X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=5160a2b12eaed0e6fb398ec3ff3805e1630b9b83;hp=5739797abf93d7d68894458feb3f12d3ad6ebda3;hpb=d0771875f23ab994c4f85fb6cd604378768df10e;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 5739797..00a2ec4 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -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
@@ -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
@@ -248,7 +244,7 @@
Selects all the sequences and residues in the
alignment.
Use <CTRL> and A (<APPLE>
and A on a MacOSX) to select all.
-
+
Deselect All (Escape)
Removes the current selection box (red dashed box) from
the alignment window. All selected sequences, residues and
@@ -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
@@ -427,12 +427,12 @@
If this box is selected then the sequence names
displayed in the sequence label area will be aligned
against the left-hand edge of the alignment display,
- rather than the left-hand edge of the alignment window.
+ rather than the left-hand edge of the alignment window.
- Show Hidden Markers
When this box is selected, positions in the
alignment where rows and columns are hidden will be
- marked by blue arrows.
+ marked by blue arrows.
- Boxes
If this is
selected the background of a residue will be coloured
using the selected background colour. Useful if used in
@@ -461,7 +461,6 @@
symbols will be rendered as a '.', highlighting
mutations in highly conserved alignments.
-
@@ -474,11 +473,10 @@
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 +505,8 @@
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.
@@ -542,44 +540,26 @@
viewer window.
- 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.
+ Calculate Tree or PCA ...
Opens the
+ calculations dialog for
+ for calculating trees or
+ principle component analysis
+ plots on the alignment or the currently selected
+ region.
- Principal Component Analysis
Shows
- a spatial clustering of the sequences based on similarity
- scores calculated with the alignment. See Principal Component Analysis.
-
- Extract Scores ... (optional)
This
- option is only visible if Jalview detects one or more
- white-space separated values in the description line of the
- alignment sequences.
When selected, these numbers are
- parsed into sequence associated annotation which can then be
- used to sort the alignment via the Sort by→Score menu.
-
- Autocalculate Consensus
For
+ Pairwise Alignments
Applies
+ Smith and Waterman algorithm to selected sequences. See pairwise
+ alignments.
+
+ Extract Scores ... (optional)
This
+ option is only visible if Jalview detects one or more
+ white-space separated values in the description line of the
+ alignment sequences.
When selected, these numbers are
+ parsed into sequence associated annotation which can then be
+ used to sort the alignment via the Sort by→Score menu.
+
+ Autocalculate Consensus
For
large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This
prevents the sometimes lengthy calculations performed after
@@ -615,7 +595,7 @@
in Jalview 2.8.1
'Standard Databases' will check sequences against
- the EBI databases plus any active DAS sequence sources<
+ 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.
@@ -626,36 +606,35 @@
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 +646,8 @@
- 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.