July 2007 Commit Log

Number of Commits:

33

Number of Active Developers:

1

jprocter 2007-07-31 18:02 #33

debugging cross references and duplicate sequence db refs

47 lines of code changed in:

• src/jalview/datamodel: DBRefEntry.java (+26 -6), Sequence.java (+10 -2), SequenceI.java (+7 -1)
• src/jalview/datamodel/xdb/embl: EmblEntry.java (+4 -4)

jprocter 2007-07-30 18:30 #32

test cc change revoked.

0 lines of code changed in:

• src/jalview/bin: Jalview.java (-1)

jprocter 2007-07-30 18:21 #31

test cc

2 lines of code changed in:

• src/jalview/bin: Jalview.java (+2 -1)

jprocter 2007-07-30 18:01 #30

javadoc

8 lines of code changed in:

• src/jalview/datamodel: Sequence.java (+8 -7)

jprocter 2007-07-30 15:13 #29

property for including debug info in classes

4 lines of code changed in:

• build.xml (+4 -1)

jprocter 2007-07-25 18:23 #28

todo comment

2 lines of code changed in:

• src/jalview/io: IdentifyFile.java (+2 -1)

jprocter 2007-07-25 18:17 #27

fix crossRef retrieval so either protein OR nucleotide

0 lines of code changed in:

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

jprocter 2007-07-25 18:17 #26

uniprot synonym

1 lines of code changed in:

• src/jalview/util: DBRefUtils.java (+1)

jprocter 2007-07-25 18:16 #25

better vamsas tree io (for when there are no nodemappings)

22 lines of code changed in:

• src/jalview/io/vamsas: Tree.java (+22 -1)

jprocter 2007-07-25 18:16 #24

uniprot synonym

0 lines of code changed in:

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

jprocter 2007-07-25 18:14 #23

bugfix for vamsas demo

818 lines of code changed in:

• src/jalview/io: NewickFile.java (+805 -801), VamsasAppDatastore.java (+13 -2)

jprocter 2007-07-25 18:14 #22

IO rearrangement for AMSAFile output

175 lines of code changed in:

• src/jalview/io: AppletFormatAdapter.java (+5 -3), FormatAdapter.java (+170 -125)

jprocter 2007-07-25 18:13 #21

bugfix for vamsas demo and IO rearrangement for AMSAFile output

12 lines of code changed in:

• src/jalview/gui: AlignFrame.java (+12 -11)

jprocter 2007-07-13 16:40 #20

ignore random stuff to do with eclipse

13 lines of code changed in:

• .cvsignore (+13)

jprocter 2007-07-13 16:37 #19

preliminary IO classes - read javadoc for purpose

0 lines of code changed in:

• src/jalview/io: ClansFile.java (new), DBRefFile.java (new), MatrixFile.java (new)

jprocter 2007-07-13 16:09 #18

pickmanager on sequence and alignment position, vamsas pick broadcast and refactor for new DBRef management and generalised source and entry retrieval mechanism for references and cross references

3992 lines of code changed in:

• src/jalview/appletgui: SeqPanel.java (+1694 -1694)
• src/jalview/gui: AlignFrame.java (+133 -4), AppJmol.java (+1), DasSourceBrowser.java (changed), FeatureSettings.java (+2 -2), PopupMenu.java (+1487 -1487), SeqPanel.java (+5 -5), SequenceFetcher.java (+604 -581), TreeCanvas.java (+2 -2)
• src/jalview/jbgui: GAlignFrame.java (+18 -1)
• src/jalview/structure: SequenceListener.java (+30 -30), StructureSelectionManager.java (+16 -8)

jprocter 2007-07-13 16:07 #17

refactor

2 lines of code changed in:

• src/MCview: PDBViewer.java (+2)

jprocter 2007-07-13 16:07 #16

new DBRef management and generalised source and entry retrieval mechanism for references and cross references

217 lines of code changed in:

• src/jalview/io: DBRefFetcher.java (del), DasSequenceFeatureFetcher.java (del), EBIFetchClient.java (del)
• src/jalview/ws: ASequenceFetcher.java (new), DBRefFetcher.java (new), DasSequenceFeatureFetcher.java (new), DbSourceProxy.java (new), DbSourceProxyImpl.java (new), EBIFetchClient.java (new), SequenceFetcher.java (new)
• src/jalview/ws/dbsources: EbiFileRetrievedProxy.java (new), EmblCdsSouce.java (new), EmblSource.java (new), EmblXmlSource.java (new), Pdb.java (new), Pfam.java (new), Uniprot.java (new 217)

jprocter 2007-07-13 16:05 #15

more semantic groupings of dbs

0 lines of code changed in:

