Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=e545ab2834bda2879cdd3cc15ab156ca968ce74f;hpb=9d50efc40c88bd65891fa009267912f50ff80cf3;p=jalview.git diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index e545ab2..e18e273 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -1,79 +1,18 @@ - -Alignment Window Menus - - -

Alignment Window File Menu

File
-
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 the European - Bioinformatics Institute. See Sequence Fetcher.

Save As
- Save the alignment to local file. A file selection window will - open, use the "Files of type:" selection box to determine which - alignment format to save as.
-
Export
- Creates an alignment graphic with the current 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.
  -
-
Output to Textbox
- 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.
- Select the format of the text by selecting one of the following menu items. -
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
-
Print
- 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.
-
Load Associated Tree
- Jalview can view trees stored in - the Newick file format, and associate them with the - alignment. Note: the ids of the tree file and your alignment - MUST be the same.
-
Load Features / Annotations
- Load files describing precalculated sequence - features or alignment - annotations.
Close
- Close the alignment window. Make sure you have - saved your alignment before you close - either as a Jalview - project or by using the Save As menu.
-

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