From 90255554ddb63f5474c11afcaba96d23ffd88a46 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 10 Apr 2006 11:27:04 +0000 Subject: [PATCH] doco changes. --- help/help.jhm | 1 + help/helpTOC.xml | 7 +++- help/html/features/annotation.html | 20 +++++------ help/html/features/annotationsFormat.html | 53 ++++++++++++++--------------- help/html/features/seqfeatures.html | 41 ++++++++++++---------- help/html/keys.html | 17 ++++++--- help/html/whatsNew.html | 9 ++--- 7 files changed, 82 insertions(+), 66 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index 4ff7a28..f3d96c4 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -15,6 +15,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 1bbe5c0..cc3555e 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -8,6 +8,7 @@ target="editInSelArea"/> + @@ -15,12 +16,16 @@ + - + + + + diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index df22d7e..447961e 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -3,14 +3,15 @@

Alignment Annotation

In addition to the definition of groups and sequence features, Jalview also - allows you to mark particular columns of an alignment and add symbols and text +

In addition to the definition of groups and sequence features, + Jalview can display symbols and graphs under the columns of an + alignment, and allow you to mark particular columns of an alignment and add symbols and text in the annotation area shown below the alignment (which may be hidden if View→Show Annotation is not ticked).

As of Jalview 2.08 precalculated annotations can be added to alignments from - the command line, drag and drop, or from the "File-> Load Features / - Annotations" menu item. See the Annotations - File Format for more details.

Web services can also add annotation to an alignment (see the + JNet web service), and as of Jalview 2.08 quantitative and symbolic + annotations can be added to an alignment via an Annotations + File for more details.

Annotation rows are added using the Annotation Label @@ -68,11 +69,8 @@ the row. Note: This cannot be undone

-Annotation is stored and retrieved using Jalview Archives. Quantitative -annnotation is also possible, but currently only possible with the -JNet web service, or by creating your own Jalview Archive (which -contains XML conforming to the Jalview-Vamsas XML schema). +User defined annotation is stored and retrieved using Jalview Archives.

Current Limitations

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index 18d773c..ba9bc99 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -53,33 +53,30 @@ All Annotations defined after a SEQUENCE_REF command will then be placed at the startIndex'th column.

Sequence associations are turned off for subsequent annotation definitions by:

SEQUENCE_REF	ALIGNMENT

LINE_GRAPH type annotations can be given a colour, - combined onto the same vertical axis, and have abscissa (lines of - constant value - so they are horizontal) at particular - values using the following lines (respectively): -

COLOUR	graph name	colour
-COMBINE	graph 1 name	graph 2 name
-GRAPHLINE	graph name	value	label	colour

An example Annotation file is given below:

#Comment lines follow the hash symbol
- JALVIEW_ANNOTATION
- SEQUENCE_REF FER1_MESCR 5
- BAR_GRAPH Bar Graph 1 ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
- LINE_GRAPH Green Values 1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
- LINE_GRAPH Red Values 2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
- BAR_GRAPH Bar Graph 2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
- NO_GRAPH Icons ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
- NO_GRAPH Purple Letters m|y|p|r|o|t|e|i|n

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

GRAPHLINE Red Values 2.6 threshold black -
-

LINE_GRAPH type annotations can be given a colour + (specified as 24 bit RGB triplet in hexadecimal or comma separated values), + combined onto the same vertical axis, and have ordinate lines (horizontal + lines at a particular vertical axis value) using the following + commands (respectively): +

COLOUR	graph_name	colour
+COMBINE	graph_1_name	graph_2_name
+GRAPHLINE	graph_name	value	label	colour

An example Annotation file is given below: +

#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF	FER1_MESCR	5
+BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
+COLOUR	Bar Graph 2	blue
+COLOUR	Red Values	255,0,0
+COLOUR	Green Values	green
+COLOUR	Purple Letters	151,52,228
+COMBINE	Green Values	Red Values
+GRAPHLINE	Red Values	2.6	threshold	black
+

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 2a57e63..2217c29 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -4,8 +4,24 @@

Sequence Features

Jalview can colour parts of a sequence based on the presence of sequence features - which may be retrieved from database records (such -as Uniprot), the result of sequence motif -searches or simply read from a sequence features file.

+as Uniprot), the result of sequence motif +searches or simply read from a sequence features file.

Sequence Feature Groups

Since Jalview 2.08, sequence features assigned to a sequence can be +organised into groups, which may indicate that the features were all retrieved +from the same database (such as Uniprot features), or generated by the +same analysis process (as might be specified in a sequence features file).

