X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=966c0053a7e4ecfff93c1337c396ba6ddbbe66a0;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 966c005..7102fd7 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,7 +1,7 @@
+
+ Alignment Window Menus
+
+
- File
- Fetch Sequence
Shows a
@@ -72,35 +73,40 @@
- 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.
-
- - Export Features
All
+- Page Setup ...
+ Open the printing system's Page Setup dialog box, to
+ control page size, layout and orientation.
+ - 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.
+
+
+ - Export Features
All
features visible on the alignment can be saved to file or
displayed in a textbox in either Jalview or GFF format
@@ -120,7 +126,7 @@
annotations.
- Close (Control W)
Close
the alignment window. Make sure you have saved your alignment
- before you close - either as a Jalview project or by using the Save
+ before you close - either from the Desktop's Save Project File menu option, or by using the Save
As menu.
@@ -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
- 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.