X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=261d723db19a957e4f213fd6ede01e48214c2cb1;hb=ecae5205f2b0ecbf25dd66f9dd04b7f20e29c028;hp=53c7e6c4ab96ab009ccb155f8515474e452f7a0b;hpb=2e2bc3fbb0231c705e5d019df9cb8e0e600ca12e;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
@@ -1,79 +1,111 @@
-
-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.
-
-
-
- - 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
- Jalview load 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.
-
-
-
-
+
+
+
+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
+
+
+ - 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.
+
+
+