Commits · ae6174a2937b2c1628f230beecbd147eacba7845 · violethaze74 / Artemis

Mar 25, 2010

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13569 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ae6174a2

Mar 23, 2010

do not set segment Name when inserting segments · dbb9cadd

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13547 ee4ac58c-ac51-4696-9907-e4b3aa274f04

dbb9cadd

Mar 22, 2010

add useSRS VM option to force object editor to use SRS · bc77e390

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13538 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bc77e390

change for history qualifier · 37b57757

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13537 ee4ac58c-ac51-4696-9907-e4b3aa274f04

37b57757

Mar 19, 2010

update · b2007475

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13536 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b2007475

fix for history qualifier · 8b4a94b1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13535 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8b4a94b1

fixes · f5b720fb

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13534 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f5b720fb

handle UTRs · aad42885

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13533 ee4ac58c-ac51-4696-9907-e4b3aa274f04

aad42885

Mar 17, 2010

allow negative data values · d04cc6fb

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13517 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d04cc6fb

Mar 16, 2010

update · f7699f80

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13491 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f7699f80

changes to handle semi-colon separators in the qualifier field of a history term · 818cb811

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13484 ee4ac58c-ac51-4696-9907-e4b3aa274f04

818cb811

Mar 15, 2010

correct user graph · 6b92982e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13481 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6b92982e

Mar 10, 2010

make stack view the default · 79342b21

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13453 ee4ac58c-ac51-4696-9907-e4b3aa274f04

79342b21

Mar 09, 2010

add main() as an example of using GFFStreamFeature · 21560f4e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13449 ee4ac58c-ac51-4696-9907-e4b3aa274f04

21560f4e

update · 29b9b18b

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13446 ee4ac58c-ac51-4696-9907-e4b3aa274f04

29b9b18b

add SNP graph · b0c7373e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13445 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b0c7373e

fix for zoomed in graph · e0a198a3

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13444 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e0a198a3

Mar 08, 2010

add tmRNA · 9d54fc2d

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13411 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9d54fc2d

add deletePolypetideDomains() to be called on deletion of polypeptide features · 987e8b91

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13410 ee4ac58c-ac51-4696-9907-e4b3aa274f04

987e8b91

fix for getting database document · e107d732

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13409 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e107d732

Mar 04, 2010

include length in header · d362be21

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13387 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d362be21

update · ff11354d

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13386 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ff11354d

write EMBL from a GFF entry · 2a2cb037

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13385 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2a2cb037

saving GFF files as EMBL · 716a88ce

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13384 ee4ac58c-ac51-4696-9907-e4b3aa274f04

716a88ce

Mar 02, 2010

colour reads by coverage plot colour · aea0aa1e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13371 ee4ac58c-ac51-4696-9907-e4b3aa274f04

aea0aa1e

change getLineAttributes() to static and protected so it can be used by BamView · 6ff63427

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13370 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6ff63427

Mar 01, 2010

fix for when additional bam files are added · 65c2fd2e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13369 ee4ac58c-ac51-4696-9907-e4b3aa274f04

65c2fd2e

update bamview · cdfb7482

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13368 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cdfb7482

for multiple bam files draw a coverage plot for each · db625caf

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13367 ee4ac58c-ac51-4696-9907-e4b3aa274f04

db625caf

fix colours in paired read display and add FL attribute to reads when using multiple bam files · d58073a6
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13366 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
d58073a6

Feb 26, 2010

update · adfbce19

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13349 ee4ac58c-ac51-4696-9907-e4b3aa274f04

adfbce19

fix for propagating id · 2d4eba01

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13348 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2d4eba01

fix insertion lines · 8897419b

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13347 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8897419b

set eagerDecode (decode SAM record entirely when reading it) to false · 69e13007

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13346 ee4ac58c-ac51-4696-9907-e4b3aa274f04

69e13007

update · 976890b2

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13345 ee4ac58c-ac51-4696-9907-e4b3aa274f04

976890b2

update to 1.14 · 4404677b

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13344 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4404677b

Feb 25, 2010

use history qualifiers rather than private qualifiers and store them as feature_cvterms · 26f6e283
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13340 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
26f6e283
use history qualifiers rather than private qualifiers and store them as feature_cvterms · a7564546
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13339 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
a7564546
use history qualifiers rather than private qualifiers and store them as feature_cvterms · 314aaa81
tjc authored 15 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13338 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
314aaa81

add history qualifiers to allowed GFF qualifiers · 894def36

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13337 ee4ac58c-ac51-4696-9907-e4b3aa274f04

894def36

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