taxeditor.git
6 years agoFix menu contributions
Patric Plitzner [Wed, 15 Jul 2015 12:09:21 +0000 (12:09 +0000)]
Fix menu contributions

6 years ago Reverted all LibrAlign changes (are now in molecular project)
Patric Plitzner [Wed, 15 Jul 2015 11:30:09 +0000 (11:30 +0000)]
 Reverted all LibrAlign changes (are now in molecular project)

6 years ago Reverted all LibrAlign changes (are now in molecular project)
Patric Plitzner [Wed, 15 Jul 2015 11:26:42 +0000 (11:26 +0000)]
 Reverted all LibrAlign changes (are now in molecular project)

6 years agoDependency refactoring
Patric Plitzner [Wed, 15 Jul 2015 11:00:51 +0000 (11:00 +0000)]
Dependency refactoring

Arranged classes and classpath in accordance to other taxeditor projects.

6 years ago - removed dependencies to LibrAlign
Patric Plitzner [Wed, 15 Jul 2015 10:43:01 +0000 (10:43 +0000)]
 - removed dependencies to LibrAlign

6 years ago - added handler to exported packages
Patric Plitzner [Wed, 15 Jul 2015 09:18:13 +0000 (09:18 +0000)]
 - added handler to exported packages

6 years ago - added molecular plugin to the feature
Patric Plitzner [Wed, 15 Jul 2015 08:48:35 +0000 (08:48 +0000)]
 - added molecular plugin to the feature

6 years ago - moved "Add..." menu item to the bottom to avoid other items not to be drawn
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

6 years ago - fixed dependencies
Patric Plitzner [Wed, 15 Jul 2015 08:47:19 +0000 (08:47 +0000)]
 - fixed dependencies

6 years agoInitial import of aggregator project files.
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.

6 years agoInitial import of aggregator project.
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.

6 years agoCleaning up
Patric Plitzner [Wed, 15 Jul 2015 07:24:38 +0000 (07:24 +0000)]
Cleaning up

Delete target folder

6 years agoMissing LibrAlign BioJava1 dependency added to molecular plugin project.
b.stoever [Tue, 14 Jul 2015 14:23:54 +0000 (14:23 +0000)]
Missing LibrAlign BioJava1 dependency added to molecular plugin project.

6 years ago - added jars to svn:ignore
Patric Plitzner [Tue, 14 Jul 2015 13:25:23 +0000 (13:25 +0000)]
 - added jars to svn:ignore

6 years agoAdd lib folder for external dependencies
Patric Plitzner [Tue, 14 Jul 2015 13:07:15 +0000 (13:07 +0000)]
Add lib folder for external dependencies

6 years agoInitial import of plugin files
Patric Plitzner [Tue, 14 Jul 2015 12:20:50 +0000 (12:20 +0000)]
Initial import of plugin files

6 years agoInitial import of separated plugin which holds all changes related to LibrAlign integ...
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

6 years agomerge-update from trunk
Patric Plitzner [Mon, 13 Jul 2015 08:20:22 +0000 (08:20 +0000)]
merge-update from trunk

6 years agoMake cell text in ReferencingObjectsView selectable
Patrick Plitzner [Wed, 8 Jul 2015 18:31:02 +0000 (20:31 +0200)]
Make cell text in ReferencingObjectsView selectable

6 years agoRemove comments
Patrick Plitzner [Wed, 8 Jul 2015 18:27:26 +0000 (20:27 +0200)]
Remove comments

6 years agomerge-update from trunk
Patric Plitzner [Wed, 8 Jul 2015 12:50:55 +0000 (12:50 +0000)]
merge-update from trunk

6 years agoExternalize cdmViewer extension point parsing
Patrick Plitzner [Wed, 8 Jul 2015 05:41:33 +0000 (07:41 +0200)]
Externalize cdmViewer extension point parsing

6 years agoAdd generic context menu for ICdmViewer framework
Patrick Plitzner [Tue, 7 Jul 2015 14:37:10 +0000 (16:37 +0200)]
Add generic context menu for ICdmViewer framework

6 years agoRefactor ICdmViewer framework
Patrick Plitzner [Tue, 7 Jul 2015 14:36:18 +0000 (16:36 +0200)]
Refactor ICdmViewer framework

