August 2006 Commit Log

Number of Commits:
164
Number of Active Developers:
2
andrew 2006-08-30 17:10

GraphHeight might be zero

2 lines of code changed in:

andrew 2006-08-30 17:09

jnet file is 1 to 1 mapping

1 lines of code changed in:

andrew 2006-08-30 17:09

Remove unnecessary separotor

2 lines of code changed in:

andrew 2006-08-30 17:08

Gap added to aa3Hash

1 lines of code changed in:

andrew 2006-08-30 17:08

User colours are case sensitive

398 lines of code changed in:

andrew 2006-08-29 16:31

Can shrink graph to zero

4 lines of code changed in:

andrew 2006-08-29 16:24

No stacktrace

0 lines of code changed in:

andrew 2006-08-29 16:23

createMapping alreadyMapped

11 lines of code changed in:

andrew 2006-08-29 16:22

Additional repaint

4 lines of code changed in:

andrew 2006-08-29 16:22

jnetfile can be loaded onto alignment

23 lines of code changed in:

andrew 2006-08-29 16:21

SequenceMapping updated

10 lines of code changed in:

andrew 2006-08-29 16:15

Jnet files sent to servlet as annotations

6 lines of code changed in:

andrew 2006-08-24 14:03

unbalanced head tag

1 lines of code changed in:

andrew 2006-08-23 09:03

volume 20

1 lines of code changed in:

andrew 2006-08-22 17:54

2.1 updates

0 lines of code changed in:

andrew 2006-08-22 17:25

add link.gif

2 lines of code changed in:

andrew 2006-08-22 16:31

2.1 update

2 lines of code changed in:

andrew 2006-08-22 15:29

To uppercase only visible

71 lines of code changed in:

jimp 2006-08-22 14:47

documentation - adding new Input data menu entries.

13 lines of code changed in:

jimp 2006-08-22 14:25

added note on column-separability

53 lines of code changed in:

jimp 2006-08-22 14:13

documentation

146 lines of code changed in:

jimp 2006-08-22 14:01

getSequenceStrings() bug fixed.

0 lines of code changed in:

andrew 2006-08-22 11:39

Remove group when hiding cols from scalePanel

10 lines of code changed in:

andrew 2006-08-22 10:11

2006

1 lines of code changed in:

andrew 2006-08-22 10:10

Put transparency back

4 lines of code changed in:

andrew 2006-08-22 10:10

make 1.1 compatible

0 lines of code changed in:

jimp 2006-08-22 09:34

hidden region recovery in JPred and new hidden region pruning function

2 lines of code changed in:

jimp 2006-08-22 09:32

off by one bug in hiden column unmarshalling

1462 lines of code changed in:

andrew 2006-08-21 16:34

header updated

790 lines of code changed in:

andrew 2006-08-21 16:29

header updated

17 lines of code changed in:

andrew 2006-08-21 15:48

validate groupPanel

2 lines of code changed in:

andrew 2006-08-21 15:39

validate groupPanel

2 lines of code changed in:

andrew 2006-08-21 15:39

Add uniprot DBref

11 lines of code changed in:

andrew 2006-08-21 15:14

Remove system.out

0 lines of code changed in:

andrew 2006-08-21 15:13

1.1 compatible

2400 lines of code changed in:

jimp 2006-08-21 14:41

Refactored Jnet and added hidden columns support.
fixed undo-redo bug, hidden columns are moved with gapped columns and delete columns and undo-redo.

3615 lines of code changed in:

jimp 2006-08-21 14:40

fixed undo-redo bug, hidden columns are moved with gapped columns and delete columns and undo-redo

2400 lines of code changed in:

jimp 2006-08-21 14:03

removeGaps method can record changes in alignment columns to pass to ColumnSelection

299 lines of code changed in:

jimp 2006-08-21 13:51

fix for truncation of sequence associated annotation mapped onto alignment

4 lines of code changed in:

jimp 2006-08-21 13:46

added shiftList to record changes in alignment column positions.

