b.stoever [Thu, 4 Dec 2014 19:19:38 +0000 (19:19 +0000)]
Removed unused imports.
b.stoever [Thu, 4 Dec 2014 19:18:26 +0000 (19:18 +0000)]
Buttons for toggling "insert/overwrite" and "insert left/right" in toolbar replaced by commands that can be updated by the AlignmentEditor.
b.stoever [Thu, 4 Dec 2014 11:25:08 +0000 (11:25 +0000)]
MultipleAlignmentsContainer now used in AlignmentEditor.
Test consensus sequence and consensus sequence data area added.
b.stoever [Tue, 2 Dec 2014 11:51:31 +0000 (11:51 +0000)]
Output style of PherogramViewPart changed. (Will user defined in future versions.)
b.stoever [Tue, 2 Dec 2014 11:32:05 +0000 (11:32 +0000)]
Missing properties added to CDMAlignmentObjectPlaceholder.
b.stoever [Wed, 26 Nov 2014 18:38:52 +0000 (18:38 +0000)]
TODO comment added to AlignmentEditor.
b.stoever [Wed, 26 Nov 2014 17:32:26 +0000 (17:32 +0000)]
PherogramView renamed to PherogramViewPart to avoid name conflict with LibrAlign component.
Adjustments to recent changes in LibrAlign on pherogram view components.
Patric Plitzner [Wed, 26 Nov 2014 14:37:34 +0000 (14:37 +0000)]
merge-update from trunk
Patric Plitzner [Wed, 26 Nov 2014 14:20:29 +0000 (14:20 +0000)]
- activated filter in factual data view for displaying only IndividualsAssociations
Patric Plitzner [Wed, 26 Nov 2014 13:52:45 +0000 (13:52 +0000)]
- removed obsolete Primer page for AmplificationWizard
- added dnaMarker to amplification designation
Patric Plitzner [Wed, 26 Nov 2014 12:50:33 +0000 (12:50 +0000)]
- re-enabled MediaViewPart for DerivateView (#4475)
Patric Plitzner [Wed, 26 Nov 2014 12:21:37 +0000 (12:21 +0000)]
- added missing service method to transient service
Patric Plitzner [Wed, 26 Nov 2014 12:19:10 +0000 (12:19 +0000)]
- moved extension point for taxon navigator context menu
- fixed DerivateSearchView layout
- added "disabled" extension point for toggling individual assciations in factual data view
Patric Plitzner [Wed, 26 Nov 2014 11:45:12 +0000 (11:45 +0000)]
- set multiline flag for LanguageStringWithLabelElement #2248
Patric Plitzner [Wed, 26 Nov 2014 08:54:43 +0000 (08:54 +0000)]
- added clear button to DerivateSearchView
- made use of cdmlib service to get associated specimen for one taxon (#4506)
b.stoever [Tue, 25 Nov 2014 18:57:54 +0000 (18:57 +0000)]
Adjustments to recent changes in LibrAlign package structure.
b.stoever [Tue, 25 Nov 2014 18:37:10 +0000 (18:37 +0000)]
URI property for PherogramView added.
PherogramViews can be opened by double clicking a pherogram in AlignmentEditor.
AlignmentEditor saves URIs for each pherogram.
Cherian Mathew [Tue, 25 Nov 2014 12:33:21 +0000 (12:33 +0000)]
added checks to makes sure no other exception is thrown within the dialog creation code #4502.
b.stoever [Tue, 25 Nov 2014 11:04:06 +0000 (11:04 +0000)]
Adjustments to recent changes in LibrAlign package structure.
Patric Plitzner [Tue, 25 Nov 2014 09:02:07 +0000 (09:02 +0000)]
- added context menu entry to taxon navigator to open associated derivates in DerivateEditor
- added taxon filter to DerivateSearchView (non-functional) (#4506)
Patric Plitzner [Mon, 24 Nov 2014 10:47:33 +0000 (10:47 +0000)]
- added some more molecular parameters to the DetailsView
Patric Plitzner [Mon, 24 Nov 2014 10:16:04 +0000 (10:16 +0000)]
- removed unused code
Patric Plitzner [Mon, 24 Nov 2014 09:12:50 +0000 (09:12 +0000)]
- converted dnaQuality from DefinedTerm to OrderedTerm (#4434)
Patric Plitzner [Mon, 24 Nov 2014 08:37:19 +0000 (08:37 +0000)]
- adapted to cdmlib changes (#4434)
b.stoever [Thu, 20 Nov 2014 16:53:26 +0000 (16:53 +0000)]
First version of PherogramView added.
b.stoever [Thu, 20 Nov 2014 15:42:02 +0000 (15:42 +0000)]
ToggleInsertOverwriteButton and ToggleLeftRightInsertionButton (currently only forward) linked to according functionality in LibrAlign.
