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cdmlib / cdmlib-model / src / main / java / eu / etaxonomy / cdm / model / molecular @ 2f54f726

# Date Author Comment
991d761f 03/09/2018 03:44 PM Patrick Plitzner

ref #6158 avoid URL redirects

fd48f996 01/30/2018 01:53 PM Andreas Müller

ref #7080 fix potential other isEmpty issues for @Embeddable classes

f1ec80f5 01/30/2018 01:50 PM Andreas Müller

cleanup

70368530 05/04/2017 11:24 PM Andreas Müller

Merge branch 'develop' into feature/cdm-4.7

Conflicts:
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/distribution/excelupdate/ExcelDistributionUpdate.java
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/MnTableCreator.java

097347e0 05/03/2017 12:39 PM pplitzner

Avoid dependency to org.codehaus.plexus.util.StringUtils

c0b73e71 05/03/2017 12:02 AM Andreas Müller

cleanup

a239e477 04/19/2017 08:43 AM Patrick Plitzner

Avoid dependency to org.codehaus.plexus.util.StringUtils

d45008d0 12/20/2016 11:49 AM Andreas Kohlbecker

ref #6190 removing svn property place holder in first line of code

90046bc4 05/25/2016 11:22 AM Andreas Müller

Remove generics from Reference in cdmlib-model #5830

ef1b5da2 04/28/2016 03:47 PM Andreas Müller

Adapt table and column names to hibernate 5 naming strategy #5369

... and some other changes to table/attribute names

974e7f9a 02/05/2016 02:04 PM Andreas Müller

Use correct column length annotation #5535

c70a7f0f 12/09/2015 05:22 PM Andreas Kohlbecker

#4716 reduicing clutter in the lucene index and solving performance problems which probably fixes #4277 and #3663

2a5361d0 12/02/2015 04:43 PM Andreas Kohlbecker

index creation without errors, most lucene search test working again
- using TextField instead of StringField to enable tokenization for some fields
- @IndexedEmbedded(includeEmbeddedObjectId=true) added where necessary

3dd6c00e 11/23/2015 04:13 PM Andreas Müller

Upgrade to hibernate 5 with persistence tests running #4716

2ae69503 11/11/2015 10:38 AM Patrick Plitzner

Add orphanRemoval to SingleReadAlignment set of Sequence #5200

455c5da0 11/10/2015 11:56 AM Patrick Plitzner

Set singleRead to null when removing SingleReadAlignment from sequence
to avoid "object would be re-saved" #5200

5189077e 10/01/2015 05:23 PM Cherian Mathew

#5281 Make SingleReadAlignment.Shift serializable

331b2aa6 09/08/2015 02:08 PM Patrick Plitzner

Set sequence to null when removing a single read #5200

ca363adb 07/01/2015 09:28 AM Patrick Plitzner

Do not set consensus sequence of single read alignment to null when
deleting the alignment

1f478638 06/08/2015 01:08 PM Cherian Mathew

Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/cdmlib into remoting-4.0

Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTerm.java
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/INameService.java...

8ee01de1 05/21/2015 05:00 PM Cherian Mathew

Merge branch 'master' of wp5.e-taxonomy.eu:/var/git/cdmlib into remoting-4.0

Conflicts:
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTerm.java
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/Reference.java...

77b3215e 05/06/2015 05:46 PM Andreas Müller

add update script and JAXB annotation for sequence positions #4743

ec3a066d 05/06/2015 05:38 PM Andreas Müller

Adding firstSeqPosition, leftCutPosition and rightCutPosition to SingleReadAlignment #4743 , Update script still missing

ae709521 03/27/2015 05:45 PM Andreas Müller

implement clone for SingleReadAlignment

370da79e 03/27/2015 05:20 PM Andreas Müller

no null return type even safer

2c099b2c 03/27/2015 03:42 PM Andreas Müller

get Shift always returns empty array instead of null #4734

903cecc9 02/03/2015 03:45 PM Cherian Mathew

added Cascade.MERGE to all fields with annotation Cascade.SAVE_UPDATE

6a46c236 12/17/2014 01:46 PM Andreas Müller

add getter and setter for reverse complement

a7621039 12/12/2014 04:25 PM Andreas Müller

javadoc for Amplification and AmplificationResult

c6423b90 12/11/2014 04:29 PM Andreas Müller

test for Amplification labelCache

73518da2 12/11/2014 04:02 PM Andreas Müller

implement Amplification.labelCache generation

747a744e 12/11/2014 03:51 PM Patrick Plitzner
  • added cascade saving for amplification result
    • made constructor protected to avoid JavaAssistEnhancementException
b1e7575d 12/10/2014 11:22 PM Andreas Müller

