Commits · 42cdbf2324abacc49b1f87519b7807516fef8287 · violethaze74 / Artemis

Sep 23, 2010

update · 42cdbf23

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14770 ee4ac58c-ac51-4696-9907-e4b3aa274f04

42cdbf23

Sep 21, 2010

add main · 03100fae

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14762 ee4ac58c-ac51-4696-9907-e4b3aa274f04

03100fae

Sep 19, 2010

changes for INDEXED_FASTA_FORMAT · d9647d6c

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14754 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d9647d6c

changes for INDEXED_FASTA_FORMAT · 921482b8

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14753 ee4ac58c-ac51-4696-9907-e4b3aa274f04

921482b8

add INDEXED_FASTA_FORMAT · fe3d961f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14752 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fe3d961f

add checkbox if IndexFastaStream · 0bf1d833

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14751 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0bf1d833

add method resetScrolls() · 8ae835aa

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14750 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8ae835aa

change fixScrollBar to protected · 3208885e

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14749 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3208885e

Sep 18, 2010

handle indexed fasta · d557ee4f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14748 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d557ee4f

Sep 09, 2010

update · c98e6b04

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14735 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c98e6b04

fix for snp and coverage plots when zooming in · 24381086

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14734 ee4ac58c-ac51-4696-9907-e4b3aa274f04

24381086

Sep 01, 2010

vcf · 84a84902

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14696 ee4ac58c-ac51-4696-9907-e4b3aa274f04

84a84902

vcf · df618e8e

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14695 ee4ac58c-ac51-4696-9907-e4b3aa274f04

df618e8e

vcf · a02b6355

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14694 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a02b6355

fix for showing new stop codons · cf32b992

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14691 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cf32b992

update · 2d601075

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14690 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2d601075

Aug 27, 2010

give a warning if the reference feature names do not match the contig names in the VCF · 48a672d8
tjc authored 14 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14677 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
48a672d8

changes for combining reference contigs in a vcf · 4cb2a65d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14676 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4cb2a65d

Aug 19, 2010

update · eca39880

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14601 ee4ac58c-ac51-4696-9907-e4b3aa274f04

eca39880

option to turn off hyperlinks · 529e9d60

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14599 ee4ac58c-ac51-4696-9907-e4b3aa274f04

529e9d60

turn hyperlink styles off in history as this causes problems · 6227f5d5

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14598 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6227f5d5

Aug 18, 2010

fix to display is_partial options when the gene is created within the current session · c9794938
tjc authored 14 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14586 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
c9794938

modify qualifier text input so that it uses an expandable text pane · 1056dfd3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14578 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1056dfd3

update · e8225fa3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14557 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e8225fa3

handle option to write unflattened gene models for GFFDocumentEntry · 7ca9479e

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14556 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7ca9479e

handle GFFDocumentEntry · 9272f9e3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14555 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9272f9e3

add getDatabaseQualifiersToRemove() · cf3d79db

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14554 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cf3d79db

Aug 16, 2010

add show_reverse_lines and show_forward_lines · 8ce19f46

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14540 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8ce19f46

Aug 10, 2010

update to 1.27 · b73189ab

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14501 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b73189ab

Jul 30, 2010

update · 569b2e5b

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14403 ee4ac58c-ac51-4696-9907-e4b3aa274f04

569b2e5b

add support for VCF v4.0 · f65c9d95

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14402 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f65c9d95

mark variants that introduce a stop codon · 7b538a5f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14395 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7b538a5f

Jul 29, 2010

support for v4.0 · 0cd9b603

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14392 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0cd9b603

Jul 26, 2010

fix for opening · b5303e5d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14328 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b5303e5d

Jul 23, 2010

use Pattern.split · 2bb779d7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14320 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2bb779d7

optionally hide variants that do not overlap CDS features · cc0849ce

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14304 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cc0849ce

Jul 22, 2010

add quality filter · 97950166

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14290 ee4ac58c-ac51-4696-9907-e4b3aa274f04

97950166

more toggle options - for insertions, deletions and multiple alleles · b9526535

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14277 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b9526535

Jul 21, 2010

initial code for identifying synonymous / non-synonymous change · f6fc5e76

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14274 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f6fc5e76

Jul 20, 2010

draw and handle range selections · 38b895e5

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14260 ee4ac58c-ac51-4696-9907-e4b3aa274f04

38b895e5

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