Commits · f8b70e04d82f9a3866f081613eb0e4d31c9f8ece · violethaze74 / Artemis

Jul 24, 2009

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11424 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f8b70e04

use a graph schema so change query to look for graph.graph · 6a50ac87

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11423 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6a50ac87

add postgres to classpath · 6f1e96ca

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11418 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6f1e96ca

update · bc86392f

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11417 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bc86392f

use String variable in IOException construction · d1317b92

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11416 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d1317b92

Jul 23, 2009

include option for opening gene builder in read only mode · 2bc2a09d

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11408 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2bc2a09d

Jul 22, 2009

Add option to read data from a graph table in the database · b4cc53d4

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11405 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b4cc53d4

ensure the Reader is closed after reading · 2b8c9549

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11404 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2b8c9549

Jul 21, 2009

In GFF3 export, lowercased the first character of non-reserved tag names... · af1be70f

gv1 authored 15 years ago

In GFF3 export, lowercased the first character of non-reserved tag names because this was breaking the Bio::FeatureIO parser, and because an uppercased non-reserved attribute name is apparently illegal according to the GFF3 specification.


git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11399 ee4ac58c-ac51-4696-9907-e4b3aa274f04

af1be70f

update · 6a664e62

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11391 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6a664e62

docs for user graph format · 50459ebd

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11390 ee4ac58c-ac51-4696-9907-e4b3aa274f04

50459ebd

add support for MSPcrunch file format · 6b39d787

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11389 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6b39d787

Jul 20, 2009

add ability to read in BLAST file format · 9b68c4bf

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11385 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9b68c4bf

add centromere and polypeptide_motif · e4932064

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11383 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e4932064

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

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