Patric Plitzner [Thu, 20 Nov 2014 13:53:04 +0000 (13:53 +0000)]
- added preference for showing Collecting Areas below Country in DetailsView (#4473)
Patric Plitzner [Thu, 20 Nov 2014 10:15:47 +0000 (10:15 +0000)]
- made use of TermType DnaQuality
Patric Plitzner [Thu, 20 Nov 2014 09:42:51 +0000 (09:42 +0000)]
- added static method to DerivateLabelProvider to get the derivate text
- refactored moving of derivates to use the operation framework.
- immplemented undo/redo
Patric Plitzner [Thu, 20 Nov 2014 09:41:33 +0000 (09:41 +0000)]
- DerivateView and BulkEditor trigger selection change event for MediaViewPart (fixes #4475)
Patric Plitzner [Thu, 20 Nov 2014 09:36:31 +0000 (09:36 +0000)]
- DerivedUnits DetailsView only shows FieldUnit data in titleCache (fixes #4474)
- Areas section is now shown below country for FieldUnits (fixes 4473)
Patric Plitzner [Thu, 20 Nov 2014 09:34:28 +0000 (09:34 +0000)]
- Rights section is now part of MediaSpecimen DetailsView (fixes #4472)
- DerivedUnits DetailsView only shows FieldUnit data in titleCache (fixes #4474)
Patric Plitzner [Tue, 18 Nov 2014 13:47:29 +0000 (13:47 +0000)]
- extended DerivateSearchView to allow multiple selection
- added context menu to open multiple elements in DerivateView
- extended DerivateView to show multiple derivate hierarchies in one view
Cherian Mathew [Tue, 18 Nov 2014 09:28:01 +0000 (09:28 +0000)]
remotingApplicationContext : now using the cachers from cdmlib
CdmServiceCacher : added unimplemented method
Katja Luther [Mon, 17 Nov 2014 12:39:46 +0000 (12:39 +0000)]
#4463 fixed
if a titlecache is updated and the position of the parsing problem is behind the actual text no position is created.
Patric Plitzner [Mon, 17 Nov 2014 09:54:35 +0000 (09:54 +0000)]
- exported eu.etaxonomy.cdm.io.csv.redlist.demo package to fix compile errors
Alexander Oppermann [Fri, 14 Nov 2014 16:29:20 +0000 (16:29 +0000)]
Added simple CSV Export to Taxonomic Editor
Patric Plitzner [Wed, 12 Nov 2014 14:35:23 +0000 (14:35 +0000)]
- updated molecular DetailsViews according to requirements
Patric Plitzner [Wed, 12 Nov 2014 08:51:52 +0000 (08:51 +0000)]
- used ImageFile instead of more generic MediaRepresentationPart when creating the Media (fixes #4402)
- fixed a typo
Patric Plitzner [Tue, 11 Nov 2014 13:11:11 +0000 (13:11 +0000)]
- moved OriginalLabelData section to 2nd position
- made text field fill horizontally
Patric Plitzner [Tue, 11 Nov 2014 08:34:23 +0000 (08:34 +0000)]
- refactored DerivateViewEditorInput to use UUIDs instead of CDM entities
- added delete operation to DerivateView (currently only deleting leafs of the derivate tree is allowed)
Katja Luther [Mon, 10 Nov 2014 08:55:43 +0000 (08:55 +0000)]
fixing problems in bulkeditor and minor
Patric Plitzner [Wed, 5 Nov 2014 12:01:42 +0000 (12:01 +0000)]
- added toolbar buttons for toggling the different insertion modes
- added menu entry to load pherogram (also possible with shortcut CTRL+O)
- added status bar indicating the current insertion mode
Patric Plitzner [Wed, 5 Nov 2014 11:59:13 +0000 (11:59 +0000)]
- merge-update from trunk
Patric Plitzner [Tue, 4 Nov 2014 14:57:28 +0000 (14:57 +0000)]
- merge-update from trunk
Patric Plitzner [Tue, 4 Nov 2014 14:54:51 +0000 (14:54 +0000)]
- fixed possible NPE
