From: tcofoegbu Date: Mon, 13 Jul 2015 16:41:47 +0000 (+0100) Subject: JAL-1788 added help documentation for biojson X-Git-Tag: Release_2_10_0~577 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3d8b21693c3c2cc27348b0fed1f5306932bc59a4;p=jalview.git JAL-1788 added help documentation for biojson --- diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html new file mode 100644 index 0000000..341e3e2 --- /dev/null +++ b/help/html/features/bioJsonFormat.html @@ -0,0 +1,52 @@ + + + +BioJson-1.0 A JSON File Format + + +

BioJson (version-1.0)

+ BioJson is a standardise JavaScript Object Notation (JSON) format for exchange of Bio-informatics Sequence Alignment data. + BioJSon-1.0 schema/documentation is available here. + You can keep up to date with BioJson development and latest news here. + +

Features supported

+ Export/Import of the following alignment elements are supported in BioJson-1.0: +

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

+ +

Features not yet supported

+ Export/Import of the following alignment elements are not supported in BioJson-1.0: +

Reference sequence
Representative sequence
Trees
3D Structures

+ + diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index 8a72d4d..16b0dc0 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -182,6 +182,10 @@

-blc FILE

Create alignment file FILE in BLC format.

+ +

-json FILE

Create alignment file FILE in JSON format.

-jalview FILE

diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html index ae56945..b457adf 100755 --- a/help/html/io/fileformats.html +++ b/help/html/io/fileformats.html @@ -77,6 +77,11 @@ THISISASEQUENCE
...
// .phy + +JSON +Data starts with '{'
Data ends with '}'

See BioJson for more info about Jalview JSON format
+.json +

The file extensions are used to associate jalview alignment icons with alignment files: diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index a2cb603..8b50d9e 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -72,6 +72,7 @@

AMSA

STH

Phylip

JSON

Print (Control P)
Jalview will print the alignment using the current fonts and colours of diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 8ad4cbd..177d56f 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -693,6 +693,7 @@ public class Jalview + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" + "-pir FILE\tCreate alignment file FILE in PIR format.\n" + "-blc FILE\tCreate alignment file FILE in BLC format.\n" + + "-json FILE\tCreate alignment file FILE in JSON format.\n" + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" + "-png FILE\tCreate PNG image FILE from alignment.\n" + "-svg FILE\tCreate SVG image FILE from alignment.\n"