From 8c0737632c158907098990b81ac702710721e9f2 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 4 Apr 2006 17:07:14 +0000 Subject: [PATCH] Modified for 2.08 --- help/html/calculations/conservation.html | 54 +++++++++++++++--------------- help/html/editing/index.html | 14 ++++++++ help/html/features/annotation.html | 49 ++++++++++++++------------- help/html/features/jalarchive.html | 36 +++++++++++--------- help/html/features/preferences.html | 6 ++-- help/html/features/search.gif | Bin 2969 -> 4924 bytes help/html/features/search.html | 14 ++++---- help/html/features/seqfeatures.html | 25 ++++++++------ help/html/keys.html | 32 ++++++++++++++++++ help/html/menus/alignmentMenu.html | 4 +++ help/html/menus/alwcalculate.html | 5 +++ help/html/menus/alwcolour.html | 32 +++++++++++------- help/html/menus/alwview.html | 10 ++++-- help/html/menus/popupMenu.html | 9 ++--- help/html/releases.html | 28 +++++++++++++--- help/html/whatsNew.html | 46 +++++++++++++------------ 16 files changed, 236 insertions(+), 128 deletions(-) diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index cf7faf5..4cfc825 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,27 +1,27 @@ - -Alignment Conservation Annotation -

Alignment Conservation Annotation

-

This is an automatically calculated quantitative alignment -annotation which measures the number of conserved physico-chemical -properties conserved for each column of the alignment. Its calculation -is based on the one used in - the AMAS method of multiple sequence alignment analysis :
-

-

-

Conservation is measured as a numerical index reflecting the -conservation of physico-chemical properties in the alignment: -Identities score highest, and the next most conserved group contain -substitutions to amino acids lying in the same physico-chemical -class.

- -

Colouring an alignment by conservation
-Conservation scores can be used to colour an alignment. This is -explained further in the help page for conservation colouring. -

- - + +Alignment Conservation Annotation +

Alignment Conservation Annotation

+

This is an automatically calculated quantitative alignment +annotation which measures the number of conserved physico-chemical +properties conserved for each column of the alignment. Its calculation +is based on the one used in + the AMAS method of multiple sequence alignment analysis :
+

+

+

Conservation is measured as a numerical index reflecting the conservation of + physico-chemical + properties in the alignment: Identities score highest, and the next most + conserved group contain substitutions to amino acids lying in the same physico-chemical + class.

+ +

Colouring an alignment by conservation
+Conservation scores can be used to colour an alignment. This is +explained further in the help page for conservation colouring. +

+ + diff --git a/help/html/editing/index.html b/help/html/editing/index.html index 734a662..8ff1cf6 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -2,6 +2,20 @@ Editing

Editing

+

Jalview 2.08 Enhancements - Editing can be restricted to the current + selection area. This allows the user to "Lock" the alignment either + side of the selection area. Any gap insertions or deletions will only affect + the current selection area.

+

+

In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, + the same number of gaps will be inserted at position 116, (between M and L). +

+

Editing is possible via the keyboard by toggling the Cursor mode on / off with + F2. A full list of keyboard editing actions is found here. +

+

Tip: For large alignments, deselect "Calculate -> + Autocalculate Consensus" to prevent the alignment performing lengthy calculations + after every edit.

Inserting / removing gaps - hold down the "Shift" key. Click a residue with the mouse and drag the residue to the right to insert gaps or to the left to remove gaps.
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 3ad7f3e..3635bbe 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -3,34 +3,37 @@

Alignment Annotation

-

In addition to the definition of groups, Jalview also allows 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). -

+

In addition to the definition of groups, Jalview also allows 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.

Annotation rows are added using the Annotation Label menu, which is obtained by clicking anywhere on the annotation row labels area (below the sequence ID area). -