taxeditor.git
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

7 years agoToggleInsertOverwriteHandler now also triggers enabling and disabling of ToggleLeftRi...
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.

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

7 years agofixing for compatibility with merged cdmlib
Cherian Mathew [Tue, 16 Jun 2015 11:53:53 +0000 (13:53 +0200)]
fixing for compatibility with merged cdmlib

7 years ago - added transient service methods
Patrick Plitzner [Mon, 15 Jun 2015 14:11:56 +0000 (16:11 +0200)]
 - added transient service methods

7 years agoadd empty folder
Andreas Müller [Mon, 15 Jun 2015 13:23:54 +0000 (15:23 +0200)]
add empty folder

7 years ago - fixed order of team members #4936
Patrick Plitzner [Mon, 15 Jun 2015 13:08:22 +0000 (15:08 +0200)]
 - fixed order of team members #4936

7 years ago - fixed NPE (#4937)
Patrick Plitzner [Mon, 15 Jun 2015 12:31:29 +0000 (14:31 +0200)]
 - fixed NPE (#4937)

7 years ago - removed inBetween target for Derivative Editor (fixes #4966)
Patrick Plitzner [Mon, 15 Jun 2015 10:46:37 +0000 (12:46 +0200)]
 - removed inBetween target for Derivative Editor (fixes #4966)

7 years agoIcons added for insert/overwrite button in AlignmentEditor tool bar.
b.stoever [Mon, 15 Jun 2015 08:52:23 +0000 (08:52 +0000)]
Icons added for insert/overwrite button in AlignmentEditor tool bar.
Insert left/right in pherogram disabled when switching to overwrite mode.

7 years ago - removed test folder
Patrick Plitzner [Mon, 15 Jun 2015 07:56:34 +0000 (09:56 +0200)]
 - removed test folder

7 years agoMerge branch 'develop' of https://dev.e-taxonomy.eu/git/taxeditor into develop
Patrick Plitzner [Mon, 15 Jun 2015 07:49:29 +0000 (09:49 +0200)]
Merge branch 'develop' of https://dev.e-taxonomy.eu/git/taxeditor into develop

7 years ago - removed test folder from classpatch
pplitzner [Mon, 15 Jun 2015 07:46:19 +0000 (09:46 +0200)]
 - removed test folder from classpatch

7 years agoAdjustments to recent changes in LibrAlign.
b.stoever [Sun, 14 Jun 2015 13:17:33 +0000 (13:17 +0000)]
Adjustments to recent changes in LibrAlign.

7 years agofix umlaute in key menus and add gitignore for rcp.target
Andreas Müller [Fri, 12 Jun 2015 15:37:21 +0000 (17:37 +0200)]
fix umlaute in key menus and add gitignore for rcp.target

7 years agoFurther adjustments to recent changes in LibrAlign.
b.stoever [Thu, 11 Jun 2015 13:39:20 +0000 (13:39 +0000)]
Further adjustments to recent changes in LibrAlign.

7 years agoAdjustments to recent changes in LibrAlign.
b.stoever [Mon, 8 Jun 2015 14:50:39 +0000 (14:50 +0000)]
Adjustments to recent changes in LibrAlign.

7 years agomerge-update from trunk
Patric Plitzner [Mon, 8 Jun 2015 11:57:53 +0000 (11:57 +0000)]
merge-update from trunk

7 years agomerge-update from trunk
Patric Plitzner [Mon, 8 Jun 2015 11:46:40 +0000 (11:46 +0000)]
merge-update from trunk

7 years agofixed manifest versions
Cherian Mathew [Mon, 8 Jun 2015 11:00:15 +0000 (13:00 +0200)]
fixed manifest versions

7 years agonew .gitignore file
Cherian Mathew [Mon, 8 Jun 2015 10:22:13 +0000 (12:22 +0200)]
new .gitignore file

7 years agoremoved test source from classpath
Cherian Mathew [Mon, 8 Jun 2015 10:20:28 +0000 (12:20 +0200)]
removed test source from classpath

7 years agofixed update to snapshot
Cherian Mathew [Mon, 8 Jun 2015 10:13:56 +0000 (12:13 +0200)]
fixed update to snapshot

7 years agocorrected cdmlib version to snapshot
Cherian Mathew [Mon, 8 Jun 2015 08:26:47 +0000 (10:26 +0200)]
corrected cdmlib version to snapshot

7 years agoUpdating develop poms back to pre merge state
Cherian Mathew [Fri, 5 Jun 2015 16:16:58 +0000 (18:16 +0200)]
Updating develop poms back to pre merge state

