X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=51ad601f62ec5b88456f49770ed66feb8e81971c;hb=bf3206cc56a3bff812f96967a81cc9cff54a57b1;hp=b006c895d35dde64bebc18b6229fcd165b71e9d5;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index b006c89..51ad601 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -33,7 +33,7 @@
- Fetch Sequence
Shows
a dialog window in which you can retrieve known ids from
- Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+ UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
Web Services provided by the European Bioinformatics
Institute. See Sequence
Fetcher
@@ -133,10 +133,9 @@
- Load Features / Annotations
Load files describing precalculated sequence features or alignment annotations.
+ href="../features/featuresFormat.html">sequence
+ features or alignment
+ annotations.
- Close (Control W)
Close
the alignment window. Make sure you have saved your
@@ -196,7 +195,7 @@
"Deselect All" to deselect all columns.
- Remove Right (Control R)
If the alignment has marked columns, the alignment will
- be trimmed to the left of the leftmost marked column. To
+ be trimmed to the right of the rightmost marked column. To
mark a column, mouse click the scale bar above the
alignment. Click again to unmark a column, or select
"Deselect All" to deselect all columns.
@@ -204,16 +203,14 @@
All columns which only contain gap characters
("-", ".") will be deleted.
You
may set the default gap character in preferences.
+ href="../features/preferences.html">preferences.
- Remove All Gaps (Control Shift E)
Gap characters ("-", ".") will be
deleted from the selected area of the alignment. If no
selection is made, ALL the gaps in the alignment will be
removed.
You may set the default gap character in preferences.
+ href="../features/preferences.html">preferences.
- Remove Redundancy (Control D)
Selecting this option brings up a window asking you to
@@ -233,8 +230,7 @@
with alignment analysis programs which require 'properly
aligned sequences' to be all the same length.
You
may set the default for Pad Gaps in the preferences.
+ href="../features/preferences.html">preferences.
Select
@@ -278,11 +274,16 @@
WARNING: This cannot be undone.
Select/Hide Columns by Annotation
Select
- or Hide columns in the alignment according to secondary
- structure, labels and values shown in alignment annotation
- rows.
+ href="../features/columnFilterByAnnotation.html">Select/Hide
+ Columns by Annotation
Select or Hide
+ columns in the alignment according to secondary structure,
+ labels and values shown in alignment annotation rows.
+ Select Highlighted Columns
Selects
+ the columns currently highlighted as a result of a find, mouse
+ over, or selection event from a linked structure viewer or other
+ application. Modifiers will work on some platforms: ALT will add
+ all but the highlighted set to the column selection, and CTRL
+ (or META) will toggle the selection.
View
@@ -310,11 +311,11 @@
- Show Sequence Features
Show
or hide sequence features on this alignment.
- 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 retrieve features from DAS annotation
+ href="../features/featuresettings.html">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 retrieve features from DAS annotation
servers.
- Sequence ID Tooltip
(application only)
This submenu's options allow the
@@ -403,22 +404,21 @@
rendering.
- Wrap
When ticked, the alignment display is "wrapped" to the width of the alignment window. This is
- useful if your alignment has only a few sequences to view
- its full width at once.
+ href="../features/wrap.html">wrapped" to
+ the width of the alignment window. This is useful if your
+ alignment has only a few sequences to view its full width at
+ once.
Additional options for display of sequence numbering
and scales are also visible in wrapped layout mode:
- - Scale Above
- Show the alignment column position scale.
- - Scale Left
- Show the sequence position for the first aligned
- residue in each row in the left column of the alignment.
- - Scale Right
- Show the sequence position for the last aligned
- residue in each row in the right-most column of the
- alignment.
+ - Scale Above
+ Show the alignment column position scale.
+ - Scale Left
Show
+ the sequence position for the first aligned residue in
+ each row in the left column of the alignment.
+ - Scale Right
+ Show the sequence position for the last aligned residue
+ in each row in the right-most column of the alignment.
- Show Sequence Limits
If this box is selected the sequence name will have
the start and end position of the sequence appended to
@@ -474,11 +474,10 @@
colour will be applied to all currently defined groups.
- Colour Text...
Opens the Colour Text
- dialog box to set a different text colour for light and dark
- background, and the intensity threshold for transition between
- them.
+ href="../colourSchemes/textcolour.html">Colour
+ Text...
Opens the Colour Text dialog box
+ to set a different text colour for light and dark background,
+ and the intensity threshold for transition between them.
- Colour Scheme options: None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
@@ -507,8 +506,8 @@
- By Annotation
Colours
the alignment on a per-column value from a specified
annotation. See Annotation Colouring.
+ href="../colourSchemes/annotationColouring.html">Annotation
+ Colouring.
- By RNA Helices
Colours
the helices of an RNA alignment loaded from a Stockholm file.
@@ -563,14 +562,14 @@
provided in this menu.
- Pairwise Alignments
Applies
Smith and Waterman algorithm to selected sequences. See pairwise alignments.
+ href="../calculations/pairwise.html">pairwise
+ alignments.
- Principal Component Analysis
Shows
a spatial clustering of the sequences based on similarity
scores calculated with the alignment. See Principal Component Analysis.
+ href="../calculations/pca.html">Principal
+ Component Analysis.
- Extract Scores ... (optional)
This
option is only visible if Jalview detects one or more
@@ -626,36 +625,35 @@
or elsewhere. You need a continuous network connection in order to
use these services through Jalview.
- - Alignment
- Align the currently selected sequences or all sequences
- in the alignment, or re-align unaligned sequences to the
- aligned sequences. Entries in this menu provide access to the
- various alignment programs supported by JABAWS. See the Multiple
- Sequence Alignment webservice client entry for more
- information.
+ - Alignment
Align the
+ currently selected sequences or all sequences in the
+ alignment, or re-align unaligned sequences to the aligned
+ sequences. Entries in this menu provide access to the various
+ alignment programs supported by JABAWS. See the
+ Multiple Sequence
+ Alignment webservice client entry for more information.
- Secondary Structure Prediction
- JPred Secondary Structure Prediction
Secondary structure prediction by network
- consensus. See the Jpred3
+ consensus. See the Jpred
client entry for more information. The behaviour of this
calculation depends on the current selection:
- If nothing is selected, and the displayed
- sequences appear to be aligned, then a JNet prediction
+ sequences appear to be aligned, then a JPred prediction
will be run for the first sequence in the alignment,
using the current alignment. Otherwise the first
sequence will be submitted for prediction.
- If just one sequence (or a region on one
sequence) has been selected, it will be submitted to
- the automatic JNet prediction server for homolog
+ the automatic JPred prediction server for homolog
detection and prediction.
- If a set of sequences are selected, and they
appear to be aligned, then the alignment will be used
- for a Jnet prediction on the first
+ for a JPred prediction on the first
sequence in the set (that is, the one that appears
first in the alignment window).
@@ -667,8 +665,8 @@
- Multi-Harmony
Performs
functional residue analysis on a protein family alignment
with sub-families defined on it. See the Multi-Harmony service entry for more information.
+ href="../webServices/shmr.html">Multi-Harmony
+ service entry for more information.