Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=b1f7a06ddb4ba1f775c4d3e803e2ce2d9b2469cf;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index b1f7a06..7102fd7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -1,31 +1,34 @@ + --> Alignment Window Menus -

- Alignment Window Menus -

+ Alignment Window Menus +

File
- Fetch Sequence
  Shows a @@ -60,47 +63,50 @@ Select the format of the text by selecting one of the following menu items.
  - FASTA -
  - MSF -
  - CLUSTAL -
  - BLC -
  - PIR -
  - PFAM -
  - FASTA
  - MSF
  - CLUSTAL
  - BLC
  - PIR
  - PFAM
  - PileUp
  - AMSA
  - STH
  - Phylip
  - JSON
- Print (Control P)
  Jalview - will print the alignment using the current fonts and colours of - your alignment. If the alignment has annotations visible, these - will be printed below the alignment. If the alignment is wrapped - the number of residues per line of your alignment will depend on - the paper width or your alignment window width, whichever is the - smaller. -
- Export Image
  Creates an - alignment graphic with the current view's annotation, alignment - background colours and group colours. If the alignment is wrapped, the output will also be - wrapped and will have the same visible residue width as the open - alignment. -
  - HTML
    Create a web page from your alignment. -
  - EPS
    Create an Encapsulated Postscript file from - your alignment. -
  - PNG
    Create a Portable Network Graphics file from - your alignment. -
- Export Features
  All +
- Page Setup ...
  + Open the printing system's Page Setup dialog box, to + control page size, layout and orientation.

@@ -201,9 +207,9 @@ the last redundancy deletion.

Pad Gaps
When selected, - the alignment will be kept at minimal width (so there no empty + the alignment will be kept at minimal width (so there are no empty columns before or after the first or last aligned residue) and all - sequences will be padded with gap characters to the before and + sequences will be padded with gap characters before and after their terminating residues.
This switch is useful when making a tree using unaligned sequences and when working with alignment analysis programs which require 'properly aligned @@ -214,42 +220,42 @@

Select
-
Find... - (Control F)
Opens the Find dialog box to - search for residues, sequence name or residue position within the - alignment and create new sequence features from the queries. -
-
Select All (Control A)
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 marked columns will - be deselected.
Use <ESCAPE> to deselect - all.
-
Invert Sequence Selection (Control I)
- Any sequence ids currently not selected will replace the - current selection. -
-
Invert Column Selection (Control Alt I)
- Any columns currently not selected will replace the current - column selection. -
-
Create Group (Control G)
- Create a group containing the currently selected sequences.
+
Find... (Control F)
+ Opens the Find dialog box to search for residues, sequence name or residue + position within the alignment and create new sequence features from the queries. + +
Select All (Control A)
+ 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 marked columns + will be deselected.
+ Use <ESCAPE> to deselect all.
+
Invert Sequence Selection (Control I)
+ Any sequence ids currently not selected will replace the + current selection.
+
Invert Column Selection (Control Alt I)
+ Any columns currently not selected will replace the current + column selection.
+
Create Group (Control G)
+ Create a group containing the currently selected sequences.

Remove Group (Shift Control G)
- Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)
-
Make Groups for selection
The currently - selected groups of the alignment will be subdivided according to - the contents of the currently selected region.
Use this to - subdivide an alignment based on the different combinations of - residues observed at specific positions. (new in jalview 2.5) -
-
Undefine Groups (Control U)
The - alignment will be reset with no defined groups.
WARNING: - This cannot be undone. -
+ Ungroup the currently selected sequence group. +
Make Groups for selection
The + currently selected groups of the alignment will be subdivided + according to the contents of the currently selected region.
Use + this to subdivide an alignment based on the different combinations + of residues at marked columns. +
+
Undefine Groups (Control U)
+ The alignment will be reset with no defined groups.
+ 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.

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 @@ -473,19 +506,25 @@

-
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
-
-
- Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu. -
+
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.