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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, 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.
- - 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
- - PileUp
- - AMSA
- - STH
- - PHYLIP
- - JSON
-
- - 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.
-
- - 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.
-
- - Load VCF File
- Load VCF annotations from a plain text or tab-indexed file.
-
This option is offered for nucleotide alignments, and requires at least one
- sequence to have known genomic coordinates.
-
Genomic coordinates are attached to entries retrieved from Ensembl.
-
Support for VCF was added in Jalview 2.11.
-
- - 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.
-
-
-
-