Patric Plitzner [Wed, 15 Jul 2015 10:43:01 +0000 (10:43 +0000)]
- removed dependencies to LibrAlign
Patric Plitzner [Wed, 15 Jul 2015 09:18:13 +0000 (09:18 +0000)]
- added handler to exported packages
Patric Plitzner [Wed, 15 Jul 2015 08:48:35 +0000 (08:48 +0000)]
- added molecular plugin to the feature
Patric Plitzner [Wed, 15 Jul 2015 08:48:17 +0000 (08:48 +0000)]
- moved "Add..." menu item to the bottom to avoid other items not to be drawn
Patric Plitzner [Wed, 15 Jul 2015 08:47:19 +0000 (08:47 +0000)]
- fixed dependencies
Patric Plitzner [Wed, 15 Jul 2015 08:44:57 +0000 (08:44 +0000)]
Initial import of aggregator project files.
The pom.xml configures which modules are aggragated.
Patric Plitzner [Wed, 15 Jul 2015 08:38:06 +0000 (08:38 +0000)]
Initial import of aggregator project.
This is used for handling the dependencies of the LibrAlign integration.
Patric Plitzner [Wed, 15 Jul 2015 07:24:38 +0000 (07:24 +0000)]
Cleaning up
Delete target folder
b.stoever [Tue, 14 Jul 2015 14:23:54 +0000 (14:23 +0000)]
Missing LibrAlign BioJava1 dependency added to molecular plugin project.
Patric Plitzner [Tue, 14 Jul 2015 13:25:23 +0000 (13:25 +0000)]
- added jars to svn:ignore
Patric Plitzner [Tue, 14 Jul 2015 13:07:15 +0000 (13:07 +0000)]
Add lib folder for external dependencies
Patric Plitzner [Tue, 14 Jul 2015 12:20:50 +0000 (12:20 +0000)]
Initial import of plugin files
Patric Plitzner [Tue, 14 Jul 2015 12:19:27 +0000 (12:19 +0000)]
Initial import of separated plugin which holds all changes related to LibrAlign integration
Patric Plitzner [Mon, 13 Jul 2015 08:20:22 +0000 (08:20 +0000)]
merge-update from trunk
Patrick Plitzner [Wed, 8 Jul 2015 18:31:02 +0000 (20:31 +0200)]
Make cell text in ReferencingObjectsView selectable
Patrick Plitzner [Wed, 8 Jul 2015 18:27:26 +0000 (20:27 +0200)]
Remove comments
Patric Plitzner [Wed, 8 Jul 2015 12:50:55 +0000 (12:50 +0000)]
merge-update from trunk
Patrick Plitzner [Wed, 8 Jul 2015 05:41:33 +0000 (07:41 +0200)]
Externalize cdmViewer extension point parsing
Patrick Plitzner [Tue, 7 Jul 2015 14:37:10 +0000 (16:37 +0200)]
Add generic context menu for ICdmViewer framework
Patrick Plitzner [Tue, 7 Jul 2015 14:36:18 +0000 (16:36 +0200)]
Refactor ICdmViewer framework
Removed unnecessary ExecutionEvent
Andreas Müller [Tue, 7 Jul 2015 13:04:55 +0000 (15:04 +0200)]
Revert incorrect fix (r24331) for taxon titleCache #5018
Patric Plitzner [Tue, 7 Jul 2015 12:57:20 +0000 (12:57 +0000)]
Fix conversion of ShiftChanges to Shifts
Cherian Mathew [Tue, 7 Jul 2015 12:13:26 +0000 (14:13 +0200)]
Make editor transient term service compatible with cdmlib term service
Patric Plitzner [Tue, 7 Jul 2015 12:11:27 +0000 (12:11 +0000)]
Use UUIDs instead of CDM objects in AlignmentEditorInput
This avoids session conflicts because the object will be loaded into the correct session when processing the editor input during initialization of the editor.
Patric Plitzner [Tue, 7 Jul 2015 11:53:57 +0000 (11:53 +0000)]
Re-load sequence to avoid session conflicts.
