June 2006 Commit Log

Number of Commits:

81

Number of Active Developers:

2

andrew 2006-06-23 17:25 #81

Uniprot may have several accession ids

0 lines of code changed in:

• src/jalview/io: DBRefFetcher.java (changed)

andrew 2006-06-23 16:33 #80

Parse HTML links from jalview features file

13 lines of code changed in:

• src/jalview/appletgui: AlignFrame.java (+7 -1), FeatureRenderer.java (+2 -54), FeatureSettings.java (+1), Tooltip.java (changed)
• src/jalview/gui: AlignFrame.java (+3 -2)
• src/jalview/io: FeaturesFile.java (changed)

andrew 2006-06-23 14:47 #79

DBRefFetcher replaces SequenceFeatureFetcher

2 lines of code changed in:

• src/jalview/gui: SequenceFetcher.java (+2 -2)

andrew 2006-06-23 14:46 #78

Check if featuresDisplayed is null

2 lines of code changed in:

• src/jalview/gui: SeqPanel.java (+2 -2)

andrew 2006-06-23 14:46 #77

Case wrapped jar file, wrapped preference true dealt with

24 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+24 -7)

andrew 2006-06-23 14:45 #76

No need for repaint

6 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+6 -5)

andrew 2006-06-23 14:45 #75

Uses FeaturesFile parser, GFF and Jalview

12 lines of code changed in:

• src/jalview/appletgui: AlignFrame.java (+12 -145)

andrew 2006-06-23 14:44 #74

++ --

2 lines of code changed in:

• src/MCview: Zsort.java (+2 -2)

andrew 2006-06-22 09:54 #73

Check featureLinks is not null

5 lines of code changed in:

• src/jalview/appletgui: FeatureSettings.java (+5 -2)

andrew 2006-06-22 09:53 #72

ParseFeaturesFile takes protocol as arg

2 lines of code changed in:

• src/jalview/bin: JalviewLite.java (+2 -2)

andrew 2006-06-22 09:52 #71

Takes AlignFrame as arg, to update progressbar

0 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-22 09:51 #70

AlignFrame is now the FeatureListener

4 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+4 -22)

andrew 2006-06-22 09:50 #69

Fetch DBRefs

89 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+67 -7)
• src/jalview/jbgui: GAlignFrame.java (+22 -3)

andrew 2006-06-22 09:50 #68

Ye olde SequenceFeatureFetcher

0 lines of code changed in:

• src/jalview/io: DBRefFetcher.java (new)

andrew 2006-06-22 09:49 #67

Renamed to DBRefFetcher

0 lines of code changed in:

• src/jalview/io: SequenceFeatureFetcher.java (del)

andrew 2006-06-22 09:48 #66

Not used in Jalview

0 lines of code changed in:

• src/org/biojava/dasobert/das: AlignmentParameters.java (del), DAS_DNA_Handler.java (del), DAS_Entry_Points_Handler.java (del), DAS_Sequence_Handler.java (del), DAS_StylesheetRetrieve.java (del), DAS_Stylesheet_Handler.java (del), DAS_Types_Handler.java (del), SequenceThread.java (del), SpiceDasSource.java (del), Xpm.java (del)
• src/org/biojava/dasobert/dasregistry: Das1Validator.java (del), DasSourceValidator.java (del)

andrew 2006-06-15 16:37 #65

Use spice-3d das1 source list for nowjalview/gui/DasSourceBrowser.java

0 lines of code changed in:

• src/jalview/gui: DasSourceBrowser.java (changed)
• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-15 15:19 #64

Fixed to trial registry at the moment

0 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-15 15:06 #63

new files

0 lines of code changed in:

• src/org/biojava/dasobert/das2/io: DAS2SourceHandler.java (new), DasSourceReader.java (new), DasSourceReaderImpl.java (new)

andrew 2006-06-15 15:06 #62

Not using AxisDasRegistry

0 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-15 15:04 #61

Not needed

0 lines of code changed in:

• src/org/biojava/dasobert/eventmodel: AlignmentListener.java (del), StructureListener.java (del)

andrew 2006-06-15 15:02 #60

check helperUrl is not null

0 lines of code changed in:

