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JAL-3070 discoverers return ServiceWithParameter, now containing logic and call code...
[jalview.git]
/
src
/
jalview
/
2019-10-02
Jim Procter
JAL-3070 discoverers return ServiceWithParameter, now...
tree
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commitdiff
2019-10-02
Jim Procter
JAL-3070 decontaminate the ‘preferred service’ methods...
tree
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commitdiff
2019-10-02
Jim Procter
JAL-3070 JAL-3062 tidy up slivka ws menu builder and...
tree
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commitdiff
2019-10-02
Jim Procter
JAL-3070 detect failed/broken annotation web service...
tree
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commitdiff
2019-10-02
Jim Procter
JAL-3070 pull up generic methods for an automatic align...
tree
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commitdiff
2019-10-02
Jim Procter
JAL-3070 TODO
tree
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commitdiff
2019-10-01
Mateusz Warowny
JAL-3066 Sequence annotation services.
tree
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commitdiff
2019-09-27
Mateusz Warowny
JAL-3066 Automatically discoverable Protein sequence...
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 oops - refactor Slivka’s service stub too :)
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 JAL-3066 JAL-3067 refactor annotation web...
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 JAL-3066 JAL-2808 allow feature filter definit...
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 allow SequenceI.findPositions(0,column+1)...
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 cope when dataset sequence is passed
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 JAL-3066 formatting
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(Alignm...
tree
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commitdiff
2019-09-24
Jim Procter
JAL-3070 tidying
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3066 JAL-3070 pull up non-jabaws specific service...
tree
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commitdiff
2019-09-23
Mateusz Warowny
JAL-3066 Annotation Service Instance stub
tree
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commitdiff
2019-09-23
Mateusz Warowny
SlivkaWSDiscoverer formatting fix
tree
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commitdiff
2019-09-23
Mateusz Warowny
JAL-3066 Move common web service methods to abstract...
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 configure annotation service manager from...
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 rename AbstractJabaCalcWorker to SeqAnnotation...
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 ensure RNAAliFold annotation rows display...
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 formatting
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 detect presence of existing JABA RNAAliFold...
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 match AbstractJabaCalcWorker’s annotation...
tree
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commitdiff
2019-09-23
Jim Procter
JAL-3070 javadoc for (mostly) jabaws specific methods
tree
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commitdiff
2019-09-20
Jim Procter
JAL-3070 rough-and-ready refactor of JABA SequenceAnnot...
tree
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commitdiff
2019-09-20
Jim Procter
JAL-3070 JAL-1379 deferred work on annotation based...
tree
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commitdiff
2019-09-19
Mateusz Warowny
JAL-3066 Auto discover multiple sequence alignment...
tree
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commitdiff
2019-09-17
Jim Procter
JAL-3432 hide the slider when validator has no min...
tree
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commitdiff
2019-09-16
Mateusz Warowny
Set the initial value of the choice field to the defaul...
tree
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commitdiff
2019-09-16
Mateusz Warowny
Add the remaining msa services to the Discoverer
tree
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commitdiff
2019-09-11
Mateusz Warowny
Change choice field to use dropbox instead of radio...
tree
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commitdiff
2019-09-11
Mateusz Warowny
Create generic msa service instance
tree
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commitdiff
2019-09-06
Mateusz Warowny
Merge remote-tracking branch 'origin/alpha/JAL-3066_Jal...
tree
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commitdiff
2019-09-06
Mateusz Warowny
JAL-3066 Working custom parameters for clustalo
tree
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commitdiff
2019-09-06
Jim Procter
JAL-3066 fix compile error (@matesuz - this will confli...
tree
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commitdiff
2019-09-06
Jim Procter
JAL_1426 JAL-3066 update Apache James mime parser and...
tree
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commitdiff
2019-09-05
Mateusz Warowny
JAL-3066 Implement clustaloWS using slivka system.
tree
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commitdiff
2019-08-13
Jim Procter
JAL-3362 keep Java 1.8 build happy by specifying generi...
tree
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commitdiff
2019-08-13
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
tree
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commitdiff
2019-08-09
gmungoc
JAL-3187 removal of variant feature (non-virtual) trans...
tree
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commitdiff
2019-08-07
gmungoc
JAL-3187 (fudge) look in both alignments for stored...
feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-08-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-31
gmungoc
JAL-3389 add .py to restored Chimera session filename...
tree
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commitdiff
2019-07-31
gmungoc
Merge branch 'bug/JAL-3388structureChooserSorting'...
tree
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commitdiff
2019-07-30
gmungoc
JAL-3198 more efficient Sequence.getDisplayId()
tree
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commitdiff
2019-07-30
gmungoc
JAL-3388 correct class for column 0 Ref Sequence
bug/JAL-3388structureChooserSorting
tree
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commitdiff
2019-07-29
gmungoc
JAL-3386 correct wrapped width calculation for headless...
