Overview

From 92ae1457a784553ccdb842b122d481ce6c5ff24f Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 8 Jun 2005 14:21:25 +0000 Subject: [PATCH] nicer help. --- help/html/features/overview.html | 10 +++--- help/html/features/search.gif | Bin 0 -> 2969 bytes help/html/features/search.html | 66 ++++++++++++++++++++++++----------- help/html/features/seqfeatures.html | 53 +++++++++++++++++++--------- help/html/features/wrap.html | 2 +- help/html/whatsNew.html | 65 ++++++++++++++++++---------------- 6 files changed, 123 insertions(+), 73 deletions(-) create mode 100755 help/html/features/search.gif diff --git a/help/html/features/overview.html b/help/html/features/overview.html index 8589e95..424ba3c 100755 --- a/help/html/features/overview.html +++ b/help/html/features/overview.html @@ -1,11 +1,11 @@ -Overview +Overview Window - -

Select the overview window to get a navigable image of the whole alignment. +View→Overview window +

Select the overview window menu item to get a navigable image of the whole alignment.

The window indicates the current viewable region of the alignment, this area - may be adjusted by clicking and dragging with the mouse.

The red box indicates the currently viewed region of the alignment, this + may be moved by clicking and dragging with the mouse.

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Search

The search box can be displayed by pressing the keys Control and F or selecting - "Search"

-Note: +

The search box is displayed by pressing Control and F or + selecting "Find..." from the "Search" menu.

"Find next" will find the next occurence of the specified + and adjust the alignment window view to show it, and "Find + all" highlights all matches for a pattern. The "Create new + group" is a quick way to highlight and group residues matching + the specified search pattern throughout the alignment.

The search will be performed on the selected region. If no region is selected, - the search will operate on the full alignment.
To clear any selection, press the "Escape" key.
The search uses regular expressions. (understands a mixture of + posix and perl style regex - see below for a summary)
Gaps are ignored when matching the query to the sequences in the + alignment.
The search is applied to both sequences and their IDs but the "Find next" + and "Find all" buttons only count the sequence matches.
If a region is selected, then search will only + be performed on that region.
To quickly clear the current selection, press the "Escape" key.

Using the "Create new group" is a quick way to group and highlight - residues with the specified search pattern throughout the alignment.

The search allows regular expression matching.

A quick Regular Expression Guide

A regular expression is not just a simple text query - although it +can be used like one, the query is not parsed literally, but +interpreted like a series of instructions defining the features of the +match. For example, a simple query like "ACDED" would +match all occurences of that string, but "ACD+ED" matches +both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query +"[ILGVMA]{;5,}" would find stretches of small, +hydrophobic amino acids of at least five residues in length. +

The table +below describes some of the regular expression syntax:

+ + + + - + - + - + - + - + - + - + - - + - +

Regular Expression Element	Effect
.	Any single character.	Matches any single character
[]	Any one of the characters in the brackets	Matches any one of the characters in the brackets
^	The start of a line (column 1).	Matches at the start of an ID or sequence
$	The end of a line	Matches at the end of an ID or sequence
*	Matches zero or more of the preceding characters or expressions.	Matches if the preceding element matches zero or more times
?	Matches zero or one of the preceding characters or expressions.	Matches if the preceding element matched once or not at all
+	Matches one or more of the preceding characters or expressions.	Matches if the preceding element matched at least once
{count}	Matches the specified number of the preceding characters or expressions. +	Matches if the preceding element matches a specified number of + times
{min,}	Matches at least the specified number of the preceding characters or - expressions.	Matches at least the specified number of the preceding element.
{min,max}	Matches between min and max of the preceding characters or expressions.	Matches if the preceding element matches between min and max + number of times.

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html index 160c1e2..4026071 100755 --- a/help/html/features/seqfeatures.html +++ b/help/html/features/seqfeatures.html @@ -1,22 +1,43 @@ Sequence Features -

Sequence Features

This displays Uniprot sequence features on the alignment if a 100% sequence - match is found.

The first step in this process is to match the id (name) of each sequence with - Uniprot. If there is no match, a Blast search is performed to try to obtain - the Uniprot Id for each sequence. You will be notified of any 100% matches with - Uniprot, which you must manually assign to each sequence in your input alignment, - then save the file.