180 lines of code changed in:

jimp 2006-08-21 13:45

remove gaps method from AlignFrame.remove_gaps_actionPerformed

344 lines of code changed in:

jimp 2006-08-21 13:43

inverse ShiftList and SequenceI.gapMap->ShiftList methods.

0 lines of code changed in:

jimp 2006-08-21 13:42

avoid null pointer exceptions

0 lines of code changed in:

jimp 2006-08-20 13:00

javadoc

331 lines of code changed in:

andrew 2006-08-18 17:54

Check colourScheme is not null - jalview prior 2.5 incompatibility

0 lines of code changed in:

andrew 2006-08-18 15:02

dont remove all representative seqs on delete groups

1 lines of code changed in:

andrew 2006-08-18 14:57

remove all representative seqs on delete groups

5 lines of code changed in:

andrew 2006-08-18 10:23

treeFile = treeFile

3 lines of code changed in:

andrew 2006-08-18 09:53

Only discover DAS sources if panel shown

0 lines of code changed in:

andrew 2006-08-18 09:52

only set new layout if 2 buttons visible

4 lines of code changed in:

andrew 2006-08-18 09:51

Jalview features format adds links as hrefs

0 lines of code changed in:

andrew 2006-08-17 15:06

H key updates

5 lines of code changed in:

andrew 2006-08-17 14:51

OptionPane invokeLater

14 lines of code changed in:

andrew 2006-08-17 14:41

If no annotation exists

16 lines of code changed in:

andrew 2006-08-17 14:41

Set bg white

3 lines of code changed in:

andrew 2006-08-17 14:40

Hold onto selected region when hiding all columns only

14 lines of code changed in:

jimp 2006-08-17 14:33

moved visible sub-alignment extraction and update from MsaWSThread to
an AlignmentView method, refactored JPredClient to new abstraction and
added flags for canMergeResults and openResultsImmediatly to web
service gui.

64 lines of code changed in:

jimp 2006-08-17 14:31

javadoc

1 lines of code changed in:

andrew 2006-08-17 13:34

Monospace check

3 lines of code changed in:

andrew 2006-08-17 13:33

1 more pixel allowed between chars and graph

4 lines of code changed in:

andrew 2006-08-17 11:14

Keys update

14 lines of code changed in:

andrew 2006-08-17 11:11

control and shift

6 lines of code changed in:

andrew 2006-08-17 11:08

Dont set group null hideCOls

2 lines of code changed in:

andrew 2006-08-17 11:08

OptionPanes invokeLater

21 lines of code changed in:

andrew 2006-08-17 11:08

Control and alt for toggle hide

43 lines of code changed in:

andrew 2006-08-16 09:05

Fire alignment changed if seqs hidden / revealed

60 lines of code changed in:

andrew 2006-08-15 13:47

Correct title for sequence parameter applets

4 lines of code changed in:

andrew 2006-08-15 13:36

Sequences can be added as parameter

20 lines of code changed in:

andrew 2006-08-15 12:14

H key added

79 lines of code changed in:

jimp 2006-08-15 12:10

make annotation label font size follow alignment font size.

3 lines of code changed in:

jimp 2006-08-15 11:59

first stage of adapting JNet client to hidden regions and new WSClient
structure.

431 lines of code changed in:

jimp 2006-08-15 11:57

fixed alignment ordering name.

0 lines of code changed in:

jimp 2006-08-15 11:57

ensure that close widget is available for jobs that cannot be
cancelled.

3 lines of code changed in:

andrew 2006-08-15 11:35

Acknowledgement

0 lines of code changed in:

andrew 2006-08-15 11:35

Setselectiongroup null on hide

3 lines of code changed in:

andrew 2006-08-15 11:34

H key to hide / reveal

20 lines of code changed in:

andrew 2006-08-15 11:34

Add key listener to scalePanel and annotationPanel

39 lines of code changed in:

andrew 2006-08-15 11:34

Select revealed seqs

71 lines of code changed in:

andrew 2006-08-15 11:00

WRITEABLE_FORMATS and READABLE_FORMATS string []

41 lines of code changed in:

andrew 2006-08-15 10:59

Move features to dataset

2 lines of code changed in:

andrew 2006-08-14 17:10

Stockholm parser added

26 lines of code changed in:

andrew 2006-08-14 17:09

Stockholm parser

0 lines of code changed in:

jimp 2006-08-14 16:23

refactored to create generic polling thread and subjobs

0 lines of code changed in:

andrew 2006-08-14 16:22

2.1 updates

10 lines of code changed in:

jimp 2006-08-14 16:22

function to indicate job has finished but no results are available.