• src/jalview/gui: DasSourceBrowser.java (changed)

andrew 2006-06-15 15:00 #59

Not needed

0 lines of code changed in:

• lib: dasobert.jar (del), dasregistry.jar (del)

andrew 2006-06-15 14:03 #58

Das client files

0 lines of code changed in:

• src/org/biojava/dasobert/das: AlignmentParameters.java (new), DAS_DNA_Handler.java (new), DAS_Entry_Points_Handler.java (new), DAS_FeatureRetrieve.java (new), DAS_Feature_Handler.java (new), DAS_Sequence_Handler.java (new), DAS_StylesheetRetrieve.java (new), DAS_Stylesheet_Handler.java (new), DAS_Types_Handler.java (new), FeatureThread.java (new), SequenceThread.java (new), SpiceDasSource.java (new), Xpm.java (new)
• src/org/biojava/dasobert/das2: Das2Capability.java (new), Das2CapabilityImpl.java (new), Das2Source.java (new), Das2SourceImpl.java (new), DasSourceConverter.java (new)
• src/org/biojava/dasobert/dasregistry: Das1Source.java (new), Das1Validator.java (new), Das2Validator.java (new), DasCoordSysComparator.java (new), DasCoordinateSystem.java (new), DasSource.java (new), DasSourceComparator.java (new), DasSourceValidator.java (new)
• src/org/biojava/dasobert/eventmodel: AlignmentListener.java (new), FeatureEvent.java (new), FeatureListener.java (new), ObjectListener.java (new), SequenceEvent.java (new), SequenceListener.java (new), StructureListener.java (new)

andrew 2006-06-15 13:57 #57

Correction - use start and end

0 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-15 13:56 #56

Dont add start and end for the moment

0 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-15 13:56 #55

Wrap alignment moved to alignFrame

0 lines of code changed in:

• src/jalview/gui: SequenceFetcher.java (-5)

andrew 2006-06-15 13:55 #54

Non positional features shown as mouse over

18 lines of code changed in:

• src/jalview/gui: IdPanel.java (+18 -2)

andrew 2006-06-15 13:55 #53

fr.findAllFeatures on init

3 lines of code changed in:

• src/jalview/gui: FeatureSettings.java (+3 -1)

andrew 2006-06-15 13:54 #52

Correct citation

2 lines of code changed in:

• src/jalview/gui: Desktop.java (+2 -2)

andrew 2006-06-15 13:54 #51

Unnecessary import

0 lines of code changed in:

• src/jalview/gui: DasSourceBrowser.java (changed)

andrew 2006-06-15 13:53 #50

FeatureRenderer synchronized featuresAdded method

33 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+12 -5), FeatureRenderer.java (+21 -4)

andrew 2006-06-15 13:52 #49

Wrap alignment moved to alignFrame

1 lines of code changed in:

• src/jalview/gui: CutAndPasteTransfer.java (+1 -6)
• src/jalview/io: FileLoader.java (-5)

andrew 2006-06-15 13:52 #48

Correct citation

15 lines of code changed in:

• src/jalview/appletgui: AlignFrame.java (+1 -1)
• src/jalview/gui: AlignFrame.java (+12 -6), SplashScreen.java (+2 -2)

andrew 2006-06-15 13:51 #47

Maintain status and position only for uniprot parsing

44 lines of code changed in:

• src/jalview/datamodel: Sequence.java (+2 -3), SequenceFeature.java (+42 -13)

andrew 2006-06-14 11:19 #46

Fileloading progressbar

46 lines of code changed in:

• src/jalview/gui: Desktop.java (+41 -2)
• src/jalview/io: FileLoader.java (+5)

andrew 2006-06-14 11:17 #45

Status is now in otherData of feature

18 lines of code changed in:

• src/jalview/appletgui: SeqPanel.java (+2 -2)
• src/jalview/datamodel: SequenceFeature.java (+7 -21)
• src/jalview/gui: AlignmentPanel.java (+5 -5), Jalview2XML.java (+1 -2), SeqPanel.java (+3 -3)

andrew 2006-06-14 11:16 #44

Sequence checks for duplicate features

0 lines of code changed in:

