taxeditor.git
4 years agoUpdated version in pom / project files to taxeditor version : 4.5.0 and cdmlib versio...
jenkins [Thu, 19 Jan 2017 10:54:35 +0000 (11:54 +0100)]
Updated version in pom / project files to taxeditor version : 4.5.0 and cdmlib version : 4.5.0

4 years agomissed to add some selection dialogs with last commit
Katja Luther [Thu, 19 Jan 2017 10:44:16 +0000 (11:44 +0100)]
missed to add some selection dialogs with last commit

4 years agofix #6342: fix exception when using ? in selection dialog
Katja Luther [Thu, 19 Jan 2017 09:39:41 +0000 (10:39 +0100)]
fix #6342: fix exception when using ? in selection dialog

4 years agoref #5474 other -> others
Andreas Müller [Wed, 18 Jan 2017 22:35:16 +0000 (23:35 +0100)]
ref #5474 other -> others

4 years agoref #5714 Fix ordering of source types
Patrick Plitzner [Wed, 18 Jan 2017 16:54:12 +0000 (17:54 +0100)]
ref #5714 Fix ordering of source types

 - order by key instead of message
 - always have either taxonomic or media source as first and the other
as second

4 years agoref #6283 Fixed potential NPE for EntitySelectionElement
Patrick Plitzner [Wed, 18 Jan 2017 15:23:01 +0000 (16:23 +0100)]
ref #6283 Fixed potential NPE for EntitySelectionElement

 - refactored constructors to always initialise the clazz variable

4 years agofix #5496 Refactor preference pages to use TermType
Patrick Plitzner [Wed, 18 Jan 2017 13:49:48 +0000 (14:49 +0100)]
fix #5496 Refactor preference pages to use TermType

4 years agoref #6333 Remove framework for exchanging an element in the details view
Patrick Plitzner [Wed, 18 Jan 2017 08:28:54 +0000 (09:28 +0100)]
ref #6333 Remove framework for exchanging an element in the details view

 - This is against the concept of the DetailsView just showing an
element which you can edit. Changing the element requires the
DetailsView to know where the element comes from

4 years agoref #6333 Add generic support for entity collection sections to allow
Patrick Plitzner [Wed, 18 Jan 2017 08:16:01 +0000 (09:16 +0100)]
ref #6333 Add generic support for entity collection sections to allow
adding existing entities

 - this is done by two abstract methods allowAddExisting() and
addExisting()

4 years agoref #6307 remove cdmserver/ from contextpath
Andreas Müller [Tue, 17 Jan 2017 22:42:10 +0000 (23:42 +0100)]
ref #6307 remove cdmserver/ from contextpath

4 years agoref #5922 Change order in supplemental data view (cont.)
Andreas Müller [Tue, 17 Jan 2017 22:29:55 +0000 (23:29 +0100)]
ref #5922 Change order in supplemental data view (cont.)

4 years agominor
Katja Luther [Tue, 17 Jan 2017 10:57:44 +0000 (11:57 +0100)]
minor

4 years agofix #6334: unsaved description needs to be removed from the taxon
Katja Luther [Tue, 17 Jan 2017 10:56:14 +0000 (11:56 +0100)]
fix #6334: unsaved description needs to be removed from the taxon

4 years agoadd missing changes
Katja Luther [Tue, 17 Jan 2017 10:52:49 +0000 (11:52 +0100)]
add missing changes

4 years agominor
Katja Luther [Tue, 17 Jan 2017 10:46:35 +0000 (11:46 +0100)]
minor

4 years agofix #5365: add delete configuration to media view
Katja Luther [Tue, 17 Jan 2017 09:59:43 +0000 (10:59 +0100)]
fix #5365: add delete configuration to media view

4 years agoremove unused bin.include
Patrick Plitzner [Fri, 13 Jan 2017 15:35:17 +0000 (16:35 +0100)]
remove unused bin.include

4 years agoSaving files before refreshing line endings
Patrick Plitzner [Fri, 13 Jan 2017 15:02:43 +0000 (16:02 +0100)]
Saving files before refreshing line endings

4 years agoMerge branch 'develop' into LibrAlign
Patrick Plitzner [Fri, 13 Jan 2017 14:32:31 +0000 (15:32 +0100)]
Merge branch 'develop' into LibrAlign

4 years agoAlternative versions for build.properties added. Current state set to "dependencies...
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.)

