Katja Luther [Tue, 17 Jan 2017 09:59:43 +0000 (10:59 +0100)]
fix #5365: add delete configuration to media view
Patrick Plitzner [Fri, 13 Jan 2017 15:35:17 +0000 (16:35 +0100)]
remove unused bin.include
Patrick Plitzner [Fri, 13 Jan 2017 15:02:43 +0000 (16:02 +0100)]
Saving files before refreshing line endings
Patrick Plitzner [Fri, 13 Jan 2017 14:32:31 +0000 (15:32 +0100)]
Merge branch 'develop' into LibrAlign
b.stoever [Fri, 13 Jan 2017 14:11:20 +0000 (15:11 +0100)]
Alternative versions for build.properties added. Current state set to "dependencies from JARs". (Can be merged to trunk in this state.)
Patrick Plitzner [Fri, 13 Jan 2017 12:51:58 +0000 (13:51 +0100)]
ref #5495 always empty details view when there is no active editor
providing a selection
b.stoever [Fri, 13 Jan 2017 12:33:36 +0000 (13:33 +0100)]
pom.xml and MANIFEST.MF updated in molecular.lib.
b.stoever [Fri, 13 Jan 2017 11:08:26 +0000 (12:08 +0100)]
Adjustments to project structure changes in JPhyloIO.
Patrick Plitzner [Fri, 13 Jan 2017 08:25:09 +0000 (09:25 +0100)]
ref #6158 Add missing git clone command to doc
Patrick Plitzner [Thu, 12 Jan 2017 16:48:11 +0000 (17:48 +0100)]
fix #6158 updated taxeditor installation documentation
Andreas Müller [Thu, 12 Jan 2017 22:57:40 +0000 (23:57 +0100)]
fix #5922 Move extensions section down
Andreas Müller [Thu, 12 Jan 2017 22:56:58 +0000 (23:56 +0100)]
cleanup
Katja Luther [Thu, 12 Jan 2017 15:49:28 +0000 (16:49 +0100)]
fix #5671: add filter element for selection dialog
Patrick Plitzner [Tue, 10 Jan 2017 15:45:06 +0000 (16:45 +0100)]
ref #6320 show pherogram title cache in single read label
Patrick Plitzner [Tue, 10 Jan 2017 15:25:07 +0000 (16:25 +0100)]
Fix icon for media derivative
Patrick Plitzner [Tue, 10 Jan 2017 14:06:19 +0000 (15:06 +0100)]
fix #6307 Show contextPath in error log
Patrick Plitzner [Tue, 10 Jan 2017 13:39:14 +0000 (14:39 +0100)]
Removed unused import
Katja Luther [Tue, 10 Jan 2017 12:57:43 +0000 (13:57 +0100)]
fix #4246: move insert node and create new key node to one menu item with submenu
Patrick Plitzner [Fri, 6 Jan 2017 15:40:11 +0000 (16:40 +0100)]
fix #5488 show only zoological nomenclatural status types not for
botanical names
- also dis some refactoring
Patrick Plitzner [Fri, 6 Jan 2017 14:49:36 +0000 (15:49 +0100)]
fix #5495 DetailsView is emptied when upon context stop i.e. when the
connection is shut down
Patrick Plitzner [Fri, 6 Jan 2017 13:36:44 +0000 (14:36 +0100)]
fix #5714 Add possibility for adding a comparator to EnumComboElement
- for Sources always have PrimaryTaxonomicSource or PrimaryMediaSource
on top depending on IdentifiableSource
Patrick Plitzner [Fri, 6 Jan 2017 10:08:09 +0000 (11:08 +0100)]
fix #5474 moved Feature and NamedArea to top level
- remaining terms are under "Other..."