Sequence Feature Inheritance

Since Jalview 2.07, sequence features are global to a set of +sequences appearing (independently or together) in many different +alignments. Practically, this means features loaded onto one alignment +can be viewed in any alignments involving the same sequences. The same +sequence appears in different alignments when a new alignment is +generated by submitting an existing set of sequences to one of the +alignment or prediction web services, and when sequences are copied +and pasted into other alignment windows.

View→Fetch Sequence Features

When this option is selected, sequence features extracted from the Uniprot record for each sequence are displayed on the alignment.

@@ -20,22 +36,11 @@ searches or simply read from a sequence featur

Toggle the display of sequence features in this alignment.

View→Feature Settings...

Once sequence features have been loaded, their display can be fully - controlled using the alignment window's Feature Settings dialog box - :

- -

features can be hidden - or have their rendering priority changed using the Feature Settings dialog. - This displays all the features loaded, the colour and whether to display the - feature or not. You can easily change the colour by clicking the colour box.
- It is important to realise that the order in which features are drawn to the - alignment may result in overlapping features being hidden. Features at the foot - of the table are rendered first. Therefore features higher up the table will - be drawn over the top of lower featrues. You can change the order of the feature - priority by dragging the feature with your mouse.
- Use the transparency setting as another way to visualise overlapping features. -

You can save all features, with their current colours and visibility - in a Jalview format file. + controlled using the alignment window's Sequence Feature Settings dialog + box. Feature colour schemes and display parameters are unique to a + particular alignment, so it is possible to colour the same sequence + features differently in different alignment views.

The Sequence Identification Process

diff --git a/help/html/keys.html b/help/html/keys.html index 802b3f2..085c343 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -61,16 +61,25 @@ columns are selected, you should use the Hi Control 'F'BothLaunches the search window -0-9CursorBegin entering a numeric parameter [p] for a cursor movement or edit command + +

The compound commands available in the Cursor mode are summarised +below. Single letter commands can be prefixed by digits to specify a repetition +number, and some more complex commands take one or more numeric +parameters (prefixing the command key and separated by commas).

+ + - + - - + +

Compound +Command	Mode	Action (and parameter description)
0-9	Cursor	Begin entering a +numeric parameter ([p]) or repetition number for a cursor movement or edit +command.
,	Cursor	Separates one or more numeric parameters ([p1],[p2]) for a command.
[p1],[p2]Return	Cursor	Move cursor to a particular column (p1) and row (p2) in the alignment. e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
[p1],[p2] Return	Cursor	Move cursor to a particular column (p1) and row (p2) in the alignment. e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
[p1]S	Cursor	Jump to the p1'th sequence in the alignment.
[p1]P	Cursor	Jump to p1'th amino acid in current sequence.
[p1]C	Cursor	Jump to p1'th column in the alignment.
Q	Cursor	Marks the top left corner of the selection area
M	Cursor	Marks the bottom right corner of the selection area
[p1]Space	Cursor	Inserts p1 gaps at the current position. p1 is optional. Hold down Control or Shift to insert gaps over a sequence group
[p1]Delete	Cursor	Remove p1 gaps at the cursor position. p1 is optional. Hold down Control or Shift to insert gaps over a sequence group
[p1] Space	Cursor	Inserts p1 gaps at the current position. p1 is optional. Hold down Control or Shift to insert gaps over a sequence group
[p1] Delete	Cursor	Remove p1 gaps at the cursor position. p1 is optional. Hold down Control or Shift to insert gaps over a sequence group

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b5f5c78..9c13b59 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -3,8 +3,9 @@

What's new ?

Jalview Version 2.08

Editing can be locked to the selection area. - Any edits made within the locked area do not affect the rest of the alignment.

Editing can be locked to the + selection area so that any edits made within the locked area do + not unexpectedly shift other parts of the alignment.

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list of keyboard controls, look here.

Create sequence features from searches. @@ -15,9 +16,9 @@

Sequence feature display and rendering has also been enhanced, with the addition of sequence feature groups (which can be used to show - or hide a set of feature types en masse) and user defined + or hide a set of features en masse) and user defined feature colours as well as transparency controls, using the Sequence Feature Settings + href="features/featuresettings.html">Sequence Feature Settings window. The Features file has also been extended to accomodate these enhancements.

Alignment annotation and colouring is also considerably -- 1.7.10.2