X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=57ffa08525b7c870ad2a09a5efcdc419f06d85bf;hb=58ecc1bd5b01acd8f8378980f369003da9db2ee9;hp=87582f81b52c807cbb6edec591e44df8e7210822;hpb=354963d0c9d69f28fa5aa642c1f13627676ff4ae;p=jalview.git
diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
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--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -24,100 +24,123 @@
-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.
- - 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.
-
+
+ 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.
+
+