Patrick Plitzner [Fri, 6 Jan 2017 07:56:28 +0000 (08:56 +0100)]
fix #5698 Duplicate ampersand to avoid conversion to mnemonic
Patrick Plitzner [Fri, 6 Jan 2017 07:39:55 +0000 (08:39 +0100)]
fix #5922 Move credits and rights section to the bottom
Katja Luther [Wed, 4 Jan 2017 14:03:37 +0000 (15:03 +0100)]
fix #4821: create OrderedTermvoc for OrderedTerms
Patrick Plitzner [Thu, 22 Dec 2016 10:09:14 +0000 (11:09 +0100)]
Fix possible NPE
Andreas Kohlbecker [Tue, 20 Dec 2016 13:28:24 +0000 (14:28 +0100)]
ref #6190 removing svn property place holder in first line of code - java files
Andreas Kohlbecker [Tue, 20 Dec 2016 13:22:26 +0000 (14:22 +0100)]
ref #6190 removing svn property place holder in first line of code - java files
Katja Luther [Tue, 20 Dec 2016 12:03:45 +0000 (13:03 +0100)]
missing changes
Katja Luther [Tue, 20 Dec 2016 11:54:30 +0000 (12:54 +0100)]
minor
Katja Luther [Tue, 20 Dec 2016 11:50:35 +0000 (12:50 +0100)]
minor to fix failing jenkins
Katja Luther [Mon, 19 Dec 2016 15:16:46 +0000 (16:16 +0100)]
more changes for configurable name details view
Katja Luther [Mon, 19 Dec 2016 15:14:51 +0000 (16:14 +0100)]
adaptions for polytomous key editing to avoid null values in children list
Katja Luther [Mon, 19 Dec 2016 15:04:23 +0000 (16:04 +0100)]
ref #6105: add name details view configuration to the cdm preferences view
Katja Luther [Mon, 19 Dec 2016 14:58:13 +0000 (15:58 +0100)]
deduplicate the nomenclatural code preference page in preferences menu
Katja Luther [Thu, 8 Dec 2016 10:57:34 +0000 (11:57 +0100)]
ref #4766: remove apply and restore defaults buttons
Katja Luther [Thu, 8 Dec 2016 10:31:19 +0000 (11:31 +0100)]
ref #4766: sortindex updater integration in admin menu
jenkins [Wed, 7 Dec 2016 12:26:21 +0000 (13:26 +0100)]
Merge branch 'hotfix/4.4.1' into develop
jenkins [Tue, 6 Dec 2016 14:40:57 +0000 (15:40 +0100)]
Updated version in pom / project files to taxeditor version : 4.4.1 and cdmlib version : 4.4.1
jenkins [Mon, 5 Dec 2016 15:19:08 +0000 (16:19 +0100)]
Merge branch 'release/4.4.0' into develop
jenkins [Mon, 5 Dec 2016 15:19:07 +0000 (16:19 +0100)]
Merge branch 'release/4.4.0'
jenkins [Mon, 5 Dec 2016 14:50:39 +0000 (15:50 +0100)]
Updated version in pom / project files to taxeditor version : 4.5.0-SNAPSHOT and cdmlib version : 4.5.0-SNAPSHOT
jenkins [Mon, 5 Dec 2016 14:50:34 +0000 (15:50 +0100)]
Updated version in pom / project files to taxeditor version : 4.4.0 and cdmlib version : 4.4.0
Katja Luther [Mon, 5 Dec 2016 09:41:23 +0000 (10:41 +0100)]
fix #6218: avoid NPE when remove text from label field
Andreas Müller [Thu, 1 Dec 2016 15:02:15 +0000 (16:02 +0100)]
fix #5971 fix NPE for not existing preference
Andreas Müller [Thu, 1 Dec 2016 14:46:12 +0000 (15:46 +0100)]
cleanup
Patrick Plitzner [Thu, 1 Dec 2016 14:37:57 +0000 (15:37 +0100)]
ref #6199 Move "open in editor" option to the bottom
Katja Luther [Thu, 1 Dec 2016 10:55:12 +0000 (11:55 +0100)]
add missing files
Katja Luther [Thu, 1 Dec 2016 08:14:09 +0000 (09:14 +0100)]
avoid NPE when reusing taxonname for taxon creation
Katja Luther [Fri, 25 Nov 2016 11:58:15 +0000 (12:58 +0100)]
ref #6219: add warning that synonym is deleted immediately
Patrick Plitzner [Thu, 24 Nov 2016 13:50:50 +0000 (14:50 +0100)]
l10n for PresenceAbsenceTermDetailElement
Patrick Plitzner [Thu, 24 Nov 2016 13:27:33 +0000 (14:27 +0100)]
ref #6216 Added button to select color instead of clicking on color
field
- resized color field
