Dashboard

Welcome Message

Welcome to Atlassian Crucible with FishEye .

To report a bug or suggest a feature please raise an issue in our public JIRA.

Customize this welcome note.

Support

You are running Crucible 4.2.1 with FishEye 4.2.1 (20161109135523 2016-11-09)

If you are experiencing any issues, please contact your administrator. You may also want to browse the documentation or search the support forums. Still stuck? You can start a support ticket at support.atlassian.com or raise a bug or feature request at jira.atlassian.com.

Customize the support message.

Wednesday 28 Jul
11:36 am

Mateusz Warowny

Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka-integration

Options
    • binary
    /j11lib/slivka-client.jar
    • -1
    • +0
    /src/jalview/ws/jws2/JPredThread.java
    • -4
    • +6
    /src/jalview/ws/slivkaws/SlivkaJPredServiceInstance.java
    • -4
    • +14
    /src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
    • -1
    • +3
    /src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
    • -55
    • +50
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
Tuesday 27 Jul
4:36 pm

Mateusz Warowny

Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

Options
    • -13
    • +28
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
2:26 pm

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

JAL-3674 Jmol seems to sometimes return a null for some commands, handle it at source

Options
    • -1
    • +4
    /src/jalview/structures/models/AAStructureBindingModel.java
2:25 pm

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

JAL-3855 suppress NPE when trying to retrieve SIFTS mappings for Alphafold PDB IDs

Options
    • -1
    • +1
    /src/jalview/structure/StructureSelectionManager.java
1:52 pm

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

JAL-3855 ALPHAFOLD database source based on the PDB retriever

Options
    • -0
    • +281
    /src/jalview/ws/dbsources/EBIAlfaFold.java
1:35 pm

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

JAL-3855 check if an alpha fold ID and retrieve using that source

Options
    • -1
    • +9
    /src/jalview/gui/AppJmol.java
    • -1
    • +8
    /src/jalview/gui/StructureViewerBase.java
1:34 pm

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

JAL-3855 check for existence of an alpha fold model when pinging the PDBe

Options
    • -0
    • +157
    /src/jalview/fts/service/alphafold/AlphafoldRestClient.java
    • -5
    • +9
    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
1:33 pm

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

JAL-3855 convenience method to check a URL will return a 200

Options
    • -0
    • +32
    /src/jalview/util/HttpUtils.java
12:00 pm

Mateusz Warowny

Merge commit '0b438477b16470202bddfecb54e0587036b37202' into alpha/JAL-3066_Jalview_212_slivka-integration

Options
Sunday 25 Jul
5:48 pm

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

JAL-3854 patched SeqSeqUtils.deUniquify to not use instanceOf - seems to work

Options
    • -2
    • +6
    /src/jalview/analysis/SeqsetUtils.java
4:23 pm

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

JAL-2994 disable tests for FileUtils path search methods on bamboo

Options
    • -2
    • +8
    /test/jalview/util/FileUtilsTest.java
4:08 pm

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

JAL-3848 slivka preferences in javascript

Options
    • -2
    • +3
    /src/jalview/jbgui/GPreferences.java
4:07 pm

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

JAL-3848 reinstate Fetch DB References submenu

Options
    • -0
    • +1
    /src/jalview/gui/AlignFrame.java
3:51 pm

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

JAL-3848 add compbio and jalview to direct connection list for J2S

Options
    • -0
    • +5
    /src/jalview/bin/Jalview.java
3:45 pm

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

JAL-3848 update jalview core with slivka classes, example file import and structure view

Options
    • -122
    • +1160
    /utils/jalviewjs/classlists/jalview.txt
3:04 pm

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

JAL-3853 - tweak test again - since failed a few commits after f6cb90d43782ca99cf2b1cbee2dc76bca3d1d466

Options
    • -1
    • +1
    /test/jalview/io/SequenceAnnotationReportTest.java
2:47 pm

