From 82bb69383ab22735cbd3440c670ae0b290fe6afd Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Sep 2015 18:24:00 +0100 Subject: [PATCH] JAL-1645 rejig bioJSON, export and whats new --- help/helpTOC.xml | 3 +- help/html/features/bioJsonFormat.html | 68 ++++++++++++++++---------- help/html/io/export.html | 85 ++++++++++++++++++++++----------- help/html/whatsNew.html | 4 +- 4 files changed, 103 insertions(+), 57 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 2580d9a..fe42110 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -16,14 +16,13 @@ - - + diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html index e12332a..09e4197 100644 --- a/help/html/features/bioJsonFormat.html +++ b/help/html/features/bioJsonFormat.html @@ -20,33 +20,49 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -BioJSON-1.0 +BioJSON in Jalviwe -

BioJSON 1.0

- BioJSON is a JavaScript Object Notation (JSON) specification for the representation and exchange of multiple sequence alignment data. - The first version of the specification was developed in 2015 and implemented in Jalview 2.9. Find out more about BioJSON - at http://jalview.github.io/biojson/. - -

Features supported

- Export and import of a single alignment along with it's properties listed below: -

Alignment Annotations
Alignment Features
Alignment Sequences
Color Scheme
Hidden Columns
Hidden Sequences
Sequence Groups

- -

Features not yet supported

- The following features are not supported in BioJSON-1.0: -

Export and import of Reference sequence
Export and import of Representative sequence
Export and import of Trees
Export and import of 3D Structures

+ BioJSON support in Jalview +

BioJSON is a JavaScript Object Notation (JSON) specification + for the representation and exchange of multiple sequence alignment + data.

Jalview 2.9 includes support for reading and writing BioJSON + v1.0 data directly, or embedded in HTML documents. It can also + generate HTML pages which employ the BioJS MSA viewer for + interactive display of BioJSON data.

+ Finding out more about BioJSON +

+ The BioJSON specification is published at http://jalview.github.io/biojson/. +

+ Jalview's Support for BioJSON v1.0 +

It is currently possible to export an alignment view along with + the following additional data:

Alignment Annotations
Alignment Features
Alignment Sequences
Color Scheme
Hidden Columns
Hidden Sequences
Sequence Groups

+ Jalview data not supported in BioJSON v1.0 +

The following data are not currently preserved on export:

Alignment Reference sequences
Representative sequence groups
Trees
3D Structures

diff --git a/help/html/io/export.html b/help/html/io/export.html index 7a3efa7..c3270c7 100755 --- a/help/html/io/export.html +++ b/help/html/io/export.html @@ -23,35 +23,66 @@ Exporting alignments as artwork -

Exporting alignments as graphics and lineart

The alignment view can be printed using -File→Print, or exported in a number of ways via the -File→Export menu: -

HTML
for viewing in a web browser -
PNG - a Portable Networks Graphics image
For low quality -diagrams and powerpoint presentations -
EPS - an Encapsulated Postscript Document
For high quality -diagrams and publications. -
SVG - a Scalable Vector Graphics document
For high quality -diagrams in publications and on the web. -
BioJS - A JavaScript based multiple sequence alignment visualiser.
For viewing in a web browser. Get more info about BioJS at http://msa.biojs.net/ -

- -

From Jalview 2.9, the HTML exporting system was re-implemented to use SVG rendering. Also, optional embedding of BioJSON data to the generated HTML file was introduced. -This is achieved using a hidden input or div element which MUST be named "seqData" as seen in the examples below: -

	<div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>
-	  OR
-	<input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/>

-HTML file embedded with BioJSON can be imported back to Jalview at a later date. During the import operation, Jalview uses an API called JSoup to traverse through the HTML file and extract the embedded BioJSON data from the target div or input element named 'seqData'. The extracted data is then parsed as a BioJSON format. - +

+ Exporting alignments as graphics and lineart +

+ The alignment view can be printed using File→Print, + or exported in a number of ways via the File→Export + menu: + +

HTML
+ for viewing in a web browser +
PNG - a Portable Networks Graphics image
+ For low quality diagrams and powerpoint presentations +
EPS - an Encapsulated Postscript Document
+ For high quality diagrams and publications. +
SVG - a Scalable Vector Graphics document
+ For high quality diagrams in publications and on the web. +
BioJS MSA - A JavaScript based multiple sequence alignment + viewer.
For interactive alignment data + visualisation in a web browser.
Get more info about the + BioJS MSA viewer at a + href="http://msa.biojs.net/">http://msa.biojs.net/ + +

+ +

+ Exporting alignments as Web Pages +

+ In Jalview 2.9, new HTML exporting options were introduced. The + standard HTML export option displays alignments as SVG documents + embedded as scollable panes. Exported pages can optionally also + include BioJSON data, + which allows Jalview to extract the original data used to create the + page. Jalview can also generate HTML pages which embed BioJSON data + and the BioJS MSA viewer, a pure javascript alignment viewer that + provides a range of interactive analysis capabiltiies. +

+ +

+ Import of BioJSON data from HTML pages +

When importing embedded data in an HTML document, Jalview + searches for a hidden input or div element named "seqData": +

+    <div name="seqData" id="seqData" style="display: none;">#valid BioJSON data#</div>
+

+ OR +

+    <input type="hidden" id="seqData" name="seqData" value='#valid BioJSON data#'/>
+

+ Jalview can also import JSON data directly if it conforms to the BioJSON specification. +

Tips for working with EPS Files

The EPS file generated by Jalview contains vector graphics which are directly editable in graphics applications such as Adobe Illustrator.

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 04fcc69..b115385 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -74,11 +74,11 @@ including the loss of pseudoknots when RNA secondary structure is shown VARNA.

Protein Secondary Structure predictions - with JPred4Jalview includes a number of new features for working + with JPred4
Jalview includes a number of new features for working with secondary structure predictions from the JPred4 server. These include the ability to automatically hide insertions and highlight mutations in an alignment with respect to a reference sequence. - Jalview 2.9's new scrollable SVG HTML export mode was also + Jalview 2.9's new scrollable SVG HTML export was also developed specifically for the JPred4 server.

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