Patrick Plitzner [Thu, 24 Nov 2016 13:26:42 +0000 (14:26 +0100)]
Align label to the middle
Katja Luther [Thu, 24 Nov 2016 12:41:57 +0000 (13:41 +0100)]
fix #4945: add propertytester for polytomouskeynode to enable menu items only if node is selected
Katja Luther [Thu, 24 Nov 2016 12:37:20 +0000 (13:37 +0100)]
fix #5971: move admin menu in front of Help
Andreas Müller [Thu, 24 Nov 2016 11:18:52 +0000 (12:18 +0100)]
Adapt labels for taxon node agent relation editing
Patrick Plitzner [Thu, 24 Nov 2016 09:25:55 +0000 (10:25 +0100)]
ref #6216 Pre-select color in ColorDialog
Patrick Plitzner [Thu, 24 Nov 2016 09:22:05 +0000 (10:22 +0100)]
fix #6216 Implement color dialog to change color of presence absence
terms
Katja Luther [Thu, 24 Nov 2016 08:52:40 +0000 (09:52 +0100)]
all polytomouskey related handler are now extended from RemotingCdmHandler
Katja Luther [Wed, 23 Nov 2016 14:04:13 +0000 (15:04 +0100)]
fix #5841: set selection to newly created keynode
Katja Luther [Wed, 23 Nov 2016 13:54:51 +0000 (14:54 +0100)]
fix #6215: check for datasource when opening preferencepage
Katja Luther [Wed, 23 Nov 2016 09:22:12 +0000 (10:22 +0100)]
fix #5971: admin menu is visible only if connected and user has role manager
Katja Luther [Mon, 21 Nov 2016 14:56:35 +0000 (15:56 +0100)]
fix #6209: adapt the message if a datasource is not available
b.stoever [Sat, 19 Nov 2016 12:29:13 +0000 (13:29 +0100)]
Additional strings externalized in molecular plugin.
Wizard for exporting single read alignments now warns and prompts if files are overwritten.
Bug fix: Changes in the format selection in the wizard now trigger validation again.
ExportSingleReadAlignmentWizardModel uses format list instead of map again.
Katja Luther [Fri, 18 Nov 2016 17:20:27 +0000 (18:20 +0100)]
ref #5971: new main menu admin with cdm preference nomenclatural code and insert polytomous key node
b.stoever [Fri, 18 Nov 2016 16:01:41 +0000 (17:01 +0100)]
Messages edited.
Support for parameters to export only single reads or only consensus implemented.
JavaDoc extended.
b.stoever [Fri, 18 Nov 2016 14:45:02 +0000 (15:45 +0100)]
Missing files from last commit added.
b.stoever [Fri, 18 Nov 2016 14:43:45 +0000 (15:43 +0100)]
Export single read alignment wizard separated into two pages.
Option to elongate sequences added.
Application information parameters of JPhyloIO set.
b.stoever [Thu, 17 Nov 2016 18:17:38 +0000 (19:17 +0100)]
Exported single read sequences are now filled up with gaps. (Will be dependent on a parameter in the future.)
Texts in ExportSequenceToFileHandler extzernalized and translated.
b.stoever [Thu, 17 Nov 2016 16:22:59 +0000 (17:22 +0100)]
Strings in ExportSingleReadAlignmentWizardPage externalized and translated.
Ben Stöver [Thu, 17 Nov 2016 12:40:59 +0000 (13:40 +0100)]
Fixes in ExportSingleReadAlignmentWizardPage layout.
Default values added to ExportSingleReadAlignmentWizardModel.
Updating values after model binding in ExportSingleReadAlignmentWizardPage implemented.
Patrick Plitzner [Thu, 17 Nov 2016 09:09:19 +0000 (10:09 +0100)]
ref #6198 removed synonym type combobox
Patrick Plitzner [Thu, 17 Nov 2016 09:06:17 +0000 (10:06 +0100)]
ref #6198 Correctly initialise ui field for pro parte and partial
Patrick Plitzner [Thu, 17 Nov 2016 09:05:40 +0000 (10:05 +0100)]
ref #6205 Move excluded notes to the bottom of the wizard
b.stoever [Wed, 16 Nov 2016 22:18:26 +0000 (23:18 +0100)]
Export single read alignment wizard validation refactored and extended.