Removed unnecessary ExecutionEvent

6 years agoRevert incorrect fix (r24331) for taxon titleCache #5018
Andreas Müller [Tue, 7 Jul 2015 13:04:55 +0000 (15:04 +0200)]
Revert incorrect fix (r24331) for taxon titleCache  #5018

6 years agoFix conversion of ShiftChanges to Shifts
Patric Plitzner [Tue, 7 Jul 2015 12:57:20 +0000 (12:57 +0000)]
Fix conversion of ShiftChanges to Shifts

6 years agoMake editor transient term service compatible with cdmlib term service
Cherian Mathew [Tue, 7 Jul 2015 12:13:26 +0000 (14:13 +0200)]
Make editor transient term service compatible with cdmlib term service

6 years agoUse UUIDs instead of CDM objects in AlignmentEditorInput
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.

6 years agoRe-load sequence to avoid session conflicts.
Patric Plitzner [Tue, 7 Jul 2015 11:53:57 +0000 (11:53 +0000)]
Re-load sequence to avoid session conflicts.

6 years agoDisplay URI parsing errors
Patrick Plitzner [Mon, 6 Jul 2015 13:11:20 +0000 (15:11 +0200)]
Display URI parsing errors

6 years agoRemove comments
Patrick Plitzner [Mon, 6 Jul 2015 13:10:59 +0000 (15:10 +0200)]
Remove comments

6 years agoAdjustments to recent module changes in bioinfweb.commons.
b.stoever [Sun, 5 Jul 2015 20:55:48 +0000 (20:55 +0000)]
Adjustments to recent module changes in bioinfweb.commons.

7 years agoAlignmentEditor.createTestContents() marked as deprecated.
b.stoever [Fri, 3 Jul 2015 14:26:11 +0000 (14:26 +0000)]
AlignmentEditor.createTestContents() marked as deprecated.

7 years agoInternalError thrown, if a single read alignment shall be saved that contains new...
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.)

7 years agoError message added, if a pherogram URL loaded from CDM cannot be processed correctly.
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.

7 years agoFixed NPE, if a single read has a pherogram object without URI.
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.

7 years ago#5056 Adapt editor to service layer 'save' method refactoring in cdmlib
Cherian Mathew [Fri, 3 Jul 2015 10:04:00 +0000 (12:04 +0200)]
#5056 Adapt editor to service layer 'save' method refactoring in cdmlib

7 years agoAdjustments to recent changes in LibrAlign.
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.)

7 years agoMake editor compatible with latest cdmlib service layer updates
Cherian Mathew [Thu, 2 Jul 2015 09:15:14 +0000 (11:15 +0200)]
Make editor compatible with latest cdmlib service layer updates

7 years agoMinor changes in implementation of AlignmentEditor.
b.stoever [Wed, 1 Jul 2015 16:06:55 +0000 (16:06 +0000)]
Minor changes in implementation of AlignmentEditor.

7 years agoShowPherogramHandler now also handles single reads without attached pherograms.
b.stoever [Wed, 1 Jul 2015 16:03:18 +0000 (16:03 +0000)]
ShowPherogramHandler now also handles single reads without attached pherograms.

7 years agoFix compile error in FeatureDistributionDetailElement
Andreas Müller [Wed, 1 Jul 2015 15:44:43 +0000 (17:44 +0200)]
Fix compile error in FeatureDistributionDetailElement

7 years agoSupport for empty alignments and single reads without pherograms added to AlignmentEd...
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.

7 years agoClass path edited to include new modules from LibrAlign and TIC.
b.stoever [Wed, 1 Jul 2015 09:34:55 +0000 (09:34 +0000)]
Class path edited to include new modules from LibrAlign and TIC.

7 years agoAdjustments to recent architecture changes in TIC and LibrAlign. (TIC top level proje...
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

7 years agomerge-update from trunk
Patric Plitzner [Wed, 1 Jul 2015 09:09:33 +0000 (09:09 +0000)]
merge-update from trunk

7 years agoFix deletion of single reads in Derivative Editor
Patrick Plitzner [Wed, 1 Jul 2015 07:16:17 +0000 (09:16 +0200)]
Fix deletion of single reads in Derivative Editor

7 years agoAdd missing transient method
Patrick Plitzner [Wed, 1 Jul 2015 07:15:39 +0000 (09:15 +0200)]
Add missing transient method

7 years agoMap preparation materials to derivation event description
Patrick Plitzner [Wed, 1 Jul 2015 07:23:39 +0000 (09:23 +0200)]
Map preparation materials to derivation event description

