From: James Procter Date: Thu, 5 Oct 2023 07:05:32 +0000 (+0100) Subject: Merge branch 'develop' into releases/Release_2_11_3_Branch X-Git-Tag: Release_2_11_3_0~6 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4ad05f84d30ed345acbb533bb51dd832c727de99;hp=1d65dccb595b609c3bc2d69be95ae24f161ddb63;p=jalview.git Merge branch 'develop' into releases/Release_2_11_3_Branch --- diff --git a/build.gradle b/build.gradle index c4ed582..8ac2757 100644 --- a/build.gradle +++ b/build.gradle @@ -1783,6 +1783,27 @@ task testTask1(type: Test) { } } +task testTask2(type: Test) { + group = "Verification" + description = "Tests that need to be isolated from the main test run" + useTestNG() { + includeGroups name + excludeGroups testng_excluded_groups.split(",") + preserveOrder true + useDefaultListeners=true + } +} +task testTask3(type: Test) { + group = "Verification" + description = "Tests that need to be isolated from the main test run" + useTestNG() { + includeGroups name + excludeGroups testng_excluded_groups.split(",") + preserveOrder true + useDefaultListeners=true + } +} + /* insert more testTaskNs here -- change N to next digit or other string */ /* task testTaskN(type: Test) { diff --git a/gradle.properties b/gradle.properties index 547304f..c2e217f 100644 --- a/gradle.properties +++ b/gradle.properties @@ -177,7 +177,7 @@ imagemagick_convert = ~/buildtools/imagemagick/bin/convert bamboo_channelbase = https://builds.jalview.org/browse bamboo_planKey = -bamboo_getdown_channel_suffix = /latest/artifact/shared/getdown-channel +bamboo_getdown_channel_suffix = /latest/artifact/shared/getdown-build-for-website/default eclipse_codestyle_file = utils/eclipse/JalviewCodeStyle.xml eclipse_extra_jdt_prefs_file = utils/eclipse/org.eclipse.jdt.core.jalview.prefs diff --git a/help/help/html/colourSchemes/annotationColouring.html b/help/help/html/colourSchemes/annotationColouring.html index 2272503..c9221a1 100755 --- a/help/help/html/colourSchemes/annotationColouring.html +++ b/help/help/html/colourSchemes/annotationColouring.html @@ -30,9 +30,17 @@

Jalview allows the columns of an alignment to be coloured using any numerical annotation rows added to that alignment.

Select "Colour" - → ".. by Annotation" to bring up the + → "by Annotation..." to bring up the Colour by Annotation settings window.
+
You can also apply Colour by annotation for a particular annotation + (or per-sequence set) by right-clicking an annotation row's label and selecting "Colour by Annotation..." or "Colour by Annotation (per Sequence)..." from the + Annotation label popup menu. (Since Jalview 2.11.3) +
+
+ +
+

The Colour by Annotation Settings Window


diff --git a/help/help/html/features/annotationsubmenucolbyannot.png b/help/help/html/features/annotationsubmenucolbyannot.png new file mode 100644 index 0000000..22f69d9 Binary files /dev/null and b/help/help/html/features/annotationsubmenucolbyannot.png differ diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index c82cb20..238366c 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -315,11 +315,11 @@
The value can also be specified as a sub-value: 
-  jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
which is equivalent to 
-  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1+SPIOL
+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1_SPIOL
    --structureviewer jmol
diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html index cebc16b..8d180ee 100644 --- a/help/help/html/features/paematrices.html +++ b/help/help/html/features/paematrices.html @@ -29,37 +29,63 @@ Jalview

-

Predicted Alignment Error matrices are produced by deep-learning - based 3D-structure prediction pipelines such as AlphaFold.

+

Predicted Alignment Error (PAE) matrices are produced by + deep-learning based 3D-structure prediction pipelines such as + AlphaFold. They reflect how reliably two parts of a model have been + positioned in space, by giving for each residue the likely error (in + Ångstroms) between that residue and every other modelled + position the pair of residues' real relative position, if the model + and real 3D structure were superimposed at that residue.

+

+ Jalview visualises PAE matrices as an alignment annotation track, + shaded from dark green to white, similar to the encoding used on the + EBI-AlphaFold website (see O04090 3D model + at EBI-AlphaFoldDB). +

+
+
Alignment of EPAS1 homologs from Human, Rat and Cow, with predicted alignment error shown in Jalview
+
Predicted Alignment Error Matrix
from https://alphafold.ebi.ac.uk/entry/Q99814
+
+

+ Importing PAE Matrices +

Jalview retrieves PAE matrices when importing predicted 3D structures from the EBI-AlphaFold database via Jalview's structure - chooser GUI. + chooser GUI. If you have produced your own models and accompanying + PAE matrices using a pipeline such as ColabFold, then you can load + them both together via the + Load PDB + File dropdown menu in the 3D structure chooser, providing it is + in a + supported PAE format.

- If you have produced your own models using a pipeline such as - ColabFold, then you can load it via the 'Add PAE matrix file' button - in the Load - PDB File dropdown menu in the 3D structure chooser, providing it is - in a supported PAE format. , - or the Command Line - Interface. See Working - with PAE Matrices for information on how they are visualised and - analysed in Jalview. + The Command Line + Interface also provides a options for importing PAE matrices along + side models, enabling the automated production of alignment figures + annotated with PAE matrices and PLDDT scores.

+

+ Showing PAE Matrix Annotations

- An additional Predicted Alignment Error file can also be - provided when importing 3D structure data. Jalview supports import of - PAE Matrices provided as AlphaFold - format JSON files - which are also produced by ColabFold. See Working with PAE Matrices for details on - what Jalview allows you to do with associated PAE matrix data. + When viewing 3D structures from the EBI-AlphaFold database or local 3D + structures with an associated PAE file, the PAE is imported as Reference + Annotation, which is not always automatically added to the alignment + view.

+

To show the PAE, right click the sequence and locate the 'Add + Reference Annotation' entry in the Sequence ID submenu, or select all + sequences and locate the option in the Selection submenu. You can do + this in any alignment window (or view) where a sequence with + associated PAE data appears.

+

- The Structure Chooser interface was introduced in Jalview - 2.9. + Support for visualision and analysis of predicted alignment + error matrices was added in Jalview 2.11.3.

diff --git a/help/help/html/features/search.html b/help/help/html/features/search.html index d559db8..6889d84 100755 --- a/help/help/html/features/search.html +++ b/help/help/html/features/search.html @@ -36,7 +36,7 @@ td {

The search box is displayed by pressing Control and F or selecting "Find..." from the "Search" menu.

- +

"Find next" will find the next occurrence of the query and adjust the alignment window view to show it, and "Find all" highlights all matches for a query. The @@ -46,18 +46,24 @@ td {