Patric Plitzner [Tue, 4 Nov 2014 13:56:39 +0000 (13:56 +0000)]
- used more pepresentative DerivationEventTypes when creating derivates via DerivatView
Patric Plitzner [Tue, 4 Nov 2014 09:41:17 +0000 (09:41 +0000)]
merge-update from trunk
Katja Luther [Thu, 30 Oct 2014 10:44:49 +0000 (10:44 +0000)]
Katja Luther [Thu, 30 Oct 2014 10:43:43 +0000 (10:43 +0000)]
fixing #2547
Patric Plitzner [Wed, 29 Oct 2014 14:50:10 +0000 (14:50 +0000)]
- fixed class cast exception
Katja Luther [Wed, 29 Oct 2014 12:18:01 +0000 (12:18 +0000)]
Patric Plitzner [Wed, 29 Oct 2014 10:39:34 +0000 (10:39 +0000)]
- added exception throwing to URI assembly in Sequence class
- handled exception in editor details view
Patric Plitzner [Wed, 29 Oct 2014 10:38:50 +0000 (10:38 +0000)]
- added elevation to section title
Patric Plitzner [Wed, 29 Oct 2014 10:38:11 +0000 (10:38 +0000)]
- applied coding conventions
Patric Plitzner [Wed, 29 Oct 2014 08:37:56 +0000 (08:37 +0000)]
- fixed possible SessionException
Patric Plitzner [Tue, 28 Oct 2014 18:25:17 +0000 (18:25 +0000)]
- adapted derivate hierarchy assembly to cdmlib3.4 changes (TissueSample, DnaSample as one class)
Cherian Mathew [Tue, 28 Oct 2014 16:52:24 +0000 (16:52 +0000)]
eu.etaxonomy.taxeditor/pom.xml : reverted addition of nebula widget jars
pom.xml : changed nebula repository to archived one
eu.etaxonomy.taxeditor/rcp.target : changed composite table jar widget to the one in the repository
Cherian Mathew [Tue, 28 Oct 2014 14:45:30 +0000 (14:45 +0000)]
removed version dependency for org.eclipse.nebula.widgets.compositetable
and added the composite table jar to the p2 update
Katja Luther [Tue, 28 Oct 2014 13:10:03 +0000 (13:10 +0000)]
fix #4450
Cherian Mathew [Tue, 28 Oct 2014 08:53:06 +0000 (08:53 +0000)]
added space between beta prefix and version
b.stoever [Mon, 27 Oct 2014 15:33:59 +0000 (15:33 +0000)]
Basic implementation for LoadPherogramHandler added. (Imported data is currently not displayed due to currently unimplemented support for adding sequences and data areas during runtime in LibrAlign.)
b.stoever [Mon, 27 Oct 2014 14:53:21 +0000 (14:53 +0000)]
Example in AlignmentEditor now relies on an editable SequenceDataProvider (and contains not more predefined base call alignment edits).
Minor changes.
b.stoever [Mon, 27 Oct 2014 14:35:52 +0000 (14:35 +0000)]
Comments added to LoadPherogramHandler.
Pherogram example file paths adjusted again. (This time the other ones are still present as comments.)
Patric Plitzner [Mon, 27 Oct 2014 13:45:51 +0000 (13:45 +0000)]
merge-update from trunk
Patric Plitzner [Mon, 27 Oct 2014 13:45:36 +0000 (13:45 +0000)]
merge-update from trunk
Patric Plitzner [Mon, 27 Oct 2014 12:48:42 +0000 (12:48 +0000)]
- fixed double exception dialog popup when not connected to data source
- fixed NPE when starting ABCD import with dirty editors
Patric Plitzner [Mon, 27 Oct 2014 10:50:11 +0000 (10:50 +0000)]
- fixed possible NPE when entering DnaQuality data
Patric Plitzner [Mon, 27 Oct 2014 09:22:29 +0000 (09:22 +0000)]
- implemented missing interface method
Cherian Mathew [Fri, 24 Oct 2014 08:22:25 +0000 (08:22 +0000)]
changed beta prefix back to beta
b.stoever [Wed, 22 Oct 2014 21:48:55 +0000 (21:48 +0000)]
Adjustments to recent changes in LibrAlign.