4 years agoref #5495 always empty details view when there is no active editor
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

4 years agopom.xml and MANIFEST.MF updated in molecular.lib.
b.stoever [Fri, 13 Jan 2017 12:33:36 +0000 (13:33 +0100)]
pom.xml and MANIFEST.MF updated in molecular.lib.

4 years agoAdjustments to project structure changes in JPhyloIO.
b.stoever [Fri, 13 Jan 2017 11:08:26 +0000 (12:08 +0100)]
Adjustments to project structure changes in JPhyloIO.

4 years agoref #6158 Add missing git clone command to doc
Patrick Plitzner [Fri, 13 Jan 2017 08:25:09 +0000 (09:25 +0100)]
ref #6158 Add missing git clone command to doc

4 years agofix #6158 updated taxeditor installation documentation
Patrick Plitzner [Thu, 12 Jan 2017 16:48:11 +0000 (17:48 +0100)]
fix #6158 updated taxeditor installation documentation

4 years agofix #5922 Move extensions section down
Andreas Müller [Thu, 12 Jan 2017 22:57:40 +0000 (23:57 +0100)]
fix #5922 Move extensions section down

4 years agocleanup
Andreas Müller [Thu, 12 Jan 2017 22:56:58 +0000 (23:56 +0100)]
cleanup

4 years agofix #5671: add filter element for selection dialog
Katja Luther [Thu, 12 Jan 2017 15:49:28 +0000 (16:49 +0100)]
fix #5671: add filter element for selection dialog

4 years agoref #6320 show pherogram title cache in single read label
Patrick Plitzner [Tue, 10 Jan 2017 15:45:06 +0000 (16:45 +0100)]
ref #6320 show pherogram title cache in single read label

4 years agoFix icon for media derivative
Patrick Plitzner [Tue, 10 Jan 2017 15:25:07 +0000 (16:25 +0100)]
Fix icon for media derivative

4 years agofix #6307 Show contextPath in error log
Patrick Plitzner [Tue, 10 Jan 2017 14:06:19 +0000 (15:06 +0100)]
fix #6307 Show contextPath in error log

4 years agoRemoved unused import
Patrick Plitzner [Tue, 10 Jan 2017 13:39:14 +0000 (14:39 +0100)]
Removed unused import

4 years agofix #4246: move insert node and create new key node to one menu item with submenu
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

4 years agofix #5488 show only zoological nomenclatural status types not for
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

4 years agofix #5495 DetailsView is emptied when upon context stop i.e. when the
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

4 years agofix #5714 Add possibility for adding a comparator to EnumComboElement
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

4 years agofix #5474 moved Feature and NamedArea to top level
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..."

4 years agofix #5698 Duplicate ampersand to avoid conversion to mnemonic
Patrick Plitzner [Fri, 6 Jan 2017 07:56:28 +0000 (08:56 +0100)]
fix #5698 Duplicate ampersand to avoid conversion to mnemonic

4 years agofix #5922 Move credits and rights section to the bottom
Patrick Plitzner [Fri, 6 Jan 2017 07:39:55 +0000 (08:39 +0100)]
fix #5922 Move credits and rights section to the bottom

4 years agofix #4821: create OrderedTermvoc for OrderedTerms
Katja Luther [Wed, 4 Jan 2017 14:03:37 +0000 (15:03 +0100)]
fix #4821: create OrderedTermvoc for OrderedTerms

4 years agoFix possible NPE
Patrick Plitzner [Thu, 22 Dec 2016 10:09:14 +0000 (11:09 +0100)]
Fix possible NPE

4 years agoref #6190 removing svn property place holder in first line of code - java files
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

4 years agoref #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

4 years agomissing changes
Katja Luther [Tue, 20 Dec 2016 12:03:45 +0000 (13:03 +0100)]
missing changes

4 years agominor
Katja Luther [Tue, 20 Dec 2016 11:54:30 +0000 (12:54 +0100)]
minor

4 years agominor to fix failing jenkins
Katja Luther [Tue, 20 Dec 2016 11:50:35 +0000 (12:50 +0100)]
minor to fix failing jenkins

4 years agomore changes for configurable name details view
Katja Luther [Mon, 19 Dec 2016 15:16:46 +0000 (16:16 +0100)]
more changes for configurable name details view