latest changes to AmplificationResult and DnaQuality

af44092f 12/10/2014 10:40 PM Andreas Müller

updating DnaQuality with typedPurificationMethod to allow both #4434 , #4552

a2c31205 12/09/2014 11:29 PM Andreas Müller

JAXB annotations for amplification results

4c96041a 12/09/2014 10:26 PM Andreas Müller

latest changes for AmplificationResult

bdfdcda2 12/09/2014 05:34 PM Andreas Müller

add labelCache to Amplification #4542

a491689c 12/09/2014 05:33 PM Andreas Müller

some bugfixes to new Amplification modelling #4541

fcab75e4 12/09/2014 05:09 PM Andreas Müller

some adaptations after trunk merge to 3.4.1

af283637 12/09/2014 05:03 PM Patrick Plitzner

merge-update from trunk

2d717c7c 12/09/2014 04:46 PM Andreas Müller

dna Quality purification method

395ccc97 12/09/2014 04:44 PM Andreas Müller

separate Amplification and AmplificationResult.java #4541

c1d8fdfa 12/04/2014 03:29 PM Patrick Plitzner
  • re-added hibernate annotation
8cd3690c 12/04/2014 01:55 PM Patrick Plitzner

-removed hibernate search annotation (copy&paste error)

b141d6fb 12/04/2014 09:43 AM Patrick Plitzner
  • fixed bidriectionality for DnaSample<->Amplification
9f976540 12/03/2014 11:55 PM Andreas Müller

fixing test for SingleReadAlignment and removal of SpecAndObs_Sequence

6571e4e5 12/03/2014 10:13 PM Andreas Müller

implement SingleReadAlignment.java #4529
not yet ready

ec352541 12/03/2014 01:22 PM Patrick Plitzner

merge-update from trunk

ccf1f2f1 12/03/2014 10:03 AM Andreas Müller

merge PresenceTerm and AbsenceTerm #4521

b71032bb 12/01/2014 02:47 PM Patrick Plitzner
  • fixed bidirectional mapping
34902b3c 11/27/2014 01:52 PM Andreas Müller

remove FIMXE on protected constructor

adac5022 11/24/2014 10:12 AM Patrick Plitzner
  • converted dnaQuality from DefinedTerm to OrderedTerm (#4434)
502ea305 11/21/2014 02:21 PM Andreas Müller

Add institution to DerivationEvent and Amplification

0e660e76 11/21/2014 01:55 PM Andreas Müller

add DnaMarker to Primer #4470

3f9e57cd 10/29/2014 11:39 AM Patrick Plitzner
  • added exception throwing to URI assembly in Sequence class
    • handled exception in editor details view
1fec1343 10/28/2014 03:27 PM Patrick Plitzner
  • made constructor protected to avoid JavaAssistEnhancementException
2c6ae9a6 10/21/2014 02:50 PM Patrick Plitzner

merge-update from trunk

1c6e6c0e 10/21/2014 01:59 PM Andreas Müller

fix init problem for DnaSample

627cb878 10/21/2014 01:21 PM Andreas Müller

bugfix for clone and setDnaSample

cc1af289 10/21/2014 12:42 PM Patrick Plitzner

merge-update from trunk

6f9c3480 10/21/2014 11:52 AM Andreas Müller

add a bit more bidirectionality to DnaSample/Sequence

eb2b587d 10/21/2014 12:25 AM Andreas Müller

cascade SingleRead.materialOrMethod

323da513 10/20/2014 08:02 PM Andreas Müller

further changes to DnaQuality #4434 and update script for ValidationFramework alpha version

