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cdmlib / cdmlib-model / src / main / java / eu / etaxonomy / cdm / model / molecular @ 747a744e

# Date Author Comment
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)

1efe13d4 03/07/2013 10:43 PM Andreas Müller

remove import

9214e186 03/07/2013 10:42 PM Andreas Müller

minor

dca4d4c1 03/07/2013 10:41 PM Andreas Müller

add lazy load GenBankAccession test

1dd924fa 03/07/2013 04:36 PM Andreas Müller

Allow Locus to be loaded by javassist (fixing #3340)

1dda33c7 02/27/2013 11:30 AM Andreas Müller

Cascade saveUpdate from Sequence to GenBankAccession

bec2153a 02/27/2013 11:23 AM Andreas Müller

Cascade saveUpdate from DNASample to Sequence

18559a66 02/26/2013 07:07 PM Andreas Müller

factory method for molecular.GenBankAccession

7cf104d0 02/26/2013 05:04 PM Andreas Müller

factory method for molecular.Locus

be034f37 02/26/2013 04:56 PM Andreas Müller

Factory method for molecular.Sequence

9a963f43 08/10/2011 04:51 PM Andreas Müller

change name of ReferencedMedia to ReferencedMediaBase (#2381)

96759d92 05/03/2011 01:43 PM Andreas Müller

added cloneable interface

9ec690dd 04/29/2011 12:27 PM Katja Luther

clone methods

f7f4a80d 04/20/2011 01:41 PM Andreas Müller

make termbase.uri and GenBankAccession.uri real java.net.URI #2340

d5345989 03/28/2011 04:17 PM Katja Luther

clone method for Sequence

1d36aa54 12/01/2010 04:17 PM Andreas Müller

merge 3.0.2 to trunk

0e3cde98 10/14/2010 10:34 AM Niels Hoffmann

making constructor private again

b1d3185d 10/13/2010 07:15 PM Niels Hoffmann

Addedfactory method and default constructor to DnaSample

a784f00f 03/10/2010 12:00 PM Katja Luther

merge cate-development2 branch with trunk

17a0cbe8 11/02/2009 01:27 PM Ben Clark

Changed public boolean supports* to JavaBeans compliant isSupports*() method signatures in Feature class
Several minor bugfixes in defined terms, validation. Indexing works on all Description Element Base subclasses.

a641fad9 10/07/2009 02:06 PM Ben Clark

Merged in changes from cate-development branch and upgraded to spring 3.0.0.RC1

57606ee3 09/21/2009 02:21 AM Andreas Müller

Intensive model change for referenceBase and subclass, smaller model changes for taxonBase and marker

43eb84c3 08/14/2009 10:14 AM Ben Clark

Added annotations to support free-text searching of occurrences & related entities

5d49833e 05/15/2009 06:24 PM Ben Clark

Annotated References, Media, and Agents, and also added more data types to the anyTypeDefs to allow more types of data to be annotated and marked etc, and added a jaxb annotation to OriginalSource.sourcedObj

4208745a 05/07/2009 01:36 PM Ben Clark

Lots of changes, but primarily:
Enabled the marshalling / unmarshalling of LSIDAuthority
Renamed the User table to UserAccount to avoid problems on SQLServer
Major refactoring of CacheStrategyGenerators so that the generic framework extends across all IIdentifiableEntities, allowing (but not requiring) the use of @Configurable and aop to inject custom cache strategy generators at runtime

b70a7f94 03/23/2009 04:39 PM Andreas Kohlbecker

reintroducing transient getters where required for cdm-remote; removing cast from inside getNomenclaturalReference(){}

ee91bcd9 02/25/2009 01:45 PM Ben Clark

Committing large number of changes relating to versioning implementation (#108)

f6765014 01/20/2009 05:59 PM Ben Clark

Major changes to the cdmlib default term loading and initialization, plus indexing of some model entities as part of #476

d3fbdf52 11/27/2008 12:45 AM Andreas Müller

Delete warnings in molecular

dc776ce0 11/26/2008 03:34 PM Anahit Babadshanjan

Fixed Hibernate mappings, JAXB annotations, and typos after model review.

b824294c 11/24/2008 11:22 AM Anahit Babadshanjan

Finished JAXB annotations for media, reference, and molecular packages

c281e68e 11/12/2008 02:02 PM Andreas Müller

persistentTitleCache -> titleCache

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