From 849a6a5ae80818bfb40f3843690c0ebee00c3d16 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Sep 2015 21:31:18 +0100 Subject: [PATCH] JAL-1645 rejig biojson/biojsmsa docs --- help/helpTOC.xml | 1 - help/html/features/bioJsonFormat.html | 28 ++++++++++++++++++++++------ help/html/features/biojsmsa.html | 22 ++++++++++++++-------- help/html/io/export.html | 16 +--------------- 4 files changed, 37 insertions(+), 30 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index fe42110..1f1a8b7 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -35,7 +35,6 @@ - diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html index 7828f50..efbfb8c 100644 --- a/help/html/features/bioJsonFormat.html +++ b/help/html/features/bioJsonFormat.html @@ -29,10 +29,12 @@

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.

+

+ 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

@@ -41,10 +43,24 @@ href="http://jalview.github.io/biojson/">http://jalview.github.io/biojson/.

+ Import of BioJSON data from HTML pages +

+

When importing embedded data in an HTML document, Jalview + searches for a hidden (usually) 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 BioJSON data directly.

+ +

Jalview's Support for BioJSON v1.0

-

BioJSON exports of an alignment view include - the following additional data:

+

BioJSON exports of an alignment view include the following + additional data:

  • Alignment Annotations
  • Alignment Features
    • diff --git a/help/html/features/biojsmsa.html b/help/html/features/biojsmsa.html index ff4d8da..f97c7b3 100644 --- a/help/html/features/biojsmsa.html +++ b/help/html/features/biojsmsa.html @@ -5,18 +5,24 @@ Exporting Alignments for viewing with the BioJS MSA Viewer

    -

    Since Jalview 2.9, HTML files can be generated from an - alignment within the Jalview desktop application that show the - alignment in an interactive viewer called 'BioJS-MSA'. The BioJS MSA - Viewer is a full-featured JavaScript based multiple sequence - alignment visualisation system created by a community of biological - data visualisation developers, and is developed independently of - Jalview.

    +

    + Since Jalview 2.9, HTML files can be generated from an alignment + within the Jalview desktop application that show the alignment in an + interactive viewer called 'BioJS-MSA'. These pages embed Jalview's + alignment data as BioJSON, which + can be imported back into Jalview, and also interpreted by the BioJS + MSA viewer. The BioJS MSA Viewer is a full-featured JavaScript based + multiple sequence alignment visualisation system created by a + community of biological data visualisation developers, and is + developed independently of Jalview. +

    To find out more about the BioJS MSA Viewer, please go to http://msa.biojs.net/. +

    +

    - Making sure your BioJS MSA exports uses the latest + Making sure your BioJS MSA export uses the latest BioJS MSA Viewer

    In order to allow Jalview to export data with the latest diff --git a/help/html/io/export.html b/help/html/io/export.html index c3270c7..71d5c55 100755 --- a/help/html/io/export.html +++ b/help/html/io/export.html @@ -69,21 +69,7 @@

    -

    - 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

    +

    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.
  • EPS files can be produced as "Text" or "Lineart". Use -- 1.7.10.2