tree
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commitdiff
2019-07-29
gmungoc
JAL-3377 more reused of SeqCanvas.computeWrappedGeometry
tree
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commitdiff
2019-07-29
gmungoc
JAL-3377 add seq-annotations gap to cheight not to...
tree
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commitdiff
2019-07-29
gmungoc
JAL-3377 Javadoc added for getWrappedHeight()
tree
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commitdiff
2019-07-29
gmungoc
JAL-3377 corrected wrapped widths height for IdCanvas
tree
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commitdiff
2019-07-29
gmungoc
JAL-3377 include seq-annotation spacing in getWrappedHe...
tree
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commitdiff
2019-07-26
gmungoc
Merge branch 'features/JAL-3375vcfValidation' into
tree
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commitdiff
2019-07-26
gmungoc
JAL-1793 only decode specific special characters in...
tree
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commitdiff
2019-07-26
gmungoc
JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature...
features/JAL-3375vcfValidation
tree
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commitdiff
2019-07-26
gmungoc
JAL-3375 format validate VCF Integer and Float fields
tree
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commitdiff
2019-07-25
gmungoc
JAL-3375 ignore '.' values for VCF data
tree
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commitdiff
2019-07-16
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-16
gmungoc
JAL-2987 tolerate null double values when formatting...
tree
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commitdiff
2019-07-15
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 can now choose number of jackhmmer iterations
merge/JAL-3285_mchmmer_with_211_develop
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 fix faulty label in a MessageManager.getString...
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 add sort by evalue and bit score
tree
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commitdiff
2019-07-12
Thomas
JAL-2629 hmmer searches now read domain rather than...
tree
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commitdiff
2019-07-11
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
tree
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commitdiff
2019-07-11
Thomas
JAL-2629 hmmer searches include seqs past inclusion...
tree
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commitdiff
2019-07-11
Thomas
JAL-2629 hmm search UI and structural improvements...
tree
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commitdiff
2019-07-10
Jim Procter
JAL-3070 standard way of storing/recovering documentati...
tree
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commitdiff
2019-07-10
Jim Procter
JAL-3070 remove final reference to Jws2Instance
tree
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commitdiff
2019-07-10
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix hmmsearch/jackhmmer assigning incorrect...
tree
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commitdiff
2019-07-10
Jim Procter
Merge branch 'tasks/JAL-3070_wsinterfaces' into alpha...
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix hmsearch and jackhmmer not being able...
tree
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commitdiff
2019-07-10
tva
JAL-2629 hmmsearch # of new sequences now only displaye...
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix incorrect hmmbuild on groups behaviour
tree
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commitdiff
2019-07-10
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
tree
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commitdiff
2019-07-10
tva
JAL-2629 fix hmmsearch/jackhmmer being unable to search...
tree
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commitdiff
2019-07-08
gmungoc
JAL-3187 derived peptide variants tweaks and tests
tree
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commitdiff
2019-07-05
tva
JAL-2629 uniquify all hmmer command sequence outputs
tree
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commitdiff
2019-07-05
gmungoc
JAL-3187 initial refactoring towards peptide variant...
tree
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commitdiff
2019-07-05
tva
JAL-2629 fix file format issues preventing hmmsearch...
tree
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commitdiff
2019-07-05
gmungoc
JAL-1793 apply URL decoding when saving VCF attribute...
tree
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commitdiff
2019-07-03
tva
JAL-2629 fix search scores being read in incorrectly
tree
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commitdiff
2019-07-03
tva
JAL-2629 fix hmm on alignment being deleted upon runnin...
tree
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commitdiff
2019-07-03
tva
JAL-2629 evalues and bit scores now conserved after...
tree
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commitdiff
2019-07-03
tva
JAL-2629 removed empty line produced under sequence...
tree
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commitdiff
2019-07-03
tva
JAL-2629 can now filter by sequence e-value or bit...
tree
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commitdiff
2019-07-02
Jim Procter
JAL-3111 JAL-3280 hide the version check preference...
tree
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commitdiff
2019-07-02
Jim Procter
Merge branch 'develop' into tasks/JAL-3311_removeVamsasMenu
tree
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commitdiff
2019-07-02
tva
JAL-2629 hmm match score colour scheme now colours...
tree
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commitdiff
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
tree
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commitdiff
2019-07-01
Ben Soares
JAL-3333 removed unused variable
tree
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commitdiff
2019-07-01
Ben Soares
JAL-3333 using floats for smoother weighting
tree
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commitdiff
2019-06-29
Ben Soares
JAL-3333 Sorry couldn't resist adding a bit of weightin...
tree
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commitdiff
2019-06-29
Ben Soares
JAL-3333 Title text now appears instantly. Altering...
tree
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commitdiff
2019-06-28
Ben Soares
Merge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceIn...
tree
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commitdiff
2019-06-28
Ben Soares
JAL-3333 changed RGB model. Tested in mojave and Windo...
tree
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commitdiff
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