From 67b2712fea5eea9212ca794d2bf7ef65f19493a7 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 5 Apr 2006 11:01:49 +0000 Subject: [PATCH] 2.08 update --- help/help.jhm | 4 ++-- help/helpTOC.xml | 2 ++ help/html/features/annotationsFormat.html | 15 +++++++++------ help/html/features/featuresFormat.html | 7 +++++-- help/html/keys.html | 4 +++- help/html/releases.html | 2 +- 6 files changed, 22 insertions(+), 12 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index 2179a73..21e28ad 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -42,8 +42,8 @@ - + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 4642f67..c148afc 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -12,6 +12,7 @@ + @@ -32,6 +33,7 @@ + diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index c2a784c..d890321 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -3,9 +3,12 @@ Annotations File Format -

Alignment Annotations File Format
+

Alignment Annotations File Format

- A precalculated annotations fiile can read onto an alignment from the command + Note: This format is primarily intended to be used for the applet, which does + not have an XML parser and where file size must be kept to a minimum to reduce + download time.

+

A precalculated annotations fiile can read onto an alignment from the command line ("-annotations"), by drag and dropping the the annotations file onto an alignment or by selecting from the File menu "Load Features / Annotations".

The File is in tab delimited format. The file must have the line JALVIEW_ANNOTATION @@ -20,11 +23,11 @@ associated with that sequence. Use SEQUENCE_REF ALIGNMENT to cancel the associtations.

The visual graphs can be coloured or combined with other graphs, or have an arbitrary line drawn at a certain value using the following lines.

-

COLOUR<tab>graph name<tab>colour
+

COLOUR<tab>graph name<tab>colour
COMBINE<tab>graph 1 name<tab>graph 2 name
GRAPHLINE<tab>graph name<tab>value<tab>label<tab>colour

An example Annotation file may look like this:

-

#Comment lines follow the hash symbol
+

#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF FER1_MESCR 5
BAR_GRAPH<tab>Bar Graph 1<tab>||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
@@ -33,12 +36,12 @@ BAR_GRAPH<tab>Bar Graph<tab>2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
NO_GRAPH<tab>Icons <tab>||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
NO_GRAPH<tab>Purple Letters<tab>m|y|p|r|o|t|e|i|n

-

COLOUR<tab>Bar Graph 2<tab>blue
+

COLOUR<tab>Bar Graph 2<tab>blue
COLOUR<tab>Red Values<tab>255,0,0
COLOUR<tab>Green Values<tab>green
COLOUR<tab>Purple Letters<tab>151,52,228
COMBINE<tab>Green Values<tab>Red Values

-

GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black +

GRAPHLINE<tab>Red Values<tab>2.6<tab>threshold<tab>black


diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 8e6ee13..a97d957 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -4,6 +4,9 @@

Sequence Features File Format

+

Note: This format is primarily intended to be used for the applet, which does + not have an XML parser and where file size must be kept to a minimum to reduce + download time.

(Prior to version 2.08 known as the "Groups file")
A precalculated Features file can read onto an alignment from the command line ("-features"), by drag and dropping the features file onto an alignment @@ -12,7 +15,7 @@

featureType<tab>colour
description<tab>sequenceId<tab>sequenceIndex<tab>start<tab>end<tab>featureType

eg
- domain red
+ domain red
metal ion-binding site 00ff00
transit peptide 0,105,215
chain 225,105,0
@@ -27,7 +30,7 @@ Your Own description here Q93XJ9_SOLTU -1 49 144 chain

An additional option in Jalview 2.08 is to group features in the following way:

-

STARTGROUP<tab>My feature groupA
+

STARTGROUP<tab>My feature groupA
....Many Feature descriptions here
ENDGROUP<tab>My feature groupA

diff --git a/help/html/keys.html b/help/html/keys.html index 86e8415..1b0339c 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -44,7 +44,9 @@
  • Q - Define the top left corner of the selection area
      • -
    • M - Define the bottom right corner of the selection area
      • +
    • M - Define the bottom right corner of the selection area
      +
      • +
    • 65,82<return> - Quick jump to column 65, sequence 82

     

     

    diff --git a/help/html/releases.html b/help/html/releases.html index f82460f..cd0b76c 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -4,7 +4,7 @@

    Release History

    - + -- 1.7.10.2
    Release
    Release
    New Features
    Issues Resolved