7 years agoMerge branch 'master' into develop
Cherian Mathew [Fri, 5 Jun 2015 16:16:57 +0000 (18:16 +0200)]
Merge branch 'master' into develop

7 years agoUpdating develop poms to hotfix version to avoid merge conflicts
Cherian Mathew [Fri, 5 Jun 2015 16:16:57 +0000 (18:16 +0200)]
Updating develop poms to hotfix version to avoid merge conflicts

7 years agoMerge branch 'hotfix/3.6.1'
Cherian Mathew [Fri, 5 Jun 2015 16:16:56 +0000 (18:16 +0200)]
Merge branch 'hotfix/3.6.1'

7 years agoupdating poms for branch'hotfix/3.6.1' with non-snapshot versions
Cherian Mathew [Fri, 5 Jun 2015 16:16:54 +0000 (18:16 +0200)]
updating poms for branch'hotfix/3.6.1' with non-snapshot versions

7 years agoversion updates for 3.6.1
Cherian Mathew [Fri, 5 Jun 2015 16:15:54 +0000 (18:15 +0200)]
version updates for 3.6.1

7 years agoupdating poms for branch '3.6.1' with snapshot versions
Cherian Mathew [Fri, 5 Jun 2015 15:55:12 +0000 (17:55 +0200)]
updating poms for branch '3.6.1' with snapshot versions

7 years agofixing classpath config
Cherian Mathew [Fri, 5 Jun 2015 15:53:49 +0000 (17:53 +0200)]
fixing classpath config

7 years agofixing classpath config
Cherian Mathew [Fri, 5 Jun 2015 15:51:50 +0000 (17:51 +0200)]
fixing classpath config

7 years agoRelease 3.6.0 merge root/tags/taxeditor/3.6.0 3.6.0
Cherian Mathew [Fri, 5 Jun 2015 14:42:11 +0000 (16:42 +0200)]
Release 3.6.0 merge

7 years agomerged jgitfow plugin
Cherian Mathew [Fri, 5 Jun 2015 14:31:17 +0000 (16:31 +0200)]
merged jgitfow plugin

7 years agomerged for gitflow plugin
Cherian Mathew [Fri, 5 Jun 2015 14:12:48 +0000 (16:12 +0200)]
merged for gitflow plugin

7 years agoadded jgitflow plugin
Cherian Mathew [Fri, 5 Jun 2015 14:07:00 +0000 (16:07 +0200)]
added jgitflow plugin

7 years ago - updating versions due to release
Patric Plitzner [Thu, 4 Jun 2015 16:43:56 +0000 (16:43 +0000)]
 - updating versions due to release

7 years agoupdated to snapshot version
Cherian Mathew [Thu, 4 Jun 2015 13:55:14 +0000 (15:55 +0200)]
updated to snapshot version

Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/taxeditor into develop

Conflicts:
eu.etaxonomy.taxeditor.cdmlib/.classpath

7 years agoUpdated version in config files to 3.6.1-SNAPSHOT attic/trunk/taxeditor/24113
edit-jenkins [Thu, 4 Jun 2015 13:49:43 +0000 (13:49 +0000)]
Updated version in config files to 3.6.1-SNAPSHOT

7 years agoMerge branch 'move-to-luna' of wp5.e-taxonomy.eu:/var/git/taxeditor into develop
Cherian Mathew [Thu, 4 Jun 2015 13:30:07 +0000 (15:30 +0200)]
Merge branch 'move-to-luna' of wp5.e-taxonomy.eu:/var/git/taxeditor into develop

Conflicts:
eu.etaxonomy.taxeditor.cdmlib/.classpath

7 years agoUpdated version in config files to 3.6.0
edit-jenkins [Thu, 4 Jun 2015 12:58:53 +0000 (12:58 +0000)]
Updated version in config files to 3.6.0

7 years ago - added wizard page listener to react on ENTER key #4853
Patric Plitzner [Thu, 4 Jun 2015 11:23:45 +0000 (11:23 +0000)]
 - added wizard page listener to react on ENTER key #4853

7 years ago - added wizard page listener to react on ENTER key #4853
Patric Plitzner [Thu, 4 Jun 2015 10:57:39 +0000 (10:57 +0000)]
 - added wizard page listener to react on ENTER key #4853

7 years ago - added context menu entry for editing classifications
Patric Plitzner [Thu, 4 Jun 2015 10:54:32 +0000 (10:54 +0000)]
 - added context menu entry for editing classifications
 - used generic extension point for cdmViewer in navigation project (#4865)