4 years agoadaptions for polytomous key editing to avoid null values in children list
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

4 years agoref #6105: add name details view configuration to the cdm preferences view
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

4 years agodeduplicate the nomenclatural code preference page in preferences menu
Katja Luther [Mon, 19 Dec 2016 14:58:13 +0000 (15:58 +0100)]
deduplicate the nomenclatural code preference page in preferences menu

4 years agoref #4766: remove apply and restore defaults buttons
Katja Luther [Thu, 8 Dec 2016 10:57:34 +0000 (11:57 +0100)]
ref #4766: remove apply and restore defaults buttons

4 years agoref #4766: sortindex updater integration in admin menu
Katja Luther [Thu, 8 Dec 2016 10:31:19 +0000 (11:31 +0100)]
ref #4766: sortindex updater integration in admin menu

4 years agoMerge branch 'hotfix/4.4.1' into develop
jenkins [Wed, 7 Dec 2016 12:26:21 +0000 (13:26 +0100)]
Merge branch 'hotfix/4.4.1' into develop

4 years agoUpdated version in pom / project files to taxeditor version : 4.4.1 and cdmlib versio...
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

4 years agoMerge branch 'release/4.4.0' into develop
jenkins [Mon, 5 Dec 2016 15:19:08 +0000 (16:19 +0100)]
Merge branch 'release/4.4.0' into develop

4 years agoMerge branch 'release/4.4.0' 4.4.0
jenkins [Mon, 5 Dec 2016 15:19:07 +0000 (16:19 +0100)]
Merge branch 'release/4.4.0'

4 years agoUpdated version in pom / project files to taxeditor version : 4.5.0-SNAPSHOT and...
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

4 years agoUpdated version in pom / project files to taxeditor version : 4.4.0 and cdmlib versio...
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

4 years agofix #6218: avoid NPE when remove text from label field
Katja Luther [Mon, 5 Dec 2016 09:41:23 +0000 (10:41 +0100)]
fix #6218: avoid NPE when remove text from label field

5 years agofix #5971 fix NPE for not existing preference
Andreas Müller [Thu, 1 Dec 2016 15:02:15 +0000 (16:02 +0100)]
fix #5971 fix NPE for not existing preference

5 years agocleanup
Andreas Müller [Thu, 1 Dec 2016 14:46:12 +0000 (15:46 +0100)]
cleanup

5 years agoref #6199 Move "open in editor" option to the bottom
Patrick Plitzner [Thu, 1 Dec 2016 14:37:57 +0000 (15:37 +0100)]
ref #6199 Move "open in editor" option to the bottom

5 years agoadd missing files
Katja Luther [Thu, 1 Dec 2016 10:55:12 +0000 (11:55 +0100)]
add missing files

5 years agoavoid NPE when reusing taxonname for taxon creation
Katja Luther [Thu, 1 Dec 2016 08:14:09 +0000 (09:14 +0100)]
avoid NPE when reusing taxonname for taxon creation

5 years agoref #6219: add warning that synonym is deleted immediately
Katja Luther [Fri, 25 Nov 2016 11:58:15 +0000 (12:58 +0100)]
ref #6219: add warning that synonym is deleted immediately

5 years agol10n for PresenceAbsenceTermDetailElement
Patrick Plitzner [Thu, 24 Nov 2016 13:50:50 +0000 (14:50 +0100)]
l10n for PresenceAbsenceTermDetailElement

5 years agoref #6216 Added button to select color instead of clicking on color
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

5 years agoAlign label to the middle
Patrick Plitzner [Thu, 24 Nov 2016 13:26:42 +0000 (14:26 +0100)]
Align label to the middle

5 years agofix #4945: add propertytester for polytomouskeynode to enable menu items only if...
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

5 years agofix #5971: move admin menu in front of Help
Katja Luther [Thu, 24 Nov 2016 12:37:20 +0000 (13:37 +0100)]
fix #5971: move admin menu in front of Help

5 years agoAdapt labels for taxon node agent relation editing
Andreas Müller [Thu, 24 Nov 2016 11:18:52 +0000 (12:18 +0100)]
Adapt labels for taxon node agent relation editing

5 years agoref #6216 Pre-select color in ColorDialog
Patrick Plitzner [Thu, 24 Nov 2016 09:25:55 +0000 (10:25 +0100)]
ref #6216 Pre-select color in ColorDialog

