Commits · ded6cf917b60228b5096adc47d3b820a4888553d · violethaze74 / Artemis

Jul 17, 2009

updates · ded6cf91

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11376 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ded6cf91

add docs on wiggle plots · 99e74805

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11374 ee4ac58c-ac51-4696-9907-e4b3aa274f04

99e74805

Jul 16, 2009

provide plot options (open, filled, heat map) to configuration · 5d6502ff

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11365 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5d6502ff

fix for mutiple wiggle data reads in a file · 07d4d0de

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11364 ee4ac58c-ac51-4696-9907-e4b3aa274f04

07d4d0de

Jul 15, 2009

add wiggle (variable and fixed step formats) to supported user plot formats · 273b47ef

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11358 ee4ac58c-ac51-4696-9907-e4b3aa274f04

273b47ef

change 2 methods to protected · be378988

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11357 ee4ac58c-ac51-4696-9907-e4b3aa274f04

be378988

Jul 13, 2009

parse colour strings that are comma or colon separated rgb values · f8053a9a

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11348 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f8053a9a

add previous_systematic_id as allowed qualifier · eb6220dd

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11346 ee4ac58c-ac51-4696-9907-e4b3aa274f04

eb6220dd

Jul 07, 2009

read line colours from the header of user plots · 63e4d4c2

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11332 ee4ac58c-ac51-4696-9907-e4b3aa274f04

63e4d4c2

read line colours from the header · 9b8d8067

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11331 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9b8d8067

add parse() to parse a string representation of a color · 616c019f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11330 ee4ac58c-ac51-4696-9907-e4b3aa274f04

616c019f

Jul 06, 2009

fix controlled curation heading positions · 589bc9fa

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11321 ee4ac58c-ac51-4696-9907-e4b3aa274f04

589bc9fa

Jul 03, 2009

add error message if a cv term is missing · ea015db6

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11299 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ea015db6

add GeneID · fda47edc

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11298 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fda47edc

Jul 02, 2009

fix so this can be run from other directories · 9f49fc98

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11290 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9f49fc98

Jul 01, 2009

update · 3c9bee41

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11263 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3c9bee41

setOpaque(false) for partial buttons · c7e9496d

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11258 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c7e9496d

Jun 30, 2009

launch gene builder · 75c1cbe7

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11252 ee4ac58c-ac51-4696-9907-e4b3aa274f04

75c1cbe7

read isFminPartial and isFmaxPartial from featureloc table · 2b44f70e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11240 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2b44f70e

record isFminPartial and isFmaxPartial fields in featureloc · c7dc8548

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11239 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c7dc8548

add partial options · f3792788

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11238 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f3792788

update · 3fceabe2

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11237 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3fceabe2

add isFminPartial and isFmaxPartial to the extra gff qualifier list · 1d60d2aa

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11236 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1d60d2aa

start to use featureloc.is_fmin_partial and featureloc.is_fmax_partial · 4acfeafd

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11235 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4acfeafd

Jun 29, 2009

new graph file format · 23ef50c9

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11230 ee4ac58c-ac51-4696-9907-e4b3aa274f04

23ef50c9

Jun 26, 2009

Changes to use line attributes to define graph line colour, style and width · a647707c

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11221 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a647707c

Define line attributes for graphs lines · 87531962

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11220 ee4ac58c-ac51-4696-9907-e4b3aa274f04

87531962

Jun 25, 2009

Tidy up the logic, and fix the quoting so that whitespace or metacharacters in... · bff05602

rh11 authored 15 years ago

Tidy up the logic, and fix the quoting so that whitespace or metacharacters in arguments don't cause problems.


git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11199 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bff05602

Jun 24, 2009

changes to the legend for multiple plots on a single graph · dd665d59

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11191 ee4ac58c-ac51-4696-9907-e4b3aa274f04

dd665d59

introduce a new user data format with the base position in the first column · 597cf405

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11188 ee4ac58c-ac51-4696-9907-e4b3aa274f04

597cf405

add bp to ID line · 46fc638a

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11187 ee4ac58c-ac51-4696-9907-e4b3aa274f04

46fc638a

add the option to set the default to display polypeptide domains by default... · c98ffd69

tjc authored 15 years ago

add the option to set the default to display polypeptide domains by default show_polypeptide_domains=yes


git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11186 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c98ffd69

use correct ID in ID line · a02ebdb5

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11184 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a02ebdb5

Jun 23, 2009

update · 1c983b3e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11168 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1c983b3e

Jun 22, 2009

update · 3b126dfb

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11158 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3b126dfb

change chado_infer_CDS_UTR to no · 587d2870

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11157 ee4ac58c-ac51-4696-9907-e4b3aa274f04

587d2870

update for inferred CDS & UTR features · 41ab5bb1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11156 ee4ac58c-ac51-4696-9907-e4b3aa274f04

41ab5bb1

Jun 19, 2009

change to chado_infer_CDS_UTR · 0517c717

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11155 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0517c717

option chado_infer_CDS_UTR · 3757426f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11154 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3757426f

update · 83925711

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11153 ee4ac58c-ac51-4696-9907-e4b3aa274f04

83925711

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