From: Jim Procter Date: Wed, 23 Nov 2016 17:44:50 +0000 (+0000) Subject: Merge branch 'develop' into releases/Release_2_10_Branch X-Git-Tag: Release_2_10_1~8 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=faa1540e197dc509d2044d4b5af39e8dd903793f;hp=3956359ebd542bc69f68fdea4ee47fac7f5e7dff;p=jalview.git Merge branch 'develop' into releases/Release_2_10_Branch --- diff --git a/AUTHORS b/AUTHORS index f0b4787..1bfc734 100644 --- a/AUTHORS +++ b/AUTHORS @@ -7,15 +7,16 @@ or might otherwise be considered author of Jalview. The people listed below are 'The Jalview Authors', who collectively own the copyright to the Jalview source code and permit it to be released under GPL. -This is the authoritative list. It was correct on 6th Oct 2016. +This is the authoritative list. It was correct on 23rd November 2016. If you are releasing a version of Jalview, please make sure any statement of authorship in the GUI reflects the list shown here. In particular, check the resources/authors.props file ! Jim Procter -Andrew Waterhouse Mungo Carstairs Tochukwu 'Charles' Ofoegbu +Kira Mourao +Andrew Waterhouse Jan Engelhardt Lauren Lui Anne Menard diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index cbef2c1..5ae00af 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -73,7 +73,10 @@ When a selection is highlighted in a Jalview window, use the Select→Select Highlighted Region or press B to add the mapped positions to the alignment window's column - selection. + selection.
Hint: Use your machine's 'switch + application' key combination (Alt-Tab on Windows and Linux, + Cmd-Tab on OSX) to quickly switch between UCSF Chimera and Jalview + before pressing 'B' to select highlighted regions.

Basic screen operations (see Selecting regions from Search Results

- Press 'B' or select the Select Highlighted Columns option - from the alignment window's select menu to add columns containing + Press 'B' or use the Select Highlighted Columns option from + the alignment window's select menu to add columns containing highlighted search results to the alignment window's column - selection. + selection. Alt-'B' will add all but the highlighted columns, and + Ctrl (or Cmd) -B will toggle the column selection for the + highlighted region.

diff --git a/help/html/keys.html b/help/html/keys.html index b79ce4d..1a5fc18 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -169,16 +169,16 @@ columns are selected, you should use the H B Both - Mark the currently highlighted columns + Add highlighted columns to current column selection Alt 'B' Both - Mark all but the currently highlighted columns + Add all but the currently highlighted columns to current selection Control 'B' Both - Toggle the marks on the currently highlighted - columns (or all others if Alt is pressed) + Toggle the column selection marks for the currently highlighted + columns (or all others if Alt is also pressed) H diff --git a/help/html/releases.html b/help/html/releases.html index abfefa2..441b394 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -70,14 +70,14 @@ Application

- Sequence ID tool tips have been tamed - (databases sorted alphabetically, abridged ID sets) + Sequence ID tool tip presents abridged + set of database cross-references, sorted alphabetically

New replacement token for creating URLs just from database cross references. Users with custom links - will receive a warning dialog asking them to update their - preferences. + will receive a warning + dialog asking them to update their preferences.
Cancel button and escape listener on @@ -85,31 +85,24 @@ Chimera session
- Jalview's chimera control window closes if + Jalview's Chimera control window closes if the Chimera it is connected to is shut down
- Custom URL links for database - cross-references are matched to database name regardless - of case -
- Select highlighted columns menu item and - keystroke (B) to mark columns containing highlighted - regions from structure selections or results of a Find - operation + New keystroke (B) and Select highlighted + columns menu item to mark columns containing + highlighted regions (e.g. from structure selections or results + of a Find operation)
Command line option for batch-generation of HTML pages rendering alignment data with the BioJS MSAviewer

- Applet + Applet

- + --> Build and deployment

Updated Jalview's Certum code signing certificate @@ -148,6 +141,11 @@ than a range in linked structure views, and treated correctly when selecting and computing trees from features
+ Custom URL links for database + cross-references are matched to database name regardless + of case +

Application @@ -202,9 +200,10 @@ lysozyme results in a PDB Client error dialog box + Build and deployment

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index 36c7c6b..088a539 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -66,10 +66,19 @@ the sequence ID for the sequence (since Jalview 2.10.1).

- If Jalview opens a project with links which include $SEQUENCE_ID$ tokens, it will present - the user with a warning message, as these links may need to be updated to use $DB_ACCESSION$, if - they were added before Jalview 2.10.1. The message lists the links which should be reviewed. - The warning can be turned off completely via a checkbox in the message dialog. + Warning dialog about updating + your configured URL links
In the desktop + prior to Jalview 2.10.1, the only way to configure custom links for + a particular database cross-reference for a sequence was to give it + a name that + exactly matched the database source, and a regular + expression for filtering out any spurious matches generated when the + custom linked was tested against the Sequence's ID string. Since the + introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$ + will not be used for database cross-reference accession strings, and + if you have custom links configured, Jalview will raise a warning + message so let you know that you may need to update your links to + use $DB_ACCESSION$.