7 years agomerge-update from trunk
Patric Plitzner [Tue, 30 Jun 2015 13:04:15 +0000 (13:04 +0000)]
merge-update from trunk

7 years agoMake background of icon transparent
Patrick Plitzner [Tue, 30 Jun 2015 11:47:51 +0000 (13:47 +0200)]
Make background of icon transparent

7 years agoAdd icon for switching to advanced media view
Patrick Plitzner [Mon, 29 Jun 2015 14:01:34 +0000 (16:01 +0200)]
Add icon for switching to advanced media view

7 years agomerge-update from trunk
Patric Plitzner [Mon, 29 Jun 2015 13:25:18 +0000 (13:25 +0000)]
merge-update from trunk

7 years agoUpdate transient services with new delete method
Cherian Mathew [Mon, 29 Jun 2015 12:52:58 +0000 (14:52 +0200)]
Update transient services with new delete method

7 years agomerge-update from trunk
Patric Plitzner [Mon, 29 Jun 2015 12:39:34 +0000 (12:39 +0000)]
merge-update from trunk

7 years agoShow abbreviated title cache for authors and refernce in taxon details
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

7 years agoShow URI parsing exceptions below URI text field (fixes #5055, #5003, #4587)
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)

7 years agoAvoid duplication of edited team member (#4997)
Patrick Plitzner [Wed, 24 Jun 2015 18:58:19 +0000 (20:58 +0200)]
Avoid duplication of edited team member (#4997)

7 years agoAdd no marker without a markerType (#4588)
Patrick Plitzner [Wed, 24 Jun 2015 19:39:38 +0000 (21:39 +0200)]
Add no marker without a markerType (#4588)

7 years agoAdd ticket number to TODO
Patrick Plitzner [Mon, 29 Jun 2015 11:41:37 +0000 (13:41 +0200)]
Add ticket number to TODO

7 years agoRefresh view after media view has been switched
Patrick Plitzner [Mon, 29 Jun 2015 10:15:24 +0000 (12:15 +0200)]
Refresh view after media view has been switched

7 years agoAdd MediaViewSwitch to media collection elements
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.

7 years agoAdd button for advanced media view to media attached to desccriptions
Patrick Plitzner [Mon, 29 Jun 2015 05:04:53 +0000 (07:04 +0200)]
Add button for advanced media view to media attached to desccriptions

7 years agoRemove duplicate code for advanced media view (#4862)
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.

7 years agoRemove comments
Patrick Plitzner [Sat, 27 Jun 2015 12:13:59 +0000 (14:13 +0200)]
Remove comments

7 years agoRemove comments
Patrick Plitzner [Wed, 24 Jun 2015 19:40:05 +0000 (21:40 +0200)]
Remove comments

7 years agoFix typo
Patrick Plitzner [Wed, 24 Jun 2015 12:18:47 +0000 (14:18 +0200)]
Fix typo

7 years ago#5036 Add missing command for polytomous key delete
Cherian Mathew [Fri, 26 Jun 2015 15:49:01 +0000 (17:49 +0200)]
#5036 Add missing command for polytomous key delete

7 years agoAdjustments to recent changes in TIC. (EDITor Code from now on written against unrele...
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.)

7 years agoFix remoting code compilation errors
Cherian Mathew [Thu, 25 Jun 2015 15:21:07 +0000 (17:21 +0200)]
Fix remoting code compilation errors

7 years agoMerge branch 'develop' of ssh://dev.e-taxonomy.eu/var/git/taxeditor into develop
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

7 years agoEmpty text fields return empty string and not null
Patrick Plitzner [Wed, 24 Jun 2015 12:19:43 +0000 (14:19 +0200)]
Empty text fields return empty string and not null

7 years agoRevert "index on develop: 6992bef Rename NonViralName authorteams to authorship ...
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.

7 years agoRename NonViralName authorteams to authorship #4968
Andreas Müller [Tue, 23 Jun 2015 16:34:38 +0000 (18:34 +0200)]
Rename NonViralName authorteams to authorship #4968

7 years agoUpdate cdmlib version to 3.6.3-SNAPSHOT
Cherian Mathew [Tue, 23 Jun 2015 16:22:30 +0000 (18:22 +0200)]
Update cdmlib version to 3.6.3-SNAPSHOT

7 years agoSome actions for adjusting pherogram displaying added.
b.stoever [Tue, 23 Jun 2015 15:58:31 +0000 (15:58 +0000)]
Some actions for adjusting pherogram displaying added.