12 lines of code changed in:

andrew 2006-08-14 16:20

New file

51 lines of code changed in:

andrew 2006-08-14 16:11

new feature added

7 lines of code changed in:

andrew 2006-08-14 16:11

Stop loading must be before JOptionPane, 1.5 bug

7 lines of code changed in:

andrew 2006-08-14 16:10

No need to check selection group size

2 lines of code changed in:

andrew 2006-08-14 16:10

findSequenceMatch returns multiple sequences

23 lines of code changed in:

andrew 2006-08-14 16:09

Do a loop for multiple seq matches

0 lines of code changed in:

andrew 2006-08-14 16:09

Correct test string

2 lines of code changed in:

jimp 2006-08-14 13:52

multiple subjobs can be cancelled and gui only allows results when a
subjob actually completes.

0 lines of code changed in:

jimp 2006-08-14 13:50

fixed off by one bug in end sequence from getSubSequence and added new
subSequence method (not properly tested yet).

20 lines of code changed in:

andrew 2006-08-14 13:30

findingFeatures flag set

12 lines of code changed in:

andrew 2006-08-14 12:08

2.1 updates

51 lines of code changed in:

andrew 2006-08-14 11:18

2.1 updates

107 lines of code changed in:

andrew 2006-08-14 11:17

2.1 new files

19 lines of code changed in:

andrew 2006-08-14 11:16

Replaced image

0 lines of code changed in:

andrew 2006-08-14 11:15

Merged with edit

0 lines of code changed in:

jimp 2006-08-14 10:51

end<start for empty sequences in Sequence[] from SeqCigar[]

1 lines of code changed in:

andrew 2006-08-14 10:02

elementAt instead of get for 1.1 compatibility

275 lines of code changed in:

jimp 2006-08-14 09:46

fixing residue clip bug in MsaWSThread and adding minimum sequence length constraints.

4 lines of code changed in:

jimp 2006-08-13 14:58

fixed end-residue bug and subjob panel names bug

1461 lines of code changed in:

jimp 2006-08-11 18:30

multiple web service jobs from visible blocks of an alignment.

163 lines of code changed in:

andrew 2006-08-11 17:34

Update overview on conservation/pid slider mouseRelease

44 lines of code changed in:

andrew 2006-08-11 17:09

alignpanel.repaint

3 lines of code changed in:

andrew 2006-08-11 17:06

Add links menu if no sequence is selected

6 lines of code changed in:

andrew 2006-08-11 17:05

popup must be added to panel before showing

2 lines of code changed in:

andrew 2006-08-11 15:32

param tree replaces treeFile

4 lines of code changed in:

andrew 2006-08-11 15:20

2.1 updates

422 lines of code changed in:

andrew 2006-08-11 15:19

new files

39 lines of code changed in:

andrew 2006-08-11 15:18

dud file

0 lines of code changed in:

andrew 2006-08-11 09:39

Desktop is null if -noDisplay is set

6 lines of code changed in:

andrew 2006-08-11 09:22

Make a new FeatureRenderer

4 lines of code changed in:

andrew 2006-08-11 09:22

AlignPanel.repaint

1 lines of code changed in:

andrew 2006-08-11 09:22

Printstacktrace

1 lines of code changed in:

andrew 2006-08-11 09:21

inFile might be null if PDB was pasted

2 lines of code changed in:

andrew 2006-08-10 15:57

Smoother drawing

16 lines of code changed in:

andrew 2006-08-10 15:57

Check selection size before making tree

13 lines of code changed in:

andrew 2006-08-10 15:57

group.getSize should be ab.alignment.getGroups

1 lines of code changed in:

andrew 2006-08-10 15:56

Check alAndColSel are not null

16 lines of code changed in:

andrew 2006-08-10 14:40

Control and shift for col selection

79 lines of code changed in:

andrew 2006-08-10 14:18

Reset button added

0 lines of code changed in:

andrew 2006-08-10 14:17

Right mouse works with cursor mode

9 lines of code changed in:

andrew 2006-08-10 14:17

Only add 1 feature settings table

62 lines of code changed in:

andrew 2006-08-10 13:58

Comment out start and end refs

0 lines of code changed in:

andrew 2006-08-10 10:50

1.1 compatible

0 lines of code changed in:

andrew 2006-08-10 10:48

file: is a URL

2 lines of code changed in:

andrew 2006-08-10 10:48

Invert column selection

173 lines of code changed in:

jimp 2006-08-09 17:21

new SequenceI method for making a sub sequence from a range on the
current sequence.

28 lines of code changed in:

jimp 2006-08-09 17:20

alignment from seqCigars will correctly mark deleted residues as
isolated insertions.

1 lines of code changed in:

jimp 2006-08-09 17:19

refactored hidden regions methods and made an AlignmentView preserve
the alignment in hidden regions.

16 lines of code changed in:

jimp 2006-08-09 17:12

fixed multiple shifts bug.

0 lines of code changed in:

andrew 2006-08-09 16:56

Must save all the feature settings

25 lines of code changed in:

andrew 2006-08-09 16:56

Check if groups have already been added or not

18 lines of code changed in:

andrew 2006-08-09 16:56

Fix for local sources with no capabilities

0 lines of code changed in:

andrew 2006-08-09 16:55

Icon drawing updated

92 lines of code changed in:

andrew 2006-08-09 16:55

Null hidden cols check

3 lines of code changed in:

andrew 2006-08-09 16:54

No need to re repaint

1 lines of code changed in:

andrew 2006-08-09 16:54

Height and info message

5 lines of code changed in:

andrew 2006-08-09 16:54

Transparency

5 lines of code changed in:

andrew 2006-08-09 16:54

Endres check for wrap alignment

1 lines of code changed in:

andrew 2006-08-09 16:53

Set the start res and start seq

3 lines of code changed in:

andrew 2006-08-09 16:53

Copy hidden cols to new alignment

36 lines of code changed in:

andrew 2006-08-09 09:51

Remove system.out

1 lines of code changed in:

andrew 2006-08-09 09:50

Make sure link menu is displayed

5 lines of code changed in:

andrew 2006-08-09 09:50

Save links and scores and keyValues for features

40 lines of code changed in:

andrew 2006-08-09 09:50

KeyValue pairs for features

0 lines of code changed in:

andrew 2006-08-09 09:49

Save links and scores and keyValues for features

11 lines of code changed in:

andrew 2006-08-08 16:45

Input Data...

2 lines of code changed in:

andrew 2006-08-08 16:44

Capitals

7 lines of code changed in:

andrew 2006-08-08 16:44

Out by 1 error on show columns

0 lines of code changed in:

andrew 2006-08-08 16:44

Applet has hidden regions

1845 lines of code changed in:

jimp 2006-08-08 12:04

removed extraneous classes.

0 lines of code changed in:

jimp 2006-08-08 10:47

locally modified biojava-dasobert package is now org.biojava.dasobert

0 lines of code changed in:

andrew 2006-08-07 16:25

Use idCanvas highlight system

1 lines of code changed in:

andrew 2006-08-07 16:25

1.1 compatible

0 lines of code changed in:

andrew 2006-08-07 16:14

Use idCanvas highlight system

18 lines of code changed in:

andrew 2006-08-07 16:13

1.1 compatible

0 lines of code changed in:

andrew 2006-08-07 15:46

Set wrapped mode even if false

6 lines of code changed in:

andrew 2006-08-07 15:37

catch out of memory error for consensus when loading groups

19 lines of code changed in:

jimp 2006-08-07 13:20

added commented out seqStrings comment.

6 lines of code changed in:

jimp 2006-08-04 15:28

recover original data for tree and pca as alignment view.

603 lines of code changed in:

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