• src/jalview/io: DasSequenceFeatureFetcher.java (changed)

andrew 2006-06-14 11:15 #43

parseAppletParam

25 lines of code changed in:

• src/jalview/appletgui: AlignViewport.java (+25 -5)

andrew 2006-06-14 11:14 #42

parseAppletParameter

75 lines of code changed in:

• src/jalview/schemes: UserColourScheme.java (+75 -25)

andrew 2006-06-09 17:37 #41

Retrieve multiple EMBL ids

21 lines of code changed in:

• src/jalview/gui: SequenceFetcher.java (+21 -11)

andrew 2006-06-09 17:22 #40

Size adjustments for MacOSX

10 lines of code changed in:

• src/jalview/gui: Preferences.java (+10 -3)

andrew 2006-06-09 17:22 #39

Remove unnecessary lines

0 lines of code changed in:

• src/jalview/gui: FeatureSettings.java (-3)

andrew 2006-06-09 17:21 #38

createColourFromName if not specified

13 lines of code changed in:

• src/jalview/gui: FeatureRenderer.java (+13 -57)

andrew 2006-06-09 17:21 #37

Export annotations as Jalview format

7 lines of code changed in:

• src/jalview/gui: AnnotationLabels.java (+7 -7)

andrew 2006-06-09 17:20 #36

Feature and annotation parsing moved to io

39 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+39 -97)

andrew 2006-06-09 17:20 #35

otherDetails

33 lines of code changed in:

• src/jalview/datamodel: SequenceFeature.java (+33 -1)

andrew 2006-06-09 17:19 #34

Remove getsfarray

1 lines of code changed in:

• src/jalview/datamodel: Sequence.java (+1 -8)

andrew 2006-06-09 17:19 #33

getSequencesArray

17 lines of code changed in:

• src/jalview/datamodel: Alignment.java (+10), AlignmentI.java (+7)

andrew 2006-06-09 17:18 #32

setAcceptAllFileFilter fixes bug on MacOSX

37 lines of code changed in:

• src/jalview/io: JalviewFileChooser.java (+37 -3)

andrew 2006-06-09 17:17 #31

Export features / annotations

45 lines of code changed in:

• src/jalview/jbgui: GAlignFrame.java (+45 -16)

andrew 2006-06-09 17:17 #30

Save text to file

56 lines of code changed in:

• src/jalview/gui: CutAndPasteTransfer.java (+35 -9)
• src/jalview/jbgui: GCutAndPasteTransfer.java (+21 -7)

andrew 2006-06-09 17:16 #29

createColourFromName

29 lines of code changed in:

• src/jalview/schemes: UserColourScheme.java (+29)

andrew 2006-06-09 17:16 #28

Function not used

1 lines of code changed in:

• src/jalview/io: EBIFetchClient.java (+1 -100)

andrew 2006-06-09 17:15 #27

readAnnotationFile

2 lines of code changed in:

• src/jalview/bin: JalviewLite.java (+2 -2)

andrew 2006-06-09 17:15 #26

parseFeaturesFile

5 lines of code changed in:

• src/jalview/bin: Jalview.java (+5 -5)

andrew 2006-06-09 17:14 #25

Annotation/feature exporter

0 lines of code changed in:

• src/jalview/gui: AnnotationExporter.java (new)
• src/jalview/io: AnnotationFile.java (new), FeaturesFile.java (new)

jimp 2006-06-08 19:17 #24

Introduced DbRefEntry to DasSourceCoordinateSystem check to only call sources for sequences with a particular DBRefEntry id (PDB or Uniprot currently)

42 lines of code changed in:

• src/jalview/gui: SequenceFetcher.java (+1 -1)
• src/jalview/io: DasSequenceFeatureFetcher.java (changed), ModellerDescription.java (+1 -1), SequenceFeatureFetcher.java (+3 -2), WSWUBlastClient.java (+2 -2)
• src/jalview/util: DBRefUtils.java (+35 -2)

jimp 2006-06-08 19:16 #23

DBRefEntry.source enum type

0 lines of code changed in:

• src/jalview/datamodel: DBRefSource.java (new)

jimp 2006-06-08 16:16 #22

bugfixed and podded.