7 years agoDelete renamed file
Cherian Mathew [Tue, 23 Jun 2015 12:45:38 +0000 (14:45 +0200)]
Delete renamed file

7 years agoPherogramViewPart that is started from within AlignmentEditor now uses a shared...
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.

7 years agoFix issues with merge conflicts
Cherian Mathew [Tue, 23 Jun 2015 11:01:02 +0000 (13:01 +0200)]
Fix issues with merge conflicts

7 years agoFixes from Katja for commit issue
Cherian Mathew [Tue, 23 Jun 2015 08:09:36 +0000 (10:09 +0200)]
Fixes from Katja for commit issue

7 years agoPosition properties of LibrAlign pherogram models are now connected to according...
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).

7 years agoFix problem with non persisted taxon titleCache change: #5018
Andreas Müller [Mon, 22 Jun 2015 14:35:17 +0000 (16:35 +0200)]
Fix problem with non persisted taxon titleCache change: #5018

7 years agoadapt service call to model change
Patrick Plitzner [Mon, 22 Jun 2015 13:50:09 +0000 (15:50 +0200)]
adapt service call to model change

7 years agoadapt transient service methods to cdmlib changes
Patrick Plitzner [Mon, 22 Jun 2015 13:49:50 +0000 (15:49 +0200)]
adapt transient service methods to cdmlib changes

7 years ago - update parent scroll form on property change (fixes #4881)
Patrick Plitzner [Mon, 22 Jun 2015 12:38:25 +0000 (14:38 +0200)]
 - update parent scroll form on property change (fixes #4881)

7 years ago - removed initial expand of sections
Patrick Plitzner [Mon, 22 Jun 2015 06:56:23 +0000 (08:56 +0200)]
 - removed initial expand of sections

7 years ago - fixed potential NPE
Patrick Plitzner [Mon, 22 Jun 2015 06:50:16 +0000 (08:50 +0200)]
 - fixed potential NPE

7 years ago - fixed potential NPE
Patrick Plitzner [Mon, 22 Jun 2015 05:54:33 +0000 (07:54 +0200)]
 - fixed potential NPE

7 years ago - changed type of "Materials & Methods" to text instead of DefinedTerm
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

7 years ago - split off "Preparation/Preservation section" from dna sample general
Patrick Plitzner [Wed, 17 Jun 2015 15:27:48 +0000 (17:27 +0200)]
 - split off "Preparation/Preservation section" from dna sample general
section

7 years agoAdjustments to recent changes in LibrAlign.
b.stoever [Mon, 22 Jun 2015 11:16:01 +0000 (11:16 +0000)]
Adjustments to recent changes in LibrAlign.

7 years agofixed conflicts from last commit
Cherian Mathew [Mon, 22 Jun 2015 09:31:26 +0000 (11:31 +0200)]
fixed conflicts from last commit

7 years agoall delete methods need an Uuid as argument
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

7 years agochange delete argument to UUID
Katja Luther [Thu, 18 Jun 2015 13:15:42 +0000 (15:15 +0200)]
change delete argument to UUID

7 years agoadd empty test folder
Andreas Müller [Fri, 19 Jun 2015 13:15:04 +0000 (15:15 +0200)]
add empty test folder

7 years agoActions for creating and updating the consensus sequence in AlignmentEditor implemented.
b.stoever [Fri, 19 Jun 2015 10:42:56 +0000 (10:42 +0000)]
Actions for creating and updating the consensus sequence in AlignmentEditor implemented.

7 years agoAbstractAlignmentEditorHandler added.
b.stoever [Fri, 19 Jun 2015 09:11:33 +0000 (09:11 +0000)]
AbstractAlignmentEditorHandler added.

7 years agoMerge remote-tracking branch 'origin/develop' into develop
Andreas Müller [Thu, 18 Jun 2015 13:22:24 +0000 (15:22 +0200)]
Merge remote-tracking branch 'origin/develop' into develop

7 years agominor
Andreas Müller [Thu, 18 Jun 2015 13:04:56 +0000 (15:04 +0200)]
minor

7 years agomerge-update from trunk
Patric Plitzner [Wed, 17 Jun 2015 13:52:06 +0000 (13:52 +0000)]
merge-update from trunk