Patrick Plitzner [Mon, 6 Jul 2015 13:11:20 +0000 (15:11 +0200)]
Display URI parsing errors
Patrick Plitzner [Mon, 6 Jul 2015 13:10:59 +0000 (15:10 +0200)]
Remove comments
b.stoever [Sun, 5 Jul 2015 20:55:48 +0000 (20:55 +0000)]
Adjustments to recent module changes in bioinfweb.commons.
b.stoever [Fri, 3 Jul 2015 14:26:11 +0000 (14:26 +0000)]
AlignmentEditor.createTestContents() marked as deprecated.
b.stoever [Fri, 3 Jul 2015 10:28:54 +0000 (10:28 +0000)]
InternalError thrown, if a single read alignment shall be saved that contains new single reads, which have been added in the AlignmentEditor. (Implementation does not make sense before the decision whether #4740, #4745 or #4746 shall be implemented.)
b.stoever [Fri, 3 Jul 2015 10:20:00 +0000 (10:20 +0000)]
Error message added, if a pherogram URL loaded from CDM cannot be processed correctly.
b.stoever [Fri, 3 Jul 2015 10:09:31 +0000 (10:09 +0000)]
Fixed NPE, if a single read has a pherogram object without URI.
Cherian Mathew [Fri, 3 Jul 2015 10:04:00 +0000 (12:04 +0200)]
#5056 Adapt editor to service layer 'save' method refactoring in cdmlib
b.stoever [Thu, 2 Jul 2015 11:11:16 +0000 (11:11 +0000)]
Adjustments to recent changes in LibrAlign.
(The additional project https://secure.bioinfweb.info/Code/svn/LibrAlign / trunk / main / info.bioinfweb.libralign.biojava1 needs to be in the workspace from now on.)
Cherian Mathew [Thu, 2 Jul 2015 09:15:14 +0000 (11:15 +0200)]
Make editor compatible with latest cdmlib service layer updates
b.stoever [Wed, 1 Jul 2015 16:06:55 +0000 (16:06 +0000)]
Minor changes in implementation of AlignmentEditor.
b.stoever [Wed, 1 Jul 2015 16:03:18 +0000 (16:03 +0000)]
ShowPherogramHandler now also handles single reads without attached pherograms.
Andreas Müller [Wed, 1 Jul 2015 15:44:43 +0000 (17:44 +0200)]
Fix compile error in FeatureDistributionDetailElement
b.stoever [Wed, 1 Jul 2015 15:34:19 +0000 (15:34 +0000)]
Support for empty alignments and single reads without pherograms added to AlignmentEditor.
DerivateLabelProvider now used to label single read sequences.
b.stoever [Wed, 1 Jul 2015 09:34:55 +0000 (09:34 +0000)]
Class path edited to include new modules from LibrAlign and TIC.
b.stoever [Wed, 1 Jul 2015 09:31:11 +0000 (09:31 +0000)]
Adjustments to recent architecture changes in TIC and LibrAlign. (TIC top level project referenced from now on.)
The following projects need to be checked out into the workspace from now on:
- https://secure.bioinfweb.info/Code/svn/commons.java/trunk/main
- https://secure.bioinfweb.info/Code/svn/TIC/trunk/main/info.bioinfweb.tic.core
- https://secure.bioinfweb.info/Code/svn/TIC/trunk/main/info.bioinfweb.tic.swt
- https://secure.bioinfweb.info/Code/svn/LibrAlign/trunk/main/info.bioinfweb.libralign.core
- https://secure.bioinfweb.info/Code/svn/LibrAlign/trunk/main/info.bioinfweb.libralign.swt
Patric Plitzner [Wed, 1 Jul 2015 09:09:33 +0000 (09:09 +0000)]
merge-update from trunk
Patrick Plitzner [Wed, 1 Jul 2015 07:16:17 +0000 (09:16 +0200)]
Fix deletion of single reads in Derivative Editor
Patrick Plitzner [Wed, 1 Jul 2015 07:15:39 +0000 (09:15 +0200)]
Add missing transient method
Patrick Plitzner [Wed, 1 Jul 2015 07:23:39 +0000 (09:23 +0200)]
Map preparation materials to derivation event description
Patric Plitzner [Tue, 30 Jun 2015 13:04:15 +0000 (13:04 +0000)]
merge-update from trunk
Patrick Plitzner [Tue, 30 Jun 2015 11:47:51 +0000 (13:47 +0200)]