View→Sequence Features

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

Currently, sequence features are rendered in red or blue, dependent + upon their type:

Features associated with a particular residue are coloured + red
e.g. an active site residue
Features which span a region are coloured blue
+e.g. a region of sequence with known structure
+
More information about the feature is given in a tooltip, which are + viewed by moving the mouse pointer over a sequence feature. The + associated text for the feature will then be displayed in a small + label will appear near the pointer.
+
After the Sequence Features option is selected, there may be some delay before + the features are actually rendered, as jalview must first determine if a + sequence is contained in uniprot and then retrieve its sequence + record. This delay should only happen once for a particular + alignment, as jalview caches uniprot records in a file in your home + directory called '.jalview.uniprot.xml'. + +
The first step in this process is to try to use the ID (name) of + each sequence as an ID search in Uniprot. If there is no match, The + EBI Blast search is used in an attempt to obtain the Uniprot Id for + each sequence. You will be notified of any 100% matches with + Uniprot, but you must then manually change the name of the sequence, + by right clicking on the sequence ID and selecting + Sequence→Edit Name, before Jalview will show its sequence + features.
- remember to save your alignment if you have updated any of the + sequence IDs! +
- The input sequence will be matched with the returned Uniprot record, the start - and end residues can then be correctly assigned to each sequence.
-
Sequence features which are 1 residue in length are coloured red. Features - which span a region are coloured blue.
-
By moving the mouse pointer over a sequence feature on the alignment a small - label will appear with the description of that sequence feature.
-
A local cache of retrieved uniprot entries is recorded on your local machine. -
+ If a uniprot record (or set of records) is found for a sequence, + then the sequence in aligned to the one in the Uniprot record + to determine the correct start and end residue positions that will be + displayed when the 'Show Full Sequence ID' option is set.
diff --git a/help/html/features/wrap.html b/help/html/features/wrap.html index 015c669..26651a3 100755 --- a/help/html/features/wrap.html +++ b/help/html/features/wrap.html @@ -3,7 +3,7 @@ Wrap Alignment -
Wrap alignment
+
View→Wrap alignment

Use this feature to wrap an alignment to the screen width.

All output (HTML, Printing, JPG etc) will also be in this wrapped format.

This is most useful when looking at alignments with less than 20 sequences. diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index dc956a9..965edea 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,30 +1,35 @@ - -What's new - -
What's new
-
If you can read this then you'll already have seen some of the recent changes - made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments - in the Java programming language. For instance Jalview is now a multi windowed - application, this keeps all your Jalview windows neatly together in one main - application window.
-
If you were familiar with the original Jalview, here is a list of important - features you should know about the current development:
-
- Editing sequences is no longer the default when mouse clicking the alignment. - Instead, mouse clicking on the alignment will create a "selection region" - which may be full sequences or groups of residues.
- To edit a sequence, the "Shift" key must be held down
- To edit groups, either the "Alt" key or the "Control" - key must be held down.
- Colours maybe applied to the background, ie the whole alignment, or to selected - regions. If the tickbox "Apply colour to all groups" is ticked (this - is the default), then the colour will be applied to all groups.
- Use the right mouse button (apple and click on the mac) to define a selected - region on the alignment as a new group.
- Conservation is automatically updated whenever the alignment is edited
- There is no "quick draw" option
- Edits can be undone! (and redone)
- - + +What's new ? + +
What's new ?
+
If you are reading this then you will already have seen some of the recent changes + made to Jalview.
+ Jalview takes advantage of some of the more recent user interface developments + in the Java programming language. For instance Jalview is now a multi windowed + application, this keeps all your Jalview windows neatly together in one main + application window.
+
If you were familiar with the original Jalview, here is a list of important + features you should know about the current development:
+
- Editing sequences is no longer the default when mouse clicking the alignment. + Instead, mouse clicking on the alignment creates a "selection region" + which may be full sequences or groups of residues.
- To insert or edit the gaps in one sequence in alignment, the + "Shift" key must be held down when dragging the mouse.
- To insert or edit gaps for a group of sequences, the + "Alt" key (or in X windows the "Control" + key) must be held down.
- Selecting colour schemes in the colour menu either sets just the + "background" colourscheme for the alignment, or - when + the tickbox "Apply colour to all groups" is ticked, + applies the scheme to the background and all groups defined on the alignment.
- Use the right mouse button (apple and click on the Mac) whilst + the pointer is within the selection area to access the "define" region menu to + define a new region, give it a name, and change its colourscheme and display + properties.
- Conservation is automatically updated whenever the alignment is edited
- There is no "quick draw" option
- Edits can be undone, and redone!
+ + -- 1.7.10.2