b998a5a0 10/20/2014 03:35 PM Andreas Müller

make primer.sequence a SequenceString #4139

0a345e59 10/18/2014 03:14 AM Andreas Müller

first implementation for DnaQuality #4434

e5f42a92 10/14/2014 09:40 AM Patrick Plitzner
  • fixed copy&paste error in Primer.change()
e2ebeba0 06/03/2014 04:35 PM Patrick Plitzner
13d17320 04/01/2014 08:50 AM Patrick Plitzner
  • added two NewInstance() methods to Amplification
    • added getUuidAndDescriptions to IAmplificationService and DAO
70d6b08b 03/25/2014 05:01 PM Patrick Plitzner
  • added removeSingleRead() method to Amplification
f295355d 03/17/2014 09:36 AM Patrick Plitzner
  • added reference to trac ticket
c09b4938 03/17/2014 08:53 AM Patrick Plitzner
43e4bbeb 03/17/2014 08:52 AM Patrick Plitzner
  • fixed a bug in the automated setting of the string length
e84380bd 03/05/2014 03:28 PM Patrick Plitzner
  • added cascading save to SequenceString of a Sequence
ec766423 03/04/2014 09:20 AM Patrick Plitzner
  • added cascading save for contig file of Sequence
824432c0 03/03/2014 09:48 AM Patrick Plitzner
  • added cascading save to pherogram (Media) of SingleRead
    • added media section to DetailsViews for Amplification (gel photo) and SingelRead (pherogram)
6388be87 02/21/2014 10:32 PM Andreas Müller

minor

9d9feae4 01/14/2014 02:10 PM Patrick Plitzner
c0ab9eed 01/14/2014 11:04 AM Andreas Müller

again bugfix for DNA URLs

b8f2227c 01/13/2014 04:24 PM Andreas Müller

fix bug for getBoldUri

0f1568df 12/18/2013 11:43 AM Andreas Müller

Bug fix for DnaSample record basis

9b842959 12/04/2013 07:41 PM Andreas Müller

add "part" to sequence setter

f352fc6f 09/13/2013 02:06 PM Andreas Müller

javadoc for amplification

101e1952 09/12/2013 01:48 PM Andreas Müller

Javadoc for molecular classes

00e9083c 09/11/2013 05:03 PM Andreas Müller

rename materialMethodTerm -> definedMaterialOrMethod

ba08dfd7 09/11/2013 04:31 PM Andreas Müller

final implementation of MaterialOrMethodEvent, Cloning, PreservationMethod, ... #3360

1d358b91 08/30/2013 05:51 PM Andreas Müller

persist Sequence direction via enum key #3686

cff58e4b 08/30/2013 11:17 AM Andreas Müller

adding FactoryMethods and Constructor to DNA classes and uuid/key for SequenceDirection

66cc80d5 08/30/2013 10:57 AM Andreas Müller

some javadoc and factory methods

10af07dc 08/27/2013 08:16 PM Andreas Müller

fix all compilation errors for app-import 3.3

1747fb8f 07/23/2013 02:46 AM Andreas Müller

update update script such that no validation errors exist anymore

5a479f39 07/22/2013 07:03 PM Andreas Müller

change some names in molecular and update the update script

f7678187 07/14/2013 02:53 PM Andreas Müller

first implementation of new molecular package #3360

0f0f606a 07/02/2013 11:02 AM Andreas Müller

make Sequence-PhylogeneticTree ManyToMany (#2540)

44a042a1 06/28/2013 01:55 PM Andreas Müller

remove ReferencedMediaBase and Figure, let PhylogeneticTree inherit from Media, remove citation and microcitation columns from DB

483579cd 06/28/2013 11:24 AM Andreas Müller

adding recordBasis to SpecimenOrObservationBase and removing some DerivedUnit classes (all #3378) and adding kindOfUnit to SpecimenOrObservationBase (except for according termType and vocabulary) #3568.

8c760302 06/25/2013 04:17 PM Andreas Müller

Remove GenBankAccession class, Spatium for EN_DASH and some minor stuff for v3.3

0a9dd700 06/21/2013 03:11 PM Andreas Müller

make Sequence.sequence a clob (#3325)

95d79c4d 04/08/2013 06:07 PM Andreas Müller

remove model changing validations fix Delete_Orphan #3379

4af7bea2 03/26/2013 07:18 PM Andreas Kohlbecker

cleaning up @Field annotations

a13c5f66 03/16/2013 01:30 AM Andreas Müller

Hibernate 4 migration. All test running except for SDDImport (Out of memory)

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