Make background of icon transparent
Patrick Plitzner [Mon, 29 Jun 2015 14:01:34 +0000 (16:01 +0200)]
Add icon for switching to advanced media view
Patric Plitzner [Mon, 29 Jun 2015 13:25:18 +0000 (13:25 +0000)]
merge-update from trunk
Cherian Mathew [Mon, 29 Jun 2015 12:52:58 +0000 (14:52 +0200)]
Update transient services with new delete method
Patric Plitzner [Mon, 29 Jun 2015 12:39:34 +0000 (12:39 +0000)]
merge-update from trunk
Patrick Plitzner [Mon, 29 Jun 2015 12:26:07 +0000 (14:26 +0200)]
Show abbreviated title cache for authors and refernce in taxon details
view
Patrick Plitzner [Wed, 24 Jun 2015 17:55:55 +0000 (19:55 +0200)]
Show URI parsing exceptions below URI text field (fixes #5055, #5003, #4587)
Patrick Plitzner [Wed, 24 Jun 2015 18:58:19 +0000 (20:58 +0200)]
Avoid duplication of edited team member (#4997)
Patrick Plitzner [Wed, 24 Jun 2015 19:39:38 +0000 (21:39 +0200)]
Add no marker without a markerType (#4588)
Patrick Plitzner [Mon, 29 Jun 2015 11:41:37 +0000 (13:41 +0200)]
Add ticket number to TODO
Patrick Plitzner [Mon, 29 Jun 2015 10:15:24 +0000 (12:15 +0200)]
Refresh view after media view has been switched
Patrick Plitzner [Mon, 29 Jun 2015 10:01:12 +0000 (12:01 +0200)]
Add MediaViewSwitch to media collection elements
Refactored code to use a static method that creates the IAction object.
This can be added by the GUI element itself.
Patrick Plitzner [Mon, 29 Jun 2015 05:04:53 +0000 (07:04 +0200)]
Add button for advanced media view to media attached to desccriptions
Patrick Plitzner [Sat, 27 Jun 2015 12:16:14 +0000 (14:16 +0200)]
Remove duplicate code for advanced media view (#4862)
Refactored code and added interface and abstract class to avoid
duplicate code.
Patrick Plitzner [Sat, 27 Jun 2015 12:13:59 +0000 (14:13 +0200)]
Remove comments
Patrick Plitzner [Wed, 24 Jun 2015 19:40:05 +0000 (21:40 +0200)]
Remove comments
Patrick Plitzner [Wed, 24 Jun 2015 12:18:47 +0000 (14:18 +0200)]
Fix typo
Cherian Mathew [Fri, 26 Jun 2015 15:49:01 +0000 (17:49 +0200)]
#5036 Add missing command for polytomous key delete
b.stoever [Fri, 26 Jun 2015 15:02:44 +0000 (15:02 +0000)]
Adjustments to recent changes in TIC. (EDITor Code from now on written against unreleased TIC 2.x.)
Cherian Mathew [Thu, 25 Jun 2015 15:21:07 +0000 (17:21 +0200)]
Fix remoting code compilation errors
Patrick Plitzner [Wed, 24 Jun 2015 12:19:58 +0000 (14:19 +0200)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/taxeditor into develop
Patrick Plitzner [Wed, 24 Jun 2015 12:19:43 +0000 (14:19 +0200)]
Empty text fields return empty string and not null
k.luther [Wed, 24 Jun 2015 11:08:18 +0000 (13:08 +0200)]
Revert "index on develop:
6992bef Rename NonViralName authorteams to authorship #4968"
This reverts commit
32cded397931ad359f7818fdfb91a113a074342e.
Andreas Müller [Tue, 23 Jun 2015 16:34:38 +0000 (18:34 +0200)]
Rename NonViralName authorteams to authorship #4968
Cherian Mathew [Tue, 23 Jun 2015 16:22:30 +0000 (18:22 +0200)]
Update cdmlib version to 3.6.3-SNAPSHOT
b.stoever [Tue, 23 Jun 2015 15:58:31 +0000 (15:58 +0000)]
Some actions for adjusting pherogram displaying added.
Cherian Mathew [Tue, 23 Jun 2015 12:45:38 +0000 (14:45 +0200)]
Delete renamed file
b.stoever [Tue, 23 Jun 2015 11:11:24 +0000 (11:11 +0000)]
PherogramViewPart that is started from within AlignmentEditor now uses a shared pherogram model to display cut positions.
