X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=e18e273bc6e63d17a8266460e4a4915b193850f3;hb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;hp=bf1fed51ab979c0587f32bd9cadb7e7639806e42;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git
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-
-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
-
-
- - 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
- - 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.
-
-
-
+