Some German translations in molecular plug-in added.
b.stoever [Wed, 16 Nov 2016 20:25:30 +0000 (21:25 +0100)]
Intermediate commit in implementing wizard validation (before moving to MultiValidator).
Plug-in dependencies added to molecular.
Patrick Plitzner [Tue, 15 Nov 2016 16:27:52 +0000 (17:27 +0100)]
fix #6199 Excluded note for excluded taxon nodes in TaxEditor
b.stoever [Tue, 15 Nov 2016 16:09:30 +0000 (17:09 +0100)]
ExportSingleReadAlignmentWizard now exposes whole format info object.
FileDialog added to ExportSingleReadAlignmentWizardPage.
Patrick Plitzner [Tue, 15 Nov 2016 14:11:23 +0000 (15:11 +0100)]
Clean up Derivate perspective
- Remove Derivate view as it is not a view but an editor (they have
their own designated area)
Patrick Plitzner [Tue, 15 Nov 2016 14:10:12 +0000 (15:10 +0100)]
Fix potential NPE
Patrick Plitzner [Tue, 15 Nov 2016 09:50:49 +0000 (10:50 +0100)]
fix #6198 Remove synonymrelationships in TaxEditor
Patrick Plitzner [Tue, 15 Nov 2016 09:12:29 +0000 (10:12 +0100)]
fix #6197 Move excluded and unplaced from Taxon to TaxonNode in
TaxEditor
Patrick Plitzner [Tue, 15 Nov 2016 08:47:38 +0000 (09:47 +0100)]
Fix possible widget is disposed exception
Patrick Plitzner [Tue, 15 Nov 2016 08:35:16 +0000 (09:35 +0100)]
Fix potential NPE
b.stoever [Mon, 14 Nov 2016 18:34:40 +0000 (19:34 +0100)]
Missing dependency Apache commons.lang added to molecular.lib.
Single read alignment export feature now makes use of wizard. (Selecting which sequences to export is not yet supported.)
b.stoever [Mon, 14 Nov 2016 16:34:28 +0000 (17:34 +0100)]
New JPhyloIO package now exported by molecular.lib.
SingleReadAlignmentPredicates renamed to SingleReadAlignmentRDFXMLConstants.
Pherogram alignment shifts are now written to single read export unsing a custom ObjectTranslator implementation.
Andreas Müller [Mon, 14 Nov 2016 15:12:53 +0000 (16:12 +0100)]
cleanup
Andreas Müller [Mon, 14 Nov 2016 15:12:40 +0000 (16:12 +0100)]
Move MoveTaxonOperationTest to navigation package and try to enable
Andreas Müller [Mon, 14 Nov 2016 13:38:03 +0000 (14:38 +0100)]
ref #5875 fix testdata in TaxEditor
Andreas Müller [Mon, 14 Nov 2016 13:27:54 +0000 (14:27 +0100)]
ref #5875 fix testdata in TaxEditor
Andreas Müller [Mon, 14 Nov 2016 13:26:39 +0000 (14:26 +0100)]
add gitignore
Andreas Müller [Mon, 14 Nov 2016 13:13:32 +0000 (14:13 +0100)]
ref #3925 fix testdata in TaxEditor
Andreas Müller [Mon, 14 Nov 2016 13:01:45 +0000 (14:01 +0100)]
ref #3925 fix testdata in TaxEditor
Andreas Müller [Mon, 14 Nov 2016 12:39:03 +0000 (13:39 +0100)]
ref #3925 fix testdata in TaxEditor
Andreas Müller [Mon, 14 Nov 2016 12:38:46 +0000 (13:38 +0100)]
Clean up
Andreas Müller [Mon, 14 Nov 2016 12:20:22 +0000 (13:20 +0100)]
ref #3925 fix testdata in TaxEditor
Andreas Müller [Mon, 14 Nov 2016 12:19:38 +0000 (13:19 +0100)]
clean up
Andreas Müller [Mon, 14 Nov 2016 12:19:13 +0000 (13:19 +0100)]
Add dataset.dtd to TaxEditor test data
Andreas Müller [Mon, 14 Nov 2016 09:57:18 +0000 (10:57 +0100)]
Try to reinstall tests for MoveTaxonOperation (maybe not yet correct)
Andreas Müller [Mon, 14 Nov 2016 09:56:33 +0000 (10:56 +0100)]
Cleanup