Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=93c7711ca92d00e8ac3e5531c06cec368235f61d;hb=2b3bd506ee1cc2d1a26a3425ccba48665179a9fb;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index e18e273..93c7711 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -16,3 +16,96 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> + +Alignment Window Menus + + + +

Alignment Window File Menu

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.
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.
Save (Control S)
+ Saves the alignment to the file it was loaded from (if available), in + the same format, updating the original in place.
Save As (Control Shift S)
+ 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.
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. 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. +
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
+
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.
+
Export Features
+ All features visible on the alignment can be saved to file or displayed + in a textbox in either Jalview or GFF format
Export Annotations
+ All annotations visible on the alignment can be saved to file or + displayed in a textbox in Jalview annotations format.
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 (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 As menu.

+ +