Commits · 96bda508164a8f8f4cfd5ab703ccb2af69a0ef89 · violethaze74 / Artemis

Jun 02, 2009

use resultMap for getOrganism · 96bda508

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10972 ee4ac58c-ac51-4696-9907-e4b3aa274f04

96bda508

implement getOrganismByCommonName() · 4f794535

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10971 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4f794535

Jun 01, 2009

allow multiple GO terms with the same id and different evidence codes · 892ba50b

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10968 ee4ac58c-ac51-4696-9907-e4b3aa274f04

892ba50b

in createFeatureFromBaseRange() use method to automatically generate a suggested ID · 06c63b4f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10967 ee4ac58c-ac51-4696-9907-e4b3aa274f04

06c63b4f

provide uniquename based on srcfeature name and base range · 5e67ae84

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10966 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5e67ae84

remove redundant imports · 223d1bb8

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10965 ee4ac58c-ac51-4696-9907-e4b3aa274f04

223d1bb8

May 29, 2009

when selecting the qualifier name to select if any values are already selected... · 6b816d22

tjc authored 15 years ago

when selecting the qualifier name to select if any values are already selected then maintain this selection


git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10953 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6b816d22

fix for highlighting default entry on Mac · 1a93c3b3

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10952 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1a93c3b3

update · 4dc86128

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10951 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4dc86128

fix key list · 49c5cc3c

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10950 ee4ac58c-ac51-4696-9907-e4b3aa274f04

49c5cc3c

speed up getFeatureByUniquename() · 5351542b

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10949 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5351542b

May 27, 2009

for new ortho/paralog genes added also optionally add ortho/paralog links to existing genes · e4c592c8
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10924 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
e4c592c8

SO term names changed · 5ae3e9e1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10916 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5ae3e9e1

May 26, 2009

add hyperling to AID · 6a48efe8

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10899 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6a48efe8

May 15, 2009

update ncbi url · 79325440

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10831 ee4ac58c-ac51-4696-9907-e4b3aa274f04

79325440

update · 7966985e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10823 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7966985e

May 14, 2009

changes to speed up getOrganismsContainingSrcFeatures · bbffb240

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10812 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bbffb240

use SwingWorker instead of SwingUtilities.invokeLater · 818d9de0

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10805 ee4ac58c-ac51-4696-9907-e4b3aa274f04

818d9de0

update · 2af709e1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10802 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2af709e1

use Feature.xml.getLazyFeatureExact in getFeatureByUniqueName · 7b6bd58b

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10801 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7b6bd58b

add getLazyFeatureExact · 5ee41bf4

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10800 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5ee41bf4

fix for manual ortholog / paralog inserts · b71a4dd9

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10799 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b71a4dd9

May 13, 2009

rename · 6800b9ae

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10797 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6800b9ae

run pfam search option · 98a4c2a1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10796 ee4ac58c-ac51-4696-9907-e4b3aa274f04

98a4c2a1

make a separate class for the progress bar · 4cce70d3

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10795 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4cce70d3

remove unused import · 3d545ada

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10794 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3d545ada

speed up gene builder opening by putting the construction of the match panel in a separate thread · e5ca1c35
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10790 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
e5ca1c35

May 12, 2009

add private to RNAs · 9dfcd733

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10785 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9dfcd733

May 08, 2009

send sequence searches to pfam · e16fc796

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10769 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e16fc796

load a pub_dbxref when a pub is created · 3a661bc2

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10763 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3a661bc2

add GmodDAO · e3853f56

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10762 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e3853f56

make PubDbXRef.xml · 91b774e8

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10761 ee4ac58c-ac51-4696-9907-e4b3aa274f04

91b774e8

fix in updateQualifierString() for updating product without evidence codes · 02277d81

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10760 ee4ac58c-ac51-4696-9907-e4b3aa274f04

02277d81

implement addDomain() to add polypeptide_domain features to the feature display · 323df007

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10752 ee4ac58c-ac51-4696-9907-e4b3aa274f04

323df007

add getNucLocation() to get nucleotide location for featurelocs in protein coordinates · 3df41726
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10751 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
3df41726

check for primary dbxref in addLazyQualifiers() · ac5afac8

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10750 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ac5afac8

add option to show polypeptide_domains in feature display · 278888f5

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10749 ee4ac58c-ac51-4696-9907-e4b3aa274f04

278888f5

May 07, 2009

change double quotes to single quotes · 5de23075

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10736 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5de23075

May 06, 2009

update · c7413e3f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10715 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c7413e3f

write an appropriate header when writing bases · 79da1cb1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10707 ee4ac58c-ac51-4696-9907-e4b3aa274f04

79da1cb1

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