X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=f5ea0914b63594934c4f5521c79beb10b67460e7;hb=2eeea2f43d7bbaafd79ebd4185b42fc60646d9e3;hp=6ffc523fd31a3f1b94af9130b1d5103e640ab1b7;hpb=cf057dc2bbe75569e3c7a1d688bee3044be73450;p=jalview.git
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Alignment Window File Menu
- - File
-
+ - Add Sequences
+ Add sequences to the visible alignment from file, URL, or cut & paste
+ window
- 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.
+ 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.
+ - 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
+ 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.
-
- - 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
- Load files describing 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.
-
-