67 lines of code changed in:

• utils: gff2annot.pl (+67 -6)

jimp 2006-06-08 14:56 #21

simplest conversion of gff to jalview annotation format files.

35 lines of code changed in:

• utils: gff2annot.pl (new 35)

andrew 2006-06-07 15:48 #20

New link image

0 lines of code changed in:

• resources/images: link.gif (changed)

andrew 2006-06-07 15:47 #19

Wrap alignment added to preferences

49 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+2 -2), CutAndPasteTransfer.java (+6 -1), Desktop.java (+2 -2), Preferences.java (+5 -1), SeqPanel.java (+3 -3), SequenceFetcher.java (+6)
• src/jalview/io: FileLoader.java (+5)
• src/jalview/jbgui: GPreferences.java (+20 -13)

andrew 2006-06-07 14:35 #18

Checks in case DasSource is null

0 lines of code changed in:

• src/jalview/gui: DasSourceBrowser.java (changed)

andrew 2006-06-07 14:03 #17

Smaller file size

0 lines of code changed in:

• resources/images: idwidth.gif (changed)

andrew 2006-06-07 14:03 #16

New link image

0 lines of code changed in:

• resources/images: link.gif (new)

andrew 2006-06-07 14:01 #15

DAS client libraries

0 lines of code changed in:

• lib: dasobert.jar (new), dasregistry.jar (new)

andrew 2006-06-07 13:59 #14

Remove unnecessary ints

1 lines of code changed in:

• src/jalview/gui: SeqCanvas.java (+1 -3)

andrew 2006-06-07 13:59 #13

DAS sources added

11 lines of code changed in:

• src/jalview/gui: Preferences.java (+11 -3)

andrew 2006-06-07 13:59 #12

PopupMenu displays URL links

26 lines of code changed in:

• src/jalview/gui: IdPanel.java (+3 -2), PopupMenu.java (+23 -14)

andrew 2006-06-07 13:58 #11

ignore begin==0 and end==0 for the moment

115 lines of code changed in:

• src/jalview/gui: FeatureSettings.java (+17 -2), SeqPanel.java (+98 -36)

andrew 2006-06-07 13:57 #10

Create random colour only if Colour is not specified

30 lines of code changed in:

• src/jalview/gui: FeatureRenderer.java (+30 -6)

andrew 2006-06-07 13:57 #9

Implements FeatureListener

15 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+15 -4)

andrew 2006-06-07 13:56 #8

new DasSequenceFetcher

5 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+5 -4)

andrew 2006-06-07 13:56 #7

DAS Settings tab added

5 lines of code changed in:

• src/jalview/jbgui: GPreferences.java (+5 -1)

andrew 2006-06-07 13:55 #6

Use a label with html instead of textarea

10 lines of code changed in:

• src/jalview/jbgui: GUserDefinedColours.java (+10 -12)

andrew 2006-06-07 13:54 #5

Remove position, add score and links

33 lines of code changed in:

• src/jalview/datamodel: SequenceFeature.java (+33 -16)

andrew 2006-06-07 13:53 #4

Parameter to show feature settings

7 lines of code changed in:

• src/jalview/bin: JalviewLite.java (+7 -1)

andrew 2006-06-07 13:52 #3

Tooltips for features, links for features added

436 lines of code changed in:

• src/jalview/appletgui: APopupMenu.java (+34 -24), AlignFrame.java (+62 -6), AlignViewport.java (+1 -1), FeatureRenderer.java (+42 -2), FeatureSettings.java (+136 -6), IdPanel.java (+35 -1), SeqCanvas.java (+8 -7), SeqPanel.java (+118 -59)

andrew 2006-06-07 13:51 #2

NEW FILES

0 lines of code changed in:

• src/jalview/appletgui: Tooltip.java (new)
• src/jalview/gui: DasSourceBrowser.java (new)
• src/jalview/io: DasSequenceFeatureFetcher.java (new)
• src/jalview/jbgui: GDasSourceBrowser.java (new)
• src/jalview/util: TableSorter.java (new)

jimp 2006-06-07 11:20 #1

broken link typo. (SEVENtwentyfour alert)

1 lines of code changed in:

• help/html/menus: alwfile.html (+1 -1)

May 2006 »