jalview/src/jalview/fts

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Friday 24 Sep 2021
5:23 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop up menu item

Options
    • -0
    • +5
    ./threedbeacons/TDB_FTSData.java
  2. … 3 more files in changeset.
2:17 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 abstract essential TDB metadata from the user configurable data array displayed in the JTable

Options
    • -0
    • +115
    ./threedbeacons/TDB_FTSData.java
    • -48
    • +1
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 1 more file in changeset.
Monday 20 Sep 2021
2:54 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 throw the exception even if it has no message

Options
    • -14
    • +15
    ./threedbeacons/TDBeaconsFTSRestClient.java
Tuesday 14 Sep 2021
2:38 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 move mock query and responses to files

Options
    • -2764
    • +57
    ./pdb/PDBFTSRestClient.java
  2. … 7 more files in changeset.
12:34 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 allow multiple URL mocks and include P01308 in 3d-beacons mocks

Options
    • -7
    • +2394
    ./pdb/PDBFTSRestClient.java
    • -2
    • +2
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 4 more files in changeset.
Sunday 12 Sep 2021
3:53 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 JalviewJS workarounds/patches

Options
    • -2
    • +3
    ./threedbeacons/TDBeaconsFTSRestClient.java
  2. … 1 more file in changeset.
Saturday 11 Sep 2021
12:10 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 ensure tests use mocked service - proper exception for mocked 400 response

Options
    • -1
    • +1
    ./pdb/PDBFTSRestClient.java
  2. … 1 more file in changeset.
Friday 10 Sep 2021
1:42 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 point at production 3d-beacons url

Options
    • -1
    • +9
    ./threedbeacons/TDBeaconsFTSRestClient.java
Monday 06 Sep 2021
2:47 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 mocking for PDBFTS for related query to UniprotFTS mock.

Options
    • -9
    • +370
    ./pdb/PDBFTSRestClient.java
    • -16
    • +1
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 2 more files in changeset.
Friday 03 Sep 2021
6:41 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 mocking for testing 3D-Beacons FTS endpoint

Options
    • -5
    • +39
    ./threedbeacons/TDBeaconsFTSRestClient.java
  2. … 1 more file in changeset.
3:36 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3855 don’t need to query Alphafold2 repository directly from PDBe FTS client since 3db client will do that

Options
    • -2
    • +6
    ./pdb/PDBFTSRestClient.java
Monday 30 Aug 2021
2:44 pm

Jim Procter

Thursday 26 Aug 2021
2:57 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'feature/JAL-3855_ebi_alphafold_import' (commit '7856e91f60adc5c2d4943bad84a5a83e1412f00c') into features/r2_11_2_JAL-3929_3dbeacons

Options
    • -5
    • +9
    ./pdb/PDBFTSRestClient.java
2:57 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'feature/JAL-3855_ebi_alphafold_import' (commit '7856e91f60adc5c2d4943bad84a5a83e1412f00c') into features/r2_11_2_JAL-3929_3dbeacons

Options
    • -5
    • +9
    ./pdb/PDBFTSRestClient.java
2:56 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 3d-beacons structure chooser logic (not yet finished)

Options
    • -4
    • +25
    ./pdb/PDBFTSRestClient.java
    • -57
    • +105
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 8 more files in changeset.
2:56 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 3d-beacons structure chooser logic (not yet finished)

Options
    • -4
    • +25
    ./pdb/PDBFTSRestClient.java
    • -57
    • +105
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 8 more files in changeset.
Wednesday 25 Aug 2021
6:10 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 proof in principle 3d-beacons sequence fetcher - still some TODOs !

Options
    • -86
    • +74
    ./threedbeacons/TDBeaconsFTSPanel.java
    • -3
    • +2
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 1 more file in changeset.
6:10 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 proof in principle 3d-beacons sequence fetcher - still some TODOs !

Options
    • -86
    • +74
    ./threedbeacons/TDBeaconsFTSPanel.java
    • -3
    • +2
    ./threedbeacons/TDBeaconsFTSRestClient.java
  3. … 1 more file in changeset.
4:26 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 fixed up the 3d-beacons data columns definitions, tests and client.

Options
    • -2
    • +2
    ./threedbeacons/TDBeaconsFTSRestClient.java
  2. … 2 more files in changeset.
4:26 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 fixed up the 3d-beacons data columns definitions, tests and client.

Options
    • -2
    • +2
    ./threedbeacons/TDBeaconsFTSRestClient.java
  2. … 2 more files in changeset.
Monday 23 Aug 2021
5:43 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3829 removed unneeded attribute in FTS core

Options
    • -9
    • +3
    ./threedbeacons/TDBeaconsFTSRestClient.java
  2. … 1 more file in changeset.
5:43 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3929 removed unneeded attribute in FTS core

Options
    • -9
    • +3
    ./threedbeacons/TDBeaconsFTSRestClient.java
  2. … 1 more file in changeset.
4:52 pm

Jim Procter

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

4:49 pm

Jim Procter

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

4:48 pm

Jim Procter

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

4:43 pm

Jim Procter

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
2:12 pm

Jim Procter

remove debugging printlns

remove debugging printlns

2:12 pm

Jim Procter

aim is normally to avoid creating query-specific data containers on the core query response class

aim is normally to avoid creating query-specific data containers on the core query response class

10:26 am

Jim Procter

? not sure this is correct

? not sure this is correct

10:24 am

Jim Procter

Needs additionally: model_category created sequence_identity uniprot_start uniprot_end resolution coverage qmean_version ? model_version

Needs additionally:
model_category
created
sequence_identity
uniprot_start
uniprot_end
resolution
coverage
qmean_version ?
model_version