Patric Plitzner [Wed, 22 Oct 2014 13:42:08 +0000 (13:42 +0000)]
- added kind of tissue to TissueSampleDetailsView
Patric Plitzner [Wed, 22 Oct 2014 13:36:31 +0000 (13:36 +0000)]
- added TODO
Patric Plitzner [Wed, 22 Oct 2014 12:59:25 +0000 (12:59 +0000)]
reintegrated taxeditor-3.4 branch into trunk
Patric Plitzner [Wed, 22 Oct 2014 12:42:13 +0000 (12:42 +0000)]
merge-update from trunk
Patric Plitzner [Wed, 22 Oct 2014 11:57:52 +0000 (11:57 +0000)]
- generalized sample designation GUI elements
- added sample designation to TissueSample details view
- added some more parameters to TissueSample details view
Patric Plitzner [Tue, 21 Oct 2014 12:45:04 +0000 (12:45 +0000)]
merge-update from trunk
Patric Plitzner [Tue, 21 Oct 2014 12:44:52 +0000 (12:44 +0000)]
- added empty "Delete Derivate" functionality to DerivateView
Patric Plitzner [Tue, 21 Oct 2014 11:44:23 +0000 (11:44 +0000)]
- removed unused package
Patric Plitzner [Tue, 21 Oct 2014 10:42:04 +0000 (10:42 +0000)]
merge-update from trunk
Patric Plitzner [Tue, 21 Oct 2014 10:41:34 +0000 (10:41 +0000)]
- extended DnaQuality details view
- refactored DateElement creation
Patric Plitzner [Tue, 21 Oct 2014 07:43:21 +0000 (07:43 +0000)]
- added more paramaters to DnaQuality details view
- fixed ordering of sample designations for DnaSamples (first is current)
Patric Plitzner [Mon, 20 Oct 2014 15:12:41 +0000 (15:12 +0000)]
- added some detail elements
Patric Plitzner [Mon, 20 Oct 2014 15:12:29 +0000 (15:12 +0000)]
- refresh after updating datasource (fixes #2117)
Patric Plitzner [Mon, 20 Oct 2014 15:11:46 +0000 (15:11 +0000)]
- adapted to cdmlib changes
Cherian Mathew [Mon, 20 Oct 2014 11:50:14 +0000 (11:50 +0000)]
deleted project from trunk to work on branch
Patric Plitzner [Mon, 20 Oct 2014 11:19:09 +0000 (11:19 +0000)]
merge-update from trunk
Cherian Mathew [Mon, 20 Oct 2014 11:08:32 +0000 (11:08 +0000)]
adding license text to feature projects since these were removed from feature.xml
Cherian Mathew [Mon, 20 Oct 2014 11:05:56 +0000 (11:05 +0000)]
added polytomous key tests and initial developments on caching
Cherian Mathew [Mon, 20 Oct 2014 10:59:37 +0000 (10:59 +0000)]
updated CDMServer and corresponding test files to use dbunit datasets with the possibility
of targetting a managed as well as external instance of the CDMServer
Cherian Mathew [Mon, 20 Oct 2014 10:57:19 +0000 (10:57 +0000)]
added required jars and setup svn:ignore property using .svnignore
Patric Plitzner [Mon, 20 Oct 2014 08:47:23 +0000 (08:47 +0000)]
- added sampleDesignation section to DnaSample details view (#4237)
- added sampleDesignation to DerivateLabelProvider
Patric Plitzner [Mon, 20 Oct 2014 08:45:19 +0000 (08:45 +0000)]
- re-enabled specimen type chooser
Patric Plitzner [Mon, 20 Oct 2014 08:21:56 +0000 (08:21 +0000)]
- adapted method calls to cdmlib changes
Patric Plitzner [Thu, 16 Oct 2014 11:08:47 +0000 (11:08 +0000)]
- removed unused extension
Patric Plitzner [Thu, 16 Oct 2014 09:23:21 +0000 (09:23 +0000)]
- added temporary shortcut "o" for opening a file chooser to load a pherogram
Patric Plitzner [Thu, 16 Oct 2014 07:50:47 +0000 (07:50 +0000)]
merge-update from trunk
Patric Plitzner [Thu, 16 Oct 2014 07:20:07 +0000 (07:20 +0000)]
merge-update from trunk
Patric Plitzner [Thu, 16 Oct 2014 07:16:53 +0000 (07:16 +0000)]
- removed visibleWhen parameter for command
Patric Plitzner [Tue, 14 Oct 2014 14:40:51 +0000 (14:40 +0000)]
- removed personal home folder