Cherian Mathew [Tue, 23 Jun 2015 11:01:02 +0000 (13:01 +0200)]
Fix issues with merge conflicts
Cherian Mathew [Tue, 23 Jun 2015 08:09:36 +0000 (10:09 +0200)]
Fixes from Katja for commit issue
b.stoever [Mon, 22 Jun 2015 16:21:47 +0000 (16:21 +0000)]
Position properties of LibrAlign pherogram models are now connected to according CDM node properties (yet untested).
Andreas Müller [Mon, 22 Jun 2015 14:35:17 +0000 (16:35 +0200)]
Fix problem with non persisted taxon titleCache change: #5018
Patrick Plitzner [Mon, 22 Jun 2015 13:50:09 +0000 (15:50 +0200)]
adapt service call to model change
Patrick Plitzner [Mon, 22 Jun 2015 13:49:50 +0000 (15:49 +0200)]
adapt transient service methods to cdmlib changes
Patrick Plitzner [Mon, 22 Jun 2015 12:38:25 +0000 (14:38 +0200)]
- update parent scroll form on property change (fixes #4881)
Patrick Plitzner [Mon, 22 Jun 2015 06:56:23 +0000 (08:56 +0200)]
- removed initial expand of sections
Patrick Plitzner [Mon, 22 Jun 2015 06:50:16 +0000 (08:50 +0200)]
- fixed potential NPE
Patrick Plitzner [Mon, 22 Jun 2015 05:54:33 +0000 (07:54 +0200)]
- fixed potential NPE
Patrick Plitzner [Wed, 17 Jun 2015 15:35:46 +0000 (17:35 +0200)]
- changed type of "Materials & Methods" to text instead of DefinedTerm
- fixed label
Patrick Plitzner [Wed, 17 Jun 2015 15:27:48 +0000 (17:27 +0200)]
- split off "Preparation/Preservation section" from dna sample general
section
b.stoever [Mon, 22 Jun 2015 11:16:01 +0000 (11:16 +0000)]
Adjustments to recent changes in LibrAlign.
Cherian Mathew [Mon, 22 Jun 2015 09:31:26 +0000 (11:31 +0200)]
fixed conflicts from last commit
Katja Luther [Thu, 18 Jun 2015 13:28:35 +0000 (15:28 +0200)]
all delete methods need an Uuid as argument
Conflicts:
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientAgentService.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientDescriptionService.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientNameService.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientOccurenceService.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientReferenceService.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientTaxonService.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientTermService.java
Katja Luther [Thu, 18 Jun 2015 13:15:42 +0000 (15:15 +0200)]
change delete argument to UUID
Andreas Müller [Fri, 19 Jun 2015 13:15:04 +0000 (15:15 +0200)]
add empty test folder
b.stoever [Fri, 19 Jun 2015 10:42:56 +0000 (10:42 +0000)]
Actions for creating and updating the consensus sequence in AlignmentEditor implemented.
b.stoever [Fri, 19 Jun 2015 09:11:33 +0000 (09:11 +0000)]
AbstractAlignmentEditorHandler added.
Andreas Müller [Thu, 18 Jun 2015 13:22:24 +0000 (15:22 +0200)]
Merge remote-tracking branch 'origin/develop' into develop
Andreas Müller [Thu, 18 Jun 2015 13:04:56 +0000 (15:04 +0200)]
minor
Patric Plitzner [Wed, 17 Jun 2015 13:52:06 +0000 (13:52 +0000)]
merge-update from trunk
b.stoever [Wed, 17 Jun 2015 13:31:53 +0000 (13:31 +0000)]
ToggleInsertOverwriteHandler now also triggers enabling and disabling of ToggleLeftRightInsertionHandler when the insert key is used instead of the tool bar button.
Actions for cutting pherograms on the left and right ends added.
Action for reverse complementing single reads added.
Minor changes.
Patrick Plitzner [Tue, 16 Jun 2015 12:04:22 +0000 (14:04 +0200)]
Merge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/taxeditor into develop
Cherian Mathew [Tue, 16 Jun 2015 11:53:53 +0000 (13:53 +0200)]
fixing for compatibility with merged cdmlib
Patrick Plitzner [Mon, 15 Jun 2015 14:11:56 +0000 (16:11 +0200)]
- added transient service methods