5 years agofix #6216 Implement color dialog to change color of presence absence
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

5 years agoall polytomouskey related handler are now extended from RemotingCdmHandler
Katja Luther [Thu, 24 Nov 2016 08:52:40 +0000 (09:52 +0100)]
all polytomouskey related handler are now extended from RemotingCdmHandler

5 years agofix #5841: set selection to newly created keynode
Katja Luther [Wed, 23 Nov 2016 14:04:13 +0000 (15:04 +0100)]
fix #5841: set selection to newly created keynode

5 years agofix #6215: check for datasource when opening preferencepage
Katja Luther [Wed, 23 Nov 2016 13:54:51 +0000 (14:54 +0100)]
fix #6215: check for datasource when opening preferencepage

5 years agofix #5971: admin menu is visible only if connected and user has role manager
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

5 years agofix #6209: adapt the message if a datasource is not available
Katja Luther [Mon, 21 Nov 2016 14:56:35 +0000 (15:56 +0100)]
fix #6209: adapt the message if a datasource is not available

5 years agoAdditional strings externalized in molecular plugin.
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.

5 years agoref #5971: new main menu admin with cdm preference nomenclatural code and insert...
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

5 years agoMessages edited.
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.

5 years agoMissing files from last commit added.
b.stoever [Fri, 18 Nov 2016 14:45:02 +0000 (15:45 +0100)]
Missing files from last commit added.

5 years agoExport single read alignment wizard separated into two pages.
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.

5 years agoExported single read sequences are now filled up with gaps. (Will be dependent on...
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.

5 years agoStrings in ExportSingleReadAlignmentWizardPage externalized and translated.
b.stoever [Thu, 17 Nov 2016 16:22:59 +0000 (17:22 +0100)]
Strings in ExportSingleReadAlignmentWizardPage externalized and translated.

5 years agoFixes in ExportSingleReadAlignmentWizardPage layout.
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.

5 years agoref #6198 removed synonym type combobox
Patrick Plitzner [Thu, 17 Nov 2016 09:09:19 +0000 (10:09 +0100)]
ref #6198 removed synonym type combobox

5 years agoref #6198 Correctly initialise ui field for pro parte and partial
Patrick Plitzner [Thu, 17 Nov 2016 09:06:17 +0000 (10:06 +0100)]
ref #6198 Correctly initialise ui field for pro parte and partial

5 years agoref #6205 Move excluded notes to the bottom of the wizard
Patrick Plitzner [Thu, 17 Nov 2016 09:05:40 +0000 (10:05 +0100)]
ref #6205 Move excluded notes to the bottom of the wizard

5 years agoExport single read alignment wizard validation refactored and extended.
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.

5 years agoIntermediate commit in implementing wizard validation (before moving to MultiValidator).
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.

5 years agofix #6199 Excluded note for excluded taxon nodes in TaxEditor
Patrick Plitzner [Tue, 15 Nov 2016 16:27:52 +0000 (17:27 +0100)]
fix #6199 Excluded note for excluded taxon nodes in TaxEditor

5 years agoExportSingleReadAlignmentWizard now exposes whole format info object.
b.stoever [Tue, 15 Nov 2016 16:09:30 +0000 (17:09 +0100)]
ExportSingleReadAlignmentWizard now exposes whole format info object.
FileDialog added to ExportSingleReadAlignmentWizardPage.

5 years agoClean up Derivate perspective
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)

5 years agoFix potential NPE
Patrick Plitzner [Tue, 15 Nov 2016 14:10:12 +0000 (15:10 +0100)]
Fix potential NPE

5 years agofix #6198 Remove synonymrelationships in TaxEditor
Patrick Plitzner [Tue, 15 Nov 2016 09:50:49 +0000 (10:50 +0100)]
fix #6198 Remove synonymrelationships in TaxEditor

5 years agofix #6197 Move excluded and unplaced from Taxon to TaxonNode in
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

5 years agoFix possible widget is disposed exception
Patrick Plitzner [Tue, 15 Nov 2016 08:47:38 +0000 (09:47 +0100)]
Fix possible widget is disposed exception

5 years agoFix potential NPE
Patrick Plitzner [Tue, 15 Nov 2016 08:35:16 +0000 (09:35 +0100)]
Fix potential NPE

5 years agoMissing dependency Apache commons.lang added to molecular.lib.
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.)