July 2006 Commit Log

Number of Commits:
161
Number of Active Developers:
2
andrew 2006-07-28 17:06

Show reveal all menu

2 lines of code changed in:

andrew 2006-07-28 17:06

findSeq in SeqPanel is used

12 lines of code changed in:

andrew 2006-07-28 17:06

Resize image if id width changes

2 lines of code changed in:

andrew 2006-07-28 17:05

No need for count

1 lines of code changed in:

andrew 2006-07-28 17:05

Resize inactive when mouse exited and no dragEvent

8 lines of code changed in:

andrew 2006-07-28 17:04

getIndex replaced with findSeq in seqPanel

1 lines of code changed in:

andrew 2006-07-28 17:04

Remove system.out

1 lines of code changed in:

andrew 2006-07-28 17:04

Scrolling fixed and selection in wrapped mode updated

16 lines of code changed in:

andrew 2006-07-28 17:03

getIndex replaced by findSeq in Seqpanel

0 lines of code changed in:

andrew 2006-07-28 14:42

Out by one error on reveal columns

0 lines of code changed in:

andrew 2006-07-28 14:26

Check height of featurePanel, not this for mousepresses

2 lines of code changed in:

andrew 2006-07-28 14:19

1.1 compatible

1 lines of code changed in:

andrew 2006-07-28 14:17

Applet doesnt have hidden columns

1 lines of code changed in:

andrew 2006-07-28 14:16

Dont set all feature descriptions on status bar

2 lines of code changed in:

andrew 2006-07-28 14:16

Dont draw all the panel if just a mouse movement

9 lines of code changed in:

andrew 2006-07-28 14:16

If colour hasnt been created, make a new one

12 lines of code changed in:

andrew 2006-07-28 12:08

Add transparency

5 lines of code changed in:

andrew 2006-07-28 12:08

output source in gff file

0 lines of code changed in:

andrew 2006-07-27 17:00

Send gapChar to print original Data

2 lines of code changed in:

andrew 2006-07-27 17:00

Remove immediate call to repaint when deleting

3 lines of code changed in:

andrew 2006-07-27 16:59

seq size cant be less than 2 for tree

4 lines of code changed in:

andrew 2006-07-27 16:58

Sends gapChar to seqData

5 lines of code changed in:

andrew 2006-07-27 16:58

remove unnecessary constructor

6 lines of code changed in:

andrew 2006-07-27 14:10

Remove unnecessary imports

0 lines of code changed in:

andrew 2006-07-27 14:10

Reset das_registry_url if null or empty

0 lines of code changed in:

andrew 2006-07-27 14:09

Dont set pdb file if it doenst exist

11 lines of code changed in:

andrew 2006-07-27 11:57

NOR the <pre> tabs

3 lines of code changed in:

andrew 2006-07-27 11:30

Use DBRefSource.PDB

0 lines of code changed in:

andrew 2006-07-27 11:29

Save PDB file to disk

54 lines of code changed in:

andrew 2006-07-27 08:53

Readline instead of bit by bit

7 lines of code changed in:

andrew 2006-07-27 08:42

Cant have col less than 0

3 lines of code changed in:

andrew 2006-07-27 08:35

Save ref to pdb file

1 lines of code changed in:

andrew 2006-07-27 08:34

Readded

48 lines of code changed in:

jimp 2006-07-26 18:40

accidental commit of a build

0 lines of code changed in:

andrew 2006-07-26 17:15

PDB file MUST have an id

4 lines of code changed in:

andrew 2006-07-26 17:14

not used

0 lines of code changed in:

andrew 2006-07-26 17:04

Load and save PDB files

98 lines of code changed in:

andrew 2006-07-26 17:03

Add file ref for pdb files

0 lines of code changed in:

jimp 2006-07-26 15:04

Ignore list created

72 lines of code changed in:

jimp 2006-07-26 14:45

Cigars for representing alignment view as used for calculation.

299 lines of code changed in:

jimp 2006-07-26 14:43

CigarBase class and derivatives.

0 lines of code changed in:

jimp 2006-07-26 14:32

Implemented CIGAR representation of an Alignment view for passing to
analysis'.

999 lines of code changed in:

jimp 2006-07-26 14:25

Compact Idiosyncratic Gapped Alignment Representation objects for internal rep of hidden alignments and views.

0 lines of code changed in:

andrew 2006-07-26 13:58

Switch to new srs url

3 lines of code changed in:

andrew 2006-07-26 13:31

seqs[j] replaces current

2 lines of code changed in:

andrew 2006-07-26 11:49

moved to org.biojava

0 lines of code changed in:

andrew 2006-07-26 11:43

back to org.biojava

4 lines of code changed in:

andrew 2006-07-26 11:43

Back to org.biojava

48 lines of code changed in:

andrew 2006-07-26 11:11

Column hide/show updated

12 lines of code changed in:

andrew 2006-07-26 11:11

Calculate overlap hidden regions

0 lines of code changed in:

andrew 2006-07-26 09:56

Remove left, right, empty cols work on hidden reps

87 lines of code changed in:

andrew 2006-07-25 16:51

ColumnSelection moved to datamodel

39 lines of code changed in:

andrew 2006-07-25 16:50

activeRow is -1

2 lines of code changed in:

andrew 2006-07-25 16:50

Odd edit bug with represented seqs fixed

12 lines of code changed in:

andrew 2006-07-25 16:50

Dont add pdb format here

1 lines of code changed in:

andrew 2006-07-25 16:49

1.1 compatible

0 lines of code changed in:

andrew 2006-07-25 16:49

Moved to datamodel

0 lines of code changed in:

andrew 2006-07-25 14:29

Output menus added

7 lines of code changed in:

andrew 2006-07-25 13:57

Repaint

3 lines of code changed in:

andrew 2006-07-25 13:57

Dont make new image unless resize

9 lines of code changed in:

andrew 2006-07-25 13:57

Reorder popupmenu

23 lines of code changed in:

andrew 2006-07-25 11:52

Renamed files not to conflict with BIOJAVA

48 lines of code changed in:

andrew 2006-07-25 11:49

jalview.biojava

4 lines of code changed in:

andrew 2006-07-25 11:25

x < endres-startres

5 lines of code changed in:

andrew 2006-07-25 10:45

Add dbrefs to mouseover

15 lines of code changed in:

andrew 2006-07-25 10:44

Must be 1.1 compliant

1 lines of code changed in:

andrew 2006-07-25 10:43

Remove associate menu

0 lines of code changed in:

andrew 2006-07-25 10:38

FileLoader replaces paste when Dropping files

15 lines of code changed in:

andrew 2006-07-25 10:37

Associate pdb files

119 lines of code changed in:

andrew 2006-07-25 10:37

pdb fetchDataAsFile

4 lines of code changed in:

andrew 2006-07-25 10:36

PDB format added

58 lines of code changed in:

andrew 2006-07-25 10:36

pdb stuff moved to popupmenu

21 lines of code changed in:

andrew 2006-07-25 10:34

Can have local file

7 lines of code changed in:

andrew 2006-07-25 10:33

If seq has a dataset, dont clear it

31 lines of code changed in:

andrew 2006-07-25 10:33

Extends AlignFile, dataset has PDBEntry added

36 lines of code changed in:

andrew 2006-07-25 10:32

Can load PDB file from disk

33 lines of code changed in:

jimp 2006-07-24 09:43

partly finished pods.

5 lines of code changed in:

andrew 2006-07-21 14:21

correct icon draw bug

2 lines of code changed in:

andrew 2006-07-21 14:21

Corrected hidden row feature render bug

19 lines of code changed in:

andrew 2006-07-21 14:20

Put DBRefFether in a new thread

0 lines of code changed in:

jimp 2006-07-21 13:42

Item added to ignoreList

2 lines of code changed in:

andrew 2006-07-21 10:54

Remove start end for now??

0 lines of code changed in:

andrew 2006-07-21 10:54

Add pdb ref

0 lines of code changed in:

andrew 2006-07-21 10:27

getViewAsString can ignore sequenceGroup

30 lines of code changed in:

andrew 2006-07-21 10:26

this.seqs = seqs

3 lines of code changed in:

andrew 2006-07-21 09:48

hidden seqs added

10 lines of code changed in:

andrew 2006-07-21 09:48

dbrefs added

17 lines of code changed in:

andrew 2006-07-21 09:48

show hide stuff moved from columnSelection

62 lines of code changed in:

andrew 2006-07-21 09:47

Saves hidden seqs and DBRefs

121 lines of code changed in:

andrew 2006-07-21 09:47

av.showHiddenMarkers check

117 lines of code changed in:

andrew 2006-07-21 09:46

Show hide cols and rows

57 lines of code changed in:

andrew 2006-07-21 09:46

Hide Selected Cols

83 lines of code changed in:

andrew 2006-07-21 09:45

DBRefs now array

22 lines of code changed in:

andrew 2006-07-21 09:44

getFullAlignment

37 lines of code changed in:

andrew 2006-07-21 09:44

Remove note

0 lines of code changed in:

andrew 2006-07-21 09:43

DBRef is an array, not vector

15 lines of code changed in:

andrew 2006-07-21 09:42

DBRefs and HiddenRegions saved

0 lines of code changed in:

jimp 2006-07-21 09:19

Ignore list created

43 lines of code changed in:

andrew 2006-07-21 08:54

Load tree from file constructor fixed

5 lines of code changed in:

jimp 2006-07-20 18:41

annotation label font size change in applet.

