Commits · 1d9be92680876f8d8b1df5d08cf496d855283a0c · violethaze74 / Artemis

Apr 26, 2010

add plasmid to list of srcfeatures · 47069fef

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13746 ee4ac58c-ac51-4696-9907-e4b3aa274f04

47069fef

Apr 15, 2010

check is_analysis and cvterm · f0db06c5

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13689 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f0db06c5

check for is_analysis flag · d26ceca7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13688 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d26ceca7

Sep 14, 2009

add caching · 9a37c7d6

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11766 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9a37c7d6

Sep 01, 2009

add deleteFeatureRelationship · 77880591

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11676 ee4ac58c-ac51-4696-9907-e4b3aa274f04

77880591

Aug 28, 2009

change to getLazyClustersByFeatureIds to include orthologs that are connected... · ac7290bd

tjc authored 15 years ago

change to getLazyClustersByFeatureIds to include orthologs that are connected with a feature_relationship and no match feature


git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11663 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ac7290bd

Aug 06, 2009

use srcfeature_id when updating and add getFeatureLocBySrcFeatureId · ab987450

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11508 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ab987450

Jul 24, 2009

use a graph schema · f8b70e04

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

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

Jun 30, 2009

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 02, 2009

use resultMap for getOrganism · 96bda508

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10972 ee4ac58c-ac51-4696-9907-e4b3aa274f04

96bda508

May 14, 2009

changes to speed up getOrganismsContainingSrcFeatures · bbffb240

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10812 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bbffb240

add getLazyFeatureExact · 5ee41bf4

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10800 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5ee41bf4

May 08, 2009

make PubDbXRef.xml · 91b774e8

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10761 ee4ac58c-ac51-4696-9907-e4b3aa274f04

91b774e8

Apr 03, 2009

changes for updating feature residues in the database · fdaa21b4

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10380 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fdaa21b4

Mar 24, 2009

reduce max number of connections in pool · 8f4dc6e6

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10268 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8f4dc6e6

Feb 04, 2009

changes to allow for FeatureCvTerm.rank column to be absent · 5b1b4cad

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9753 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5b1b4cad

remove organism join for statements mapping to map-feature-with-residues-result · 8d1ba6d8

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9752 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8d1ba6d8

Dec 10, 2008

add OrganismProp · a14d27d9

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9582 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a14d27d9

Nov 25, 2008

fix for similarity · d7e3ce0c

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9431 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d7e3ce0c

Nov 21, 2008

remove join that is not needed from getTopLevelOrganisms · 71f66f5d

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9412 ee4ac58c-ac51-4696-9907-e4b3aa274f04

71f66f5d

Nov 17, 2008

add getTopLevelFeatures · 69f13ce0

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9370 ee4ac58c-ac51-4696-9907-e4b3aa274f04

69f13ce0

add getTopLevelOrganisms and getOrganismsContainingSrcFeatures · 67ac9dab

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9369 ee4ac58c-ac51-4696-9907-e4b3aa274f04

67ac9dab

update order of xml · 6e88e163

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9368 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6e88e163

Oct 15, 2008

remover order from getFeature · 02b35232

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9034 ee4ac58c-ac51-4696-9907-e4b3aa274f04

02b35232

Oct 14, 2008

speed up getFeature · c038d8ef

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9006 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c038d8ef

Sep 25, 2008

optimise getResidueFeatures · f3699eb3

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8894 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f3699eb3

change getLazySimilarityMatches and getLazySimilarityMatchesByFeatureIds to... · 495eb12f

tjc authored 16 years ago

change getLazySimilarityMatches and getLazySimilarityMatchesByFeatureIds to speed up loading similarity and polypeptide domains that are featureLoc'ed


git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8882 ee4ac58c-ac51-4696-9907-e4b3aa274f04

495eb12f

add getFeatureLocsByListOfIds · 04b9ba65

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8881 ee4ac58c-ac51-4696-9907-e4b3aa274f04

04b9ba65

Sep 24, 2008

example DBCP transactionManager · 57423163

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8879 ee4ac58c-ac51-4696-9907-e4b3aa274f04

57423163

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

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

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

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

Sep 15, 2008

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 08, 2008

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

Aug 07, 2008

add ping query to SimpleDataSource · bc526837

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8485 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bc526837

Aug 05, 2008

use Pool.TimeToWait · ad7faa05

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8463 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ad7faa05

Aug 01, 2008

retrieve the features that are featureloced to feaure · 140473d1

tjc authored 16 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8424 ee4ac58c-ac51-4696-9907-e4b3aa274f04

140473d1

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