Commits · 48d0d7bc3ce51556b698aa26274e717f7bc37b15 · violethaze74 / Artemis

Sep 23, 2008

use getLazyFeatureNoResiduesById · 48d0d7bc

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8876 ee4ac58c-ac51-4696-9907-e4b3aa274f04

48d0d7bc

updates for getGeneFeature · d613f0d1

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8874 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d613f0d1

add getLazyFeatureNoResiduesById · 844eff4d

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8873 ee4ac58c-ac51-4696-9907-e4b3aa274f04

844eff4d

Sep 22, 2008

add getFeaturePubsByFeature() · eeac18a4

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8872 ee4ac58c-ac51-4696-9907-e4b3aa274f04

eeac18a4

fix getFeaturePubsByFeature · 07d93fcd

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8871 ee4ac58c-ac51-4696-9907-e4b3aa274f04

07d93fcd

optimise · 0cf1d564

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8870 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0cf1d564

Sep 19, 2008

add codon_start to properties panel · b80aa509

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8864 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b80aa509

change to use feature.name as the primary name · be6734f4

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8863 ee4ac58c-ac51-4696-9907-e4b3aa274f04

be6734f4

change to using feature.name as the primary name · 5579d884

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8862 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5579d884

Sep 18, 2008

new contructor to open gene builder by supplying the gene name · 51e682d9

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8859 ee4ac58c-ac51-4696-9907-e4b3aa274f04

51e682d9

test for null value when retieving featurepubs · fee6365f

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8858 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fee6365f

load CvTerms in a separate thread when opening standalone gene editor · 3a907ff7

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8857 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3a907ff7

fix for lazy loading · f64fada0

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8856 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f64fada0

Sep 16, 2008

add ignore obsolete option · 615845d3

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8852 ee4ac58c-ac51-4696-9907-e4b3aa274f04

615845d3

add ignore obsolete flag and remove CDS on non-coding transcript · 49f7baf4

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8851 ee4ac58c-ac51-4696-9907-e4b3aa274f04

49f7baf4

use GeneUtils.getNonCodingTranscripts() to get array on non-coding transcripts · 7c89c28e

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8850 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7c89c28e

add option to ignore obsolete genes · efda8ad9

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8849 ee4ac58c-ac51-4696-9907-e4b3aa274f04

efda8ad9

add non-coding transcript array · f0a820f9

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8848 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f0a820f9

polypeptide analysis mappings · c4ee019c

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8847 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c4ee019c

fix for writing EMBL in database mode · e1343c17

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8846 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e1343c17

Sep 15, 2008

fix for creating tree nodes · f3f5e520

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8819 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f3f5e520

fix getFeatureCvTermsByFeature() · 728b6836

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8818 ee4ac58c-ac51-4696-9907-e4b3aa274f04

728b6836

Sep 12, 2008

prompt on delete · db7df969

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8797 ee4ac58c-ac51-4696-9907-e4b3aa274f04

db7df969

add track deletion option · 19068a1c

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8790 ee4ac58c-ac51-4696-9907-e4b3aa274f04

19068a1c

update track manager when dragging and droping · 819cf655

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8787 ee4ac58c-ac51-4696-9907-e4b3aa274f04

819cf655

change default graph colours · 695191a5

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8786 ee4ac58c-ac51-4696-9907-e4b3aa274f04

695191a5

update · c4a36522

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8785 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c4a36522

Sep 11, 2008

limit NCBI search to one selected feature · 896a3a85

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8769 ee4ac58c-ac51-4696-9907-e4b3aa274f04

896a3a85

add getNCBIPrograms() · 05ba8dc8

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8768 ee4ac58c-ac51-4696-9907-e4b3aa274f04

05ba8dc8

add ncbi searches · 3400dfdc

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8767 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3400dfdc

include Run menu for all operating systems · cbd56eda

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8766 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cbd56eda

update · a505696c

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8765 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a505696c

Sep 10, 2008

fix · a90c1e9d

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8764 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a90c1e9d

fix for non-database gff · 8a400b78

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8762 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8a400b78

show unique keys that are ignored · d97b1856

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8761 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d97b1856

Sep 08, 2008

strip translation qualifiers from CDS · 59f90c28

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8744 ee4ac58c-ac51-4696-9907-e4b3aa274f04

59f90c28

look for supercontigs · 92513a4c

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8743 ee4ac58c-ac51-4696-9907-e4b3aa274f04

92513a4c

sort gene before CDS · 79145cdc

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8742 ee4ac58c-ac51-4696-9907-e4b3aa274f04

79145cdc

Sep 04, 2008

added option to save genbank tabular format · bc7fcd74

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8732 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bc7fcd74

five-column, tab-delimited table of feature locations and qualifiers · a636c821

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8731 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a636c821

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