X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=1e1cfdc4b9fb14042b293bc8f3623bee1040474f;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 1e1cfdc..7102fd7 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,31 +1,34 @@
+ -->
Alignment Window Menus
-
- Alignment Window Menus
-
-
View
@@ -277,38 +283,10 @@
selected, the view will automatically scroll to display the
highlighted sequence position corresponding to the position under
the mouse pointer in a linked alignment or structure view.
- Show Annotations
If this
- is selected the "Annotation Panel" will be displayed
- below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values
- as bar charts.
-
- Autocalculated Annotation
Settings
- for the display of autocalculated annotation.
-
- - Apply to all groups
When
- ticked, any modification to the current settings will be applied
- to all autocalculated annotation.
- - Show Consensus Histogram
- Enable or disable the display of the histogram above the
- consensus sequence.
- - Show Consensus Logo
Enable
- or disable the display of the Consensus Logo above the consensus
- sequence.
- - Normalise Consensus Logo
- When enabled, scales all logo stacks to the same height,
- making it easier to compare symbol diversity in highly variable
- regions.
- - Group Conservation
When
- ticked, display a conservation row for all groups (only available
- for protein alignments).
- - Apply to all groups
When
- ticked, display a consensus row for all groups.
-
Show Sequence Features
Show
or hide sequence features on this alignment.
- Seqence
+ Sequence
Feature Settings...
Opens the
Sequence Feature Settings dialog box to control the colour and
display of sequence features on the alignment, and configure and
@@ -331,6 +309,61 @@
using the mouse.
+ Annotations (Since Jalview 2.8.2)
+
+ - Show Annotations
If this
+ is selected the "Annotation Panel" will be displayed
+ below the alignment. The default setting is to display the
+ conservation calculation, quality calculation and consensus values
+ as bar charts.
+
+ - Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for example, Consensus,
+ or secondary structure prediction from alignment).
+ - Hide Alignment Related
+ Hide all annotations that are for the alignment as a whole.
+ - Show Sequence Related
+ Show all annotations that are for individual sequences.
+ - Hide Sequence Related
+ Hide all annotations that are for individual sequences.
+ - You can also selectively show or hide annotations from the Popup
+ or Annotation menus.
+ - Sort by Sequence
Sort sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).
+ - Sort by Label
Sort sequence-specific annotations by label
+ (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+ allowing you to make a manual ordering of the annotations.
+ - Autocalculated Annotation
Settings
+ for the display of autocalculated annotation.
+
+ - Show first
+ Show autocalculated annotations above sequence-specific annotations.
+ Note this also applies to other annotations for the alignment, for example secondary
+ structure prediction from alignment.
+ - Show last
+ Show autocalculated / alignment annotations below sequence-specific annotations.
+ - Apply to all groups
When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.
+ - Show Consensus Histogram
+ Enable or disable the display of the histogram above the
+ consensus sequence.
+ - Show Consensus Logo
Enable
+ or disable the display of the Consensus Logo above the consensus
+ sequence.
+ - Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
+ - Group Conservation
When
+ ticked, display a conservation row for all groups (only available
+ for protein alignments).
+ - Group Consensus
When
+ ticked, display a consensus row for all groups.
+
+
+
+
Alignment Window Format Menu
- Font...
Opens the
@@ -473,25 +506,32 @@
- Calculate Tree
Functions
- for calculating trees on the alignment or the currently selected
- region. See calculating
- trees.
-
- - Average Distance Using % Identity
- - Neighbour Joining Using % Identity
- - Average Distance Using Blosum62
- - Neighbour Joining Using Blosum62
-
-
-
+ Calculate Tree
Functions
+ for calculating trees on the alignment or the currently
+ selected region. See calculating
+ trees.
+
+
+ - Neighbour Joining Using PAM250
+ - Neighbour Joining Using Sequence
+ Feature Similarity
+ - Neighbour Joining Using Blosum62
+ - Neighbour Joining Using % Identity
+ - Average Distance Using PAM250
+ - Average Distance Using Sequence
+ Feature Similarity
+ - Average Distance Using Blosum62
+ - Average Distance Using % Identity
+
Note: Since Version 2.8.1, a number of
+ additional similarity measures for tree calculation are
+ provided in this menu.
Pairwise Alignments
Applies
Smith and Waterman algorithm to selected sequences. See pairwise alignments.
Principal Component Analysis
Shows
- a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See Principal
+ a spatial clustering of the sequences based on similarity scores calculated with
+ the alignment. See Principal
Component Analysis.
Extract Scores ... (optional)
This
@@ -509,28 +549,36 @@
Sort With New Tree
When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.
-
+ Show Flanking Regions
Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides.
+
Web Service Menu
This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:
- Fetch DB References
This
- will use any of the database services that Jalview is aware of
- (e.g. DAS sequence servers and the WSDBFetch service provided by
- the EBI) to verify the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment.
'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.
- - Envision2 Services
Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the EnVision2 web
- application. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- ENFIN.
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+
+ - 'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment.
Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !
Added in Jalview 2.8.1
+
+ - 'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<
+
Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+
Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or