X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=7102fd740ba47d30f6b6ea14f736d070e0b5b62f;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=5bf9e608b68c2986a38c551174388a9cfa465918;hpb=0943de76f6a7435894e72479671642c05f2f3687;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 5bf9e60..7102fd7 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -24,10 +24,11 @@ -

- Alignment Window Menus -

+ Alignment Window Menus +

File
- Fetch Sequence
  Shows a @@ -74,34 +75,38 @@
- Phylip

-
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.
+
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.
+
SVG
+ Create a Scalable Vector Graphics file from your alignment for embedding in web pages.
+
BioJS
+ Create a BioJS MSA Viewer HTML file from your 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
@@ -121,7 +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.

@@ -215,42 +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
@@ -501,19 +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.