Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwfile.html;h=0605040e6eb8a39aa1faed7af13776a4cf26bbd1;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=e545ab2834bda2879cdd3cc15ab156ca968ce74f;hpb=9d50efc40c88bd65891fa009267912f50ff80cf3;p=jalview.git diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index e545ab2..0605040 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -1,79 +1,120 @@ - -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. - -
- 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.
-

- - + + + +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
+
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. +
- 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.
- SVG
  + Create a Scalable Vector Graphics file from your alignment for embedding in web pages.
+
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.

+ +