Regular Expression Substitution
A url may diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 448430d..e8b9c96 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,69 +24,37 @@
- What's new in Jalview 2.10.0b1 ? + What's new in Jalview 2.10.1 ?

- Jalview 2.10.0b1 is a patch release for 2.10, the next major release - in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release - Notes, but the highlights are below. + Jalview 2.10.1 was released on 24th November 2016. Full details are + in the Jalview 2.10.1 + Release Notes, but the highlights are below. This is also the + first release to include contributions from Kira Mourão, who + joined Jalview's core development team in October 2016.
- Drag and drop reinstated for the Jalview desktop on - Windows, Linux and older OSX systems.
- Problems loading local PDB files have been fixed
- Conservation shading can be disabled for PID and consensus - based colour scheme
-
Major highlights of the 2.10.0 Release
-
- Ensembl sequence fetcher
  Annotated - Genes, transcripts and proteins can be retrieved via Jalview's new - Ensembl REST - client. Support for import of Ensembl data allows: -
  - Aligned locus view
    Transcripts - retrieved for a gene identifier via the Ensembl or - EnsemblGenomes sequence databases are automatically aligned to - their reference genome, and introns hidden from the view.
  - Sequence variant data
    Jalview - propagates variant annotation on genomic regions onto - transcripts and protein products, complete with associated - metadata such as clinical significance.
- Ensembl and ENA 'show cross-references' - support
  The Calculations menu's 'Show - cross-references' now offers Ensembl as well as EMBLCDS and - Uniprot when CDS/Protein mapping data is available for download or - display. This allows variant annotation to be added directly to an - alignment of UniProt sequences.
- Working with structures -
  - More accurate structure mappings
    - Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) - to match structures - to UniProt sequences, even for structures containing - multiple copies of a sequence.
  - Import structures as mmCIF
    Jalview - now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large - structures to be imported, such as the HIV virus capsid - assembly.
  - Chimera users will need to upgrade to - 1.11.1
    If you use Chimera to view structures - downloaded by Jalview 2.10, you will need to make sure you are - running the latest version of Chimera.
- UniProt Free Text Search
  The new - search dialog for UniProt allows you to browse and retrieve - sequences with free-text search, or structured queries.
- Reference sequence alignment view
  - Jalview 2.9 introduced support for reference sequences. In 2.10, - when a reference sequence is defined for the alignment, the - alignment column ruler is now numbered according to the reference - sequence. The reference sequence for alignment views can also be - saved and restored from Jalview projects.
- More memory efficient
  We've slimmed + down the consensus analysis data structures used by Jalview so + even wider alignments can be worked with.
- Select highlighted region
  Press 'B' + or use the new menu option in the alignment window's Select menu + to mark columns containing highlighted regions generated from + structure selections, mouse-overs, or resulting from a + Find operation.
- New custom link mechanism for opening URLs + for database cross references.
  If you have customised URL + links in your Jalview preferences, then you may already have seen + the Update your links + warning dialog.
- New command line export option for BioJS + MSAviewer
  A number of small bugs with the HTML export + functions from the Jalview desktop were also fixed.
- Small but significant changes to the + physicochemical properties and consensus calculations
  Threonine + is no longer considered a non-hydrophobic residue in the protein + conservation calculation, and minor bugs addressed in PID and + consensus colouring.
diff --git a/resources/authors.props b/resources/authors.props index bcb07cf..3488ac6 100644 --- a/resources/authors.props +++ b/resources/authors.props @@ -1,4 +1,4 @@ YEAR=2016 -AUTHORS=J Procter, M Carstairs, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton -AUTHORFNAMES=Jim Procter, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton +AUTHORS=J Procter, M Carstairs, TC Ofoegbu, K Mourao, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton +AUTHORFNAMES=Jim Procter, Mungo Carstairs, Tochukwu 'Charles' Ofoegbu, Kira Mourao, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton \ No newline at end of file diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 9a58965..6360dc7 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -126,7 +126,7 @@ action.colour = Colour action.calculate = Calculate action.select_all = Select all action.select_highlighted_columns = Select Highlighted Columns -tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-B to toggle, and Alt-B to mark all but highlighted columns +tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns action.deselect_all = Deselect all action.invert_selection = Invert selection action.using_jmol = Using Jmol diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 9c2436c..e5b5e27 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -122,6 +122,8 @@ action.change_font_tree_panel = Cambiar fuente (panel del action.colour = Color action.calculate = Calcular action.select_all = Seleccionar Todo +action.select_highlighted_columns = Seleccionar columnas resaltadas +tooltip.select_highlighted_columns = Presione B para marcar las columnas resaltadas, Ctrl (o Cmd)-B para cambiarlas, y Alt-B para marcar todas menos las columnas resaltadas action.deselect_all = Deseleccionar Todo action.invert_selection = Invertir selección action.using_jmol = Usar Jmol