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

JAL-3848 update swingJS runtime and transpiler to 3.3.1

Options
    • binary
    /swingjs/SwingJS-site.zip
    • -271
    • +256
    /swingjs/differences.txt
    • binary
    /swingjs/net.sf.j2s.core-j11.jar
    • binary
    /swingjs/net.sf.j2s.core.jar
    • -1
    • +1
    /swingjs/timestamp
    • -0
    • +10
    /swingjs/ver/3.3.1-j11/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.3.1-j11/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.3.1-j11/_j2sclasslist.txt
    • -0
    • +1526
    /swingjs/ver/3.3.1-j11/differences.txt
    • binary
    /swingjs/ver/3.3.1-j11/net.sf.j2s.core-j11.jar
    • -0
    • +1
    /swingjs/ver/3.3.1-j11/timestamp
    • -0
    • +10
    /swingjs/ver/3.3.1/DEV_NOTES.txt
    • binary
    /swingjs/ver/3.3.1/SwingJS-site.zip
    • -0
    • +412
    /swingjs/ver/3.3.1/_j2sclasslist.txt
    • -0
    • +1526
    /swingjs/ver/3.3.1/differences.txt
    • binary
    /swingjs/ver/3.3.1/net.sf.j2s.core.jar
    • -0
    • +1
    /swingjs/ver/3.3.1/timestamp
2:16 pm

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

Merge branch 'improvement/JAL-3848_slivka_0.8' of https://source.jalview.org/git/jalview into improvement/JAL-3848_slivka_0.8

Options
Friday 23 Jul
1:12 pm

Mateusz Warowny

JAL-3848 Update slivka client javajs library.

Options
    • binary
    /utils/jalviewjs/libjs/slivka-client-site.zip
Thursday 22 Jul
8:44 pm

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

JAL-3848 enable slivka services dialog in JalviewJS

Options
    • -2
    • +4
    /src/jalview/gui/Preferences.java
8:41 pm

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

JAL-3853 JAL-1870 toggle to enable/disable posterior probability transparency when rendering per sequence annotation row scores .. needs more work

Options
    • -0
    • +21
    /src/jalview/gui/AnnotationColourChooser.java
    • -0
    • +1
    /src/jalview/gui/AnnotationRowFilter.java
8:40 pm

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

JAL-3853 JAL-1870 patch tests for annotation colour gradient without transparency/per sequence annotation score encoding

Options
    • -3
    • +13
    /src/jalview/schemes/AnnotationColourGradient.java
8:37 pm

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

JAL-1950 patch groovy bootstrap for importing hmmer3 json

Options
    • -2
    • +2
    /examples/groovy/hmmertestimport.groovy
8:36 pm

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

JAL-3853 patch sequence annotation report code and tweak the test. When merging from 2.11.2 develop there will be conflicts that need merging re HTMLXML tags

Options
    • -8
    • +15
    /src/jalview/io/SequenceAnnotationReport.java
    • -1
    • +1
    /test/jalview/io/SequenceAnnotationReportTest.java
6:04 pm

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

JAL-3848 ensure annotation from a service gets a calcId so it can be updated and tracked across multiple views - nb - service.getId() probably isn’t the right value to use for this!

Options
    • -1
    • +22
    /src/jalview/io/AnnotationFile.java
    • -1
    • +1
    /src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
6:02 pm

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

JAL-3848 don’t include sequence limits in sequence id as it confuses slivka-0.8’s jalview-feature-file creation script

Options
    • -2
    • +5
    /src/jalview/ws/slivkaws/SlivkaWSInstance.java
6:00 pm

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

JAL-3848 - actually test the Slivka and JABAWS disorder services - nb still need asserts to verify the disorder annotation from Slivka looks like Jabaws

Options
    • -3
    • +18
    /test/jalview/ws/jabaws/DisorderAnnotExportImport.java
Wednesday 21 Jul
5:08 pm

Mateusz Warowny

JAL-3848 print exception for failed align jobs

Options
    • -0
    • +1
    /src/jalview/ws/gui/MsaWSThread.java
5:06 pm

Mateusz Warowny

JAL-3848 add latest slivka-client fixes.

Options
    • binary
    /j11lib/slivka-client.jar
12:50 pm

Ben Soares

JAL-3850 fixed full class name

Options
    • -2
    • +2
    /build.gradle