November 2008 Commit Log

Number of Commits:

41

Number of Active Developers:

1

jprocter 2008-11-12 17:08 #41

beginning documentation for new hidecol/hiderep and representation capabilities

1 lines of code changed in:

• help/html/features: annotationsFormat.html (+1 -1)

jprocter 2008-11-12 17:08 #40

todo for documenting selection sharing

1 lines of code changed in:

• help/html/features: multipleViews.html (+1)

jprocter 2008-11-12 17:07 #39

autoscroll option

10 lines of code changed in:

• help/html/menus: alignmentMenu.html (+5), alwview.html (+5)

jprocter 2008-11-12 17:07 #38

new capabilities and note on 'try vamsas'

13 lines of code changed in:

• help/html/vamsas: index.html (+13 -1)

jprocter 2008-11-12 17:07 #37

new features/resolved for 2.4.1.

11 lines of code changed in:

• help/html: releases.html (+11 -1)

jprocter 2008-11-12 17:05 #36

refactored to propery separate addToDocument,addFromDocument, updateToDocument, updateToJalview and conflict processes

578 lines of code changed in:

• src/jalview/io/vamsas: Datasetsequence.java (new), DatastoreItem.java (+243 -2), Dbref.java (+121 -65), LocalDocSyncObject.java (+5 -4), Rangetype.java (+17 -2), Sequencefeature.java (new), Sequencemapping.java (+96 -54), Tree.java (+96 -47)

jprocter 2008-11-12 17:05 #35

new viewport IDs and jalview XML storage/sync in vamsas appdata and refactored more code to use of jalview.io.vamsas.DatastoreItem

470 lines of code changed in:

• src/jalview/io: VamsasAppDatastore.java (+470 -285)

jprocter 2008-11-12 17:04 #34

selection sending and receiving, autoscrolling to highlighted position, new viewport IDs and jalview XML storage/sync in vamsas appdata

1623 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+144 -37), AlignViewport.java (+144 -6), Jalview2XML.java (+928 -295), VamsasApplication.java (+407 -15)

jprocter 2008-11-12 17:02 #33

selection sending and receiving, autoscrolling to highlighted position

59 lines of code changed in:

• src/jalview/gui: AlignmentPanel.java (+59 -18)

jprocter 2008-11-12 17:01 #32

selection sending

10 lines of code changed in:

• src/jalview/gui: IdPanel.java (+2 -2), PopupMenu.java (+2 -1), RotatableCanvas.java (+3 -2), ScalePanel.java (+3 -1)

jprocter 2008-11-12 17:01 #31

selection sending and receiving, autoscrolling to highlighted position

56 lines of code changed in:

• src/jalview/gui: SeqPanel.java (+56 -3)

jprocter 2008-11-12 17:00 #30

new ID constructor and selection sending

3 lines of code changed in:

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

jprocter 2008-11-12 17:00 #29

new constructors for setting IDs

15 lines of code changed in:

• src/jalview/gui: AppJmol.java (+15 -1)

jprocter 2008-11-12 16:59 #28

new window discovery and alignment view navigation methods

95 lines of code changed in:

• src/jalview/gui: Desktop.java (+95 -5)

jprocter 2008-11-12 16:58 #27

jar inputstream provider enabling multiple jar entries to be unmarshalled without closing the input stream

0 lines of code changed in:

• src/jalview/gui: Jalview2XML_V1.java (changed)
• src/jalview/util: jarInputStreamProvider.java (new)

jprocter 2008-11-12 16:57 #26

automatic scrolling switch

21 lines of code changed in:

• src/jalview/jbgui: GAlignFrame.java (+21)

jprocter 2008-11-12 16:13 #25

updated library supporting exchange of selection messages

0 lines of code changed in:

• lib: vamsas-client.jar (changed)

jprocter 2008-11-12 15:20 #24

automatic scrolling option added to view

53 lines of code changed in:

• src/jalview/appletgui: AlignFrame.java (+14 -1), AlignViewport.java (+5 -1), AlignmentPanel.java (+30 -7), SeqPanel.java (+4)

jprocter 2008-11-12 11:54 #23

jdk1.2 compatibility

7 lines of code changed in:

• src/jalview/datamodel: SequenceGroup.java (+6 -2)
• src/jalview/structure: StructureSelectionManager.java (+1 -1)

jprocter 2008-11-12 11:27 #22

minor translation bug

0 lines of code changed in:

• src/jalview/analysis: Dna.java (changed)

jprocter 2008-11-12 11:25 #21

javadoc

31 lines of code changed in:

• src/jalview/structure: SelectionListener.java (+19 -18), SelectionSource.java (+12 -11)

jprocter 2008-11-12 11:18 #20

jalview XML schema update for 2.4.1 (or 2.5?) introducing IDs for views and treepanels and proper reconstruction of dataset/Alignment relationships

9848 lines of code changed in:

• schemas: jalview.xsd (+13), vamsas.xsd (+9 -3)
• src/jalview/binding: Alignment.java (+154 -180), Annotation.java (+417 -459), AnnotationElement.java (+276 -305), Colour.java (+154 -179), Feature.java (+275 -304), FeatureSettings.java (+260 -289), Features.java (+100 -123), JGroup.java (+724 -760), JSeq.java (+608 -645), JalviewModel.java (+205 -233), JalviewModelSequence.java (+907 -955), JalviewUserColours.java (+283 -313), Pdbentry.java (+311 -344), PdbentryItem.java (+180 -195), Pdbids.java (+100 -123), Property.java (+154 -180), Sequence.java (+100 -123), SequenceSet.java (+499 -538), SequenceType.java (+179 -206), Setting.java (+235 -262), Tree.java (+805 -843), UserColourScheme.java (+100 -124), UserColours.java (+154 -181), VAMSAS.java (+566 -602), VamsasModel.java (+100 -122), Viewport.java (+1417 -1463)
• src/jalview/schemabinding/version2: .castor.cdr (changed), AlcodMap.java (changed), Alcodon.java (changed), AlcodonFrame.java (changed), Annotation.java (changed), AnnotationColours.java (changed), AnnotationElement.java (changed), Colour.java (changed), DBRef.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), Group.java (changed), HiddenColumns.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), MapListFrom.java (changed), MapListTo.java (changed), MapListType.java (changed), Mapping.java (changed), MappingChoice.java (changed), OtherData.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceSetProperties.java (+155 -183), SequenceType.java (changed), Setting.java (changed), StructureState.java (+408 -413), ThresholdLine.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)
• src/jalview/schemabinding/version2/descriptors: AlcodMapDescriptor.java (changed), AlcodonDescriptor.java (changed), AlcodonFrameDescriptor.java (changed), AnnotationColoursDescriptor.java (changed), AnnotationDescriptor.java (changed), AnnotationElementDescriptor.java (changed), ColourDescriptor.java (changed), DBRefDescriptor.java (changed), FeatureDescriptor.java (changed), FeatureSettingsDescriptor.java (changed), FeaturesDescriptor.java (changed), GroupDescriptor.java (changed), HiddenColumnsDescriptor.java (changed), JGroupDescriptor.java (changed), JSeqDescriptor.java (changed), JalviewModelDescriptor.java (changed), JalviewModelSequenceDescriptor.java (changed), JalviewUserColoursDescriptor.java (changed), MapListFromDescriptor.java (changed), MapListToDescriptor.java (changed), MapListTypeDescriptor.java (changed), MappingChoiceDescriptor.java (changed), MappingDescriptor.java (changed), OtherDataDescriptor.java (changed), PdbentryDescriptor.java (changed), PdbentryItemDescriptor.java (changed), PdbidsDescriptor.java (changed), PropertyDescriptor.java (changed), SequenceDescriptor.java (changed), SequenceSetDescriptor.java (changed), SequenceSetPropertiesDescriptor.java (changed), SequenceTypeDescriptor.java (changed), SettingDescriptor.java (changed), StructureStateDescriptor.java (changed), ThresholdLineDescriptor.java (changed), TreeDescriptor.java (changed), UserColourSchemeDescriptor.java (changed), UserColoursDescriptor.java (changed), VAMSASDescriptor.java (changed), VamsasModelDescriptor.java (changed), ViewportDescriptor.java (changed)

jprocter 2008-11-12 11:14 #19

new listener/sender for selection events

59 lines of code changed in:

• src/jalview/structure: SelectionListener.java (new 18), SelectionSource.java (new 11), StructureSelectionManager.java (+30)

jprocter 2008-11-12 11:11 #18

gracefully translate ambigous nucleotides as 'X'

8 lines of code changed in:

• src/jalview/schemes: ResidueProperties.java (+8 -2)

jprocter 2008-11-12 11:10 #17

bugfix to safely deal with server exception resulting in null document

0 lines of code changed in:

• src/jalview/ws/ebi: EBIFetchClient.java (changed)

jprocter 2008-11-12 11:09 #16

added todo regarding import of GFF2 key=value attributes

0 lines of code changed in:

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

jprocter 2008-11-12 11:09 #15

avoid exception if search returns valid object but does not match any sequences

2 lines of code changed in:

• src/jalview/analysis: Finder.java (+2 -2)

jprocter 2008-11-12 11:07 #14

new copy constructor and intersect method

58 lines of code changed in:

• src/jalview/datamodel: SequenceGroup.java (+58 -1)

jprocter 2008-11-12 11:03 #13

involvesSequence to check if searchResults intersect with a specific sequence

23 lines of code changed in:

• src/jalview/datamodel: SearchResults.java (+23 -1)

jprocter 2008-11-12 11:03 #12

javadoc and new method to get alignment sequence index using a SearchResults object

29 lines of code changed in:

• src/jalview/datamodel: Alignment.java (+21 -2), AlignmentI.java (+8 -1)

jprocter 2008-11-04 13:31 #11

bugfix db ref retrieve routine so it removes dead query strings properly

0 lines of code changed in:

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

jprocter 2008-11-04 13:29 #10

implemented embl validation properly

0 lines of code changed in:

• src/jalview/ws/dbsources: EmblCdsSouce.java (changed)

jprocter 2008-11-04 13:18 #9

implemented embl validation properly

0 lines of code changed in:

• src/jalview/ws/dbsources: EmblSource.java (changed)

jprocter 2008-11-04 11:48 #8

links for non-positional features

18 lines of code changed in:

• help/html/features: featuresFormat.html (+18 -5)

jprocter 2008-11-04 11:48 #7

comment about escaping regex properly

4 lines of code changed in:

• help/html/features: preferences.html (+4 -1)

jprocter 2008-11-04 11:47 #6

optional display of database refs and non-positional feature tooltips

5 lines of code changed in:

• help/html/menus: alignmentMenu.html (+5)

jprocter 2008-11-04 11:47 #5

optional display of database refs and non-positional features

4 lines of code changed in:

• help/html/menus: alwview.html (+4)

jprocter 2008-11-04 11:46 #4

links for non-positional features

4 lines of code changed in:

• help/html/menus: popupMenu.html (+4 -1)

jprocter 2008-11-04 11:44 #3

beginning of implementation of new properties for hide/show groups and sequence representatives via the annotation file

86 lines of code changed in:

• help/html/features: annotationsFormat.html (+10 -2)
• src/jalview/datamodel: SequenceGroup.java (+76 -3)
• src/jalview/io: AnnotationFile.java (changed)

jprocter 2008-11-04 09:16 #2

bugfix for transfer of user defined colourscheme from applet to application via jnlp launch

16 lines of code changed in:

• src/jalview/schemes: ColourSchemeProperty.java (+16 -10)

jprocter 2008-11-04 09:15 #1

application specific validIOformat method

23 lines of code changed in:

• src/jalview/io: FormatAdapter.java (+23 -1)

October 2008 »