2 lines of code changed in:

andrew 2006-07-19 16:33

Make new seq[] when modifying hidden bits

5 lines of code changed in:

andrew 2006-07-19 16:32

Remove b keystroke

3 lines of code changed in:

andrew 2006-07-19 16:22

showTranslation is not a checkbox

1 lines of code changed in:

andrew 2006-07-19 16:21

Merge new frame buttons added

113 lines of code changed in:

andrew 2006-07-19 16:20

Output to text window added

42 lines of code changed in:

andrew 2006-07-19 16:20

Correct highlighted res height

2 lines of code changed in:

andrew 2006-07-19 16:20

Save output use whole alignment

32 lines of code changed in:

andrew 2006-07-19 16:19

Original tree data output in PFAM format

13 lines of code changed in:

andrew 2006-07-19 11:57

Count uniprot refs

0 lines of code changed in:

andrew 2006-07-19 11:41

Highlight hidden columns after revealing

16 lines of code changed in:

andrew 2006-07-19 11:40

datasetSeq bug

2 lines of code changed in:

andrew 2006-07-19 11:40

Check for all gapped seqs

29 lines of code changed in:

andrew 2006-07-19 11:39

Use Selection group to define sequence range to fetch features

0 lines of code changed in:

andrew 2006-07-19 09:11

Copy works with selection area

6 lines of code changed in:

andrew 2006-07-18 16:50

Modified for hidden region/group calculation

83 lines of code changed in:

andrew 2006-07-18 16:32

Use selection area with hidden columns in calculations

347 lines of code changed in:

andrew 2006-07-18 16:31

omitHiddenColumns

21 lines of code changed in:

andrew 2006-07-18 16:31

Button to view original data

30 lines of code changed in:

andrew 2006-07-18 16:30

Takes strings, not seqs

8 lines of code changed in:

andrew 2006-07-18 16:30

getSelectionAsNewSequence added

57 lines of code changed in:

andrew 2006-07-18 16:30

Takes a string, not sequence

3 lines of code changed in:

andrew 2006-07-18 16:29

Works on strings, not seqs

86 lines of code changed in:

andrew 2006-07-18 16:28

Takes string[] instead of seq[]

2 lines of code changed in:

jimp 2006-07-18 15:12

use of GapChars

2 lines of code changed in:

andrew 2006-07-17 11:02

Towards an auto dbref fetcher

24 lines of code changed in:

andrew 2006-07-17 11:00

Dasobert updates, labels and prefix changes

0 lines of code changed in:

andrew 2006-07-14 09:58

Just fetch features for selected seqs

0 lines of code changed in:

andrew 2006-07-13 18:01

DAS feature retrieval updated

256 lines of code changed in:

andrew 2006-07-13 18:00

Selected DAS sources may differ from default

0 lines of code changed in:

andrew 2006-07-13 17:59

Sequence is private

5 lines of code changed in:

andrew 2006-07-12 12:52

Launch full app parameter takes servlet URL

9 lines of code changed in:

andrew 2006-07-12 12:22

Das source browser

35 lines of code changed in:

andrew 2006-07-12 12:21

Authority, type and labels

0 lines of code changed in:

andrew 2006-07-12 12:20

sequences are private in SequenceGroup

528 lines of code changed in:

andrew 2006-07-12 12:19

Append start and end

0 lines of code changed in:

andrew 2006-07-07 17:50

Dont discard label if different to H or E

0 lines of code changed in:

andrew 2006-07-07 14:34

Redundant Remove Redundancy Removed

0 lines of code changed in:

andrew 2006-07-07 14:30

Sequence numbering maintained

29 lines of code changed in:

andrew 2006-07-07 14:09

Changeable background colour

695 lines of code changed in:

andrew 2006-07-07 14:08

Make sure bond has a colour

4 lines of code changed in:

andrew 2006-07-07 14:08

Make sure atom has a colour

4 lines of code changed in:

andrew 2006-07-07 14:07

Highlight sequences before seleting

184 lines of code changed in:

andrew 2006-07-07 14:07

Corrected for hidden rows

53 lines of code changed in:

andrew 2006-07-07 14:06

Row might have height of zero

11 lines of code changed in:

andrew 2006-07-07 14:05

check control down if c pressed in cursor mode

4 lines of code changed in:

andrew 2006-07-07 14:05

changeColour is public

9 lines of code changed in:

andrew 2006-07-07 14:04

Coms might be null

4 lines of code changed in:

andrew 2006-07-07 14:03

New panel layouts

34 lines of code changed in:

andrew 2006-07-07 14:03

Offsets

4 lines of code changed in:

andrew 2006-07-07 14:02

Optimised PID method

28 lines of code changed in:

andrew 2006-07-07 14:02

Make 1.1 compatible

12 lines of code changed in:

andrew 2006-07-07 14:02

Move position of stopLoading for 1.5 people

3 lines of code changed in:

andrew 2006-07-07 14:01

make 1.1 compatible

0 lines of code changed in:

andrew 2006-07-07 14:01

Dont write graph type twice

0 lines of code changed in:

andrew 2006-07-07 14:00

Checks on drawing characters and if sequence ref has been deleted

23 lines of code changed in:

andrew 2006-07-07 14:00

Colour argument added, to mirror applet view

25 lines of code changed in:

andrew 2006-07-07 13:58

Prepare for launchFullApplication

68 lines of code changed in:

andrew 2006-07-07 13:56

Highlight sequences to be deleted before deleting, and apply button exists

206 lines of code changed in:

andrew 2006-07-07 13:56

Check row.annotations is not null

5 lines of code changed in:

andrew 2006-07-07 13:55

SelectionGroup is initially null

1 lines of code changed in:

andrew 2006-07-07 13:55

Replaced by AnnotationFile

0 lines of code changed in:

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