Commits · 5ee41bf47e3a5a33946ce4c475a2d5dbabddb59d · violethaze74 / Artemis

May 14, 2009

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

May 05, 2009

add option for writing out a combination of upstream, feature and downstream bases · e157916d

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10706 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e157916d

Apr 30, 2009

grey out panel when view is being scrolled · 10da7141

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10685 ee4ac58c-ac51-4696-9907-e4b3aa274f04

10da7141

speed up opening options panel · c9a482b7

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10684 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c9a482b7

Apr 29, 2009

set busy cursor when opening · 2bc388a9

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10676 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2bc388a9

improve look · d39440a8

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10675 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d39440a8

add new file selection panel · 6154e816

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10672 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6154e816

fix ticks · 8bda7002

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10671 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8bda7002

Apr 27, 2009

fix when running with no args · f53ed2d0

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10666 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f53ed2d0

fix opening Artemis · 286fe80f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10661 ee4ac58c-ac51-4696-9907-e4b3aa274f04

286fe80f

Apr 24, 2009

include option to ignore methylation sites · 66339866

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10646 ee4ac58c-ac51-4696-9907-e4b3aa274f04

66339866

Apr 23, 2009

set proxySet to true · c0ddc674

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10620 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c0ddc674

update · c8097585

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10610 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c8097585

add proxy settings to options dialog · c69d3277

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10602 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c69d3277

Apr 22, 2009

close with system.exit() · 3247cad1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10595 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3247cad1

capitalise the evidence codes · baec5c60

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10590 ee4ac58c-ac51-4696-9907-e4b3aa274f04

baec5c60

correct typo in ISO evidence code · 91df9439

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10589 ee4ac58c-ac51-4696-9907-e4b3aa274f04

91df9439

fix for updating uniquename on child features · 8300e968

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10584 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8300e968

update · c8bb073a

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10582 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c8bb073a

change to menu for clarity · d8d6f53f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10581 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d8d6f53f

add a filter to search for multiple systematic name qualifiers · ee88e79f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10580 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ee88e79f

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