 15:01

rightalign and italic ids docs

134 lines of code changed in:

jprocter 2007-05-08 14:48

added jmol documentation

64 lines of code changed in:

andrew 2007-05-08 14:47

check for null annotations

12 lines of code changed in:

andrew 2007-05-08 14:47

set picking label

5 lines of code changed in:

andrew 2007-05-08 12:01

state jmol 11.0.2

50 lines of code changed in:

andrew 2007-05-08 11:58

More issues resolved

3 lines of code changed in:

andrew 2007-05-08 11:58

instant update when seq colour is pressed

17 lines of code changed in:

andrew 2007-05-08 11:44

must specify .CA

3 lines of code changed in:

andrew 2007-05-08 11:09

remove system.out

11 lines of code changed in:

andrew 2007-05-08 11:08

small sphere for alpha carbon

6 lines of code changed in:

andrew 2007-05-08 09:18

addElement

4 lines of code changed in:

andrew 2007-05-08 08:56

mirror image recitified

10 lines of code changed in:

andrew 2007-05-07 16:16

2.3 updates

772 lines of code changed in:

andrew 2007-05-07 15:12

Can compile and obfuscate applet with Jmol

34 lines of code changed in:

andrew 2007-05-07 14:59

Image size must allow for scale height

3 lines of code changed in:

andrew 2007-05-07 14:59

dif is never used

1 lines of code changed in:

andrew 2007-05-07 14:59

Allow for large font sizes

2 lines of code changed in:

andrew 2007-05-07 14:58

dont use gold highlights

6 lines of code changed in:

andrew 2007-05-07 14:58

Max width for tooltip

40 lines of code changed in:

andrew 2007-05-07 14:58

still trying to prevent null painting

3 lines of code changed in:

andrew 2007-05-07 14:58

Use id hash to add pdb mappings back to alignment

31 lines of code changed in:

andrew 2007-05-07 14:57

tIndex prevented deletion of last annotation

2 lines of code changed in:

andrew 2007-05-07 14:57

Dont use gold colouring for highlight

6 lines of code changed in:

andrew 2007-05-07 14:56

Use PDB id for grouping mappings

9 lines of code changed in:

andrew 2007-05-07 14:56

Dont use gold colouring for highlight

3 lines of code changed in:

andrew 2007-05-07 14:55

PDBViewer available if necessary

249 lines of code changed in:

andrew 2007-05-04 14:56

Check bounds of loaded comp

4 lines of code changed in:

andrew 2007-05-04 14:55

remove system.out

1 lines of code changed in:

andrew 2007-05-04 14:34

added

963 lines of code changed in:

andrew 2007-05-04 14:33

Add dbrefs before zero length features

14 lines of code changed in:

andrew 2007-05-04 14:33

lastCommand check

1 lines of code changed in:

andrew 2007-05-04 14:32

Rename AppJMol to AppJmol - also AppJmol works with independant sequence sets

34 lines of code changed in:

andrew 2007-05-04 14:30

Renamed to AppJmol

0 lines of code changed in:

andrew 2007-05-04 11:48

New example file for version 2.3

10 lines of code changed in:

andrew 2007-05-04 11:32

Splash screen is not added using normal method, prevents null paint bug

41 lines of code changed in:

andrew 2007-05-04 11:31

Annotations do not extend when full alignment is adjusted

8 lines of code changed in:

andrew 2007-05-03 15:41

pdb id toUpperCase

2 lines of code changed in:

andrew 2007-05-03 15:40

optimize repaints

2 lines of code changed in:

andrew 2007-05-03 15:40

remove system.out

0 lines of code changed in:

andrew 2007-05-03 15:40

optimize repaints

28 lines of code changed in:

jprocter 2007-05-02 16:20

feature locations are retrieved by associated accession string and public debug report request in case embl parsing fails

403 lines of code changed in:

jprocter 2007-05-02 16:19

feature locations are retrieved by associated accession string

53 lines of code changed in:

jprocter 2007-05-02 15:30

public debug report log message to gather any cases where Das coordinate frame mapping fails

0 lines of code changed in:

jprocter 2007-05-02 15:28

fixed getIntervals bug to ensure it returns range from start of token at fromPosition to end of token in toPosition in the direction from fromPosition to toPosition

4 lines of code changed in:

jprocter 2007-05-02 15:27

documentation and proxy call to util.MapList.getToWord(mpos)

6 lines of code changed in:

jprocter 2007-05-02 14:46

extractScores menu item disabled for release

1 lines of code changed in:

jprocter 2007-05-02 14:41

only return non-empty subsequences when getting selection as new sequences

31 lines of code changed in:

andrew 2007-05-02 14:03

Allow expansion of textarea for many sequence input

582 lines of code changed in:

andrew 2007-05-02 14:02

AMSA input set padgaps true

19 lines of code changed in:

andrew 2007-05-02 14:02

convert space to gapchar

3 lines of code changed in:

jprocter 2007-05-02 13:25

undo stackempty error fix, refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation, convenience method for getting alignment object array for all views

54 lines of code changed in:

jprocter 2007-05-02 13:24

refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation

4381 lines of code changed in:

jprocter 2007-05-02 13:23

copy only the sequence associated alignment annotation displayed in the current view

3 lines of code changed in:

jprocter 2007-05-02 13:21

subsequence bound checks and constructor for selectively duplicating sequence associated alignment annotation in copy constructor

26 lines of code changed in:

jprocter 2007-05-02 13:20

return flag indicating if annotations were actually deleted from alignment

2 lines of code changed in:

jprocter 2007-05-02 13:19

checks for negative start column in restrict

8 lines of code changed in:

jprocter 2007-05-02 13:19

return flag indicating if annotations were actually deleted from alignment

3 lines of code changed in:

andrew 2007-05-02 11:47

Padgaps is false by default

2 lines of code changed in:

andrew 2007-05-01 17:34

setVisible flag sent to EditNameDialog

29 lines of code changed in:

andrew 2007-05-01 17:33

Pad gaps method

18 lines of code changed in:

andrew 2007-05-01 17:33

Make sure annots are alignment width

5 lines of code changed in:

andrew 2007-05-01 15:18

use jalviewLite to addFrame

1 lines of code changed in:

andrew 2007-05-01 15:18

remove system.out

3 lines of code changed in:

andrew 2007-05-01 14:58

set chains available

4 lines of code changed in:

andrew 2007-05-01 14:37

Multiple views/hidden region/undo out of index bug

8 lines of code changed in:

andrew 2007-05-01 13:25

Can specify PDB chain to map sequence to - only used by applet so far

152 lines of code changed in:

jprocter 2007-05-01 12:47

javadoc

1 lines of code changed in:

jprocter 2007-05-01 12:46

removeAlignmentAnnotation only removes annotation objects referenced by the alignmentI and will do nothing otherwise.

16 lines of code changed in:

jprocter 2007-05-01 11:42

sort-by-score works of sequence-annotation, not alignment annotation vector

10 lines of code changed in:

andrew 2007-05-01 11:04

Save seqset properties

194 lines of code changed in:

andrew 2007-05-01 11:03

Seqset properties saved

6 lines of code changed in:

jprocter 2007-05-01 10:51

2.3 what's new

328 lines of code changed in:

jprocter 2007-05-01 10:50

preliminary EMBL and mapping documentation

9 lines of code changed in:

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