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

jprocter 2007-07-13 16:04 #14

debugged mappings and translated sequence recovery

519 lines of code changed in:

• src/jalview/datamodel: DBRefEntry.java (+14), Mapping.java (+275 -79)
• src/jalview/datamodel/xdb/embl: EmblEntry.java (+224 -132), EmblFeatureLocations.java (+6 -3)

jprocter 2007-07-13 16:03 #13

preliminary states for pca distribution io

50 lines of code changed in:

• src/jalview/datamodel: SequencePoint.java (+50 -43)

jprocter 2007-07-13 16:03 #12

preliminary methods for detecting internal sequence nodes

167 lines of code changed in:

• src/jalview/datamodel: SequenceNode.java (+167 -149)

jprocter 2007-07-13 16:02 #11

bugfix

5 lines of code changed in:

• src/jalview/datamodel: SequenceFeature.java (+5 -6)

jprocter 2007-07-13 16:01 #10

mapping bug fixes

4 lines of code changed in:

• src/jalview/datamodel: AlignedCodonFrame.java (changed), Alignment.java (+4 -2)

jprocter 2007-07-13 16:00 #9

basic idea for recognising that a feature is a coding region.

0 lines of code changed in:

• src/jalview/datamodel: FeatureProperties.java (changed)

jprocter 2007-07-13 15:59 #8

bugfixes, partially working code for translation using existing translation associated with aligned sequences

0 lines of code changed in:

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

jprocter 2007-07-13 15:58 #7

comments for future viz/detection of internal sequence nodes.

8 lines of code changed in:

• src/jalview/analysis: NJTree.java (+8 -4)

jprocter 2007-07-13 15:58 #6

updated to iscb demo vamsas-client version

792 lines of code changed in:

• lib: vamsas-client.jar (changed)
• src/jalview/gui: VamsasApplication.java (+18 -1)
• src/jalview/io: VamsasAppDatastore.java (+774 -576)

jprocter 2007-07-13 15:57 #5

refactored form of vamsas document interaction code

894 lines of code changed in:

• src/jalview/io/vamsas: DatastoreItem.java (+88), Dbref.java (new 115), Rangetype.java (new 270), Sequencemapping.java (new 245), Tree.java (+176 -9)

jprocter 2007-07-13 15:56 #4

methods for traversing database reference space

0 lines of code changed in:

• src/jalview/analysis: CrossRef.java (new)

jprocter 2007-07-13 15:55 #3

new search method for finding references like other references.

37 lines of code changed in:

• src/jalview/util: DBRefUtils.java (+37)

jprocter 2007-07-13 15:54 #2

bugfix and comments

45 lines of code changed in:

• src/jalview/util: MapList.java (+45 -2)

jprocter 2007-07-13 15:53 #1

moved to castor-1.1-cycle - a specially patched version of castor relating to jira bugs : http://jira.codehaus.org/browse/CASTOR-2027 http://jira.codehaus.org/browse/CASTOR-2012 http://jira.codehaus.org/browse/CASTOR-2011

23 lines of code changed in:

• build.xml (+23 -3)
• lib: castor-1.1-cycle-xml.jar (new), castor-1.1-xml.jar (del)
• src/jalview/binding: Alignment.java (changed), Annotation.java (changed), AnnotationElement.java (changed), Colour.java (changed), Feature.java (changed), FeatureSettings.java (changed), Features.java (changed), JGroup.java (changed), JSeq.java (changed), JalviewModel.java (changed), JalviewModelSequence.java (changed), JalviewUserColours.java (changed), Pdbentry.java (changed), PdbentryItem.java (changed), Pdbids.java (changed), Property.java (changed), Sequence.java (changed), SequenceSet.java (changed), SequenceType.java (changed), Setting.java (changed), Tree.java (changed), UserColourScheme.java (changed), UserColours.java (changed), VAMSAS.java (changed), VamsasModel.java (changed), Viewport.java (changed)
• src/jalview/schemabinding/version2: .castor.cdr (changed), SequenceSetProperties.java (changed), StructureState.java (changed)
• src/jalview/schemabinding/version2/descriptors: 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), 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)
• utils: castor-1.1-codegen-anttask.jar (del), castor-1.1-codegen.jar (del), castor-1.1-cycle-codegen-anttask.jar (new), castor-1.1-cycle-codegen.jar (new)

June 2007 »