From: amwaterhouse Date: Fri, 11 Aug 2006 14:20:25 +0000 (+0000) Subject: 2.1 updates X-Git-Tag: Release_2_1~99 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=152502648d18fd539602fe0e060c8b9288bc4183;p=jalview.git 2.1 updates --- diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index 6ffc523..f5ea091 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -4,76 +4,73 @@

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. +
- HTML
  + Create a web page from your + alignment.
- EPS
  + Create an Encapsulated Postscript + file from your alignment.
- PNG
  + Create a Portable Network Graphics + file from your 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. - -
- HTML
  - Create a web page - from your alignment.
- EPS
  - Create an Encapsulated - Postscript file from your alignment.
- PNG
  - Create a Portable Network - Graphics file from your 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.
-