X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=9d2ad33915f44a82fe31c003dc0d4293449d70de;hb=9efb6cb466bc1f3365843ac03907cff5e50e58b0;hp=eb45924051412e0e0dd737410416b1c474ad1766;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git
diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
index eb45924..9d2ad33 100755
--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -1,4 +1,24 @@
+
Alignment Window Menus
@@ -8,16 +28,17 @@
- Fetch Sequence
Shows a dialog window in which you can select known ids from
- Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
+ Uniprot, EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services provided by
the European Bioinformatics Institute. See Sequence Fetcher.
- Add Sequences
Add sequences to the visible alignment from file, URL, or cut &
paste window
- Reload
- Reloads the alignment from the original file, if available.
Warning:
- This will delete any edits, analyses and colourings applied since the
- alignment was last saved, and cannot be undone.
+ Reloads the alignment from the original file, if available.
+ Warning: This will delete any edits, analyses and
+ colourings applied since the alignment was last saved, and cannot be
+ undone.
- Save (Control S)
Saves the alignment to the file it was loaded from (if available), in
the same format, updating the original in place.
@@ -26,9 +47,11 @@
open, use the "Files of type:" selection box to determine
which alignment format to save as.
- Output to Textbox
- The alignment will be displayed in plain text in a new window
+ The alignment will be displayed in plain text in a new window,
which you can "Copy and Paste" using the pull down menu, or
- your standard operating system copy and paste keys.
+ your standard operating system copy and paste keys. The output window
+ also has a "New Window" button to import the
+ (possibly edited) text as a new alignment.
Select the format of the text by selecting one of the following menu
items.
@@ -38,8 +61,15 @@
- BLC
- PIR
- PFAM
+ - PileUp
+ - AMSA
+ - STH
+ - Phylip
+ - 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,
@@ -47,8 +77,8 @@
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.
@@ -62,6 +92,8 @@
- 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.
Export Features