Publish alignment as a Web-link
[Menu-bar>Protein>File>Export proteins and alignments]
With this dialog a Web-Link can be formed which loads the proteins from the public databases into STRAP and displays an alignment.
When the link is clicked on a computer with Java, the alignment will be displayed in STRAP.
Depending on the purpose of the link and on how much information should be transfered
two different types are available:
- A compact URL
- A Web form
In both types, proteins that are stored in protein databases are
included by database reference. This has the advantage that always the most recent
version of the protein file is loaded and the current state of
sequence features and cross links are available.
Single URL
Since the URL contains the information in a compact form in a single line, not all information is stored.
The advantage is that the can not only be included in web-pages, but also in e-mails, Office-documents.
The generation of the URL is conducted in two steps:
-
The parameter String is written into the first text-field and can be modified by the user.
The following table summarizes the "|"-separated fields.
separated fields of protein entries
| No | Description | Example |
|---|
| 1 | URL of protein file or database colon ID | EMBL:M57965 |
|---|
| 2 | Protein name. Optionally with exclamation mark and residue subset. | b_myosin_heavy_chain |
|---|
| 3 | Icon | http://www.ebi.ac.uk/thornton.../duc_temp.gif |
|---|
| 4 | Residue selections. Supported 3D-styles: sticks, spheres and dots. | #00FFFF,sticks,16-20,#FF00FF,spheres,40-50 |
|---|
| 5 | Coding sequence of a nucleotide sequence | reverse,40-100 |
|---|
The 5th field is required only for nucleotide sequence files. It contains either the index of the CDS such as "#1" for the first or "#2" for the second CDS or the
CDS expression directly.
-
From the text in the first text-field the web-link will be generated using and written into the 2nd text-field.
The generated URL acts as a hyperlink and can be tested by clicking. A new STRAP session will be opened in web-mode and an alignment will be loaded with the specified information.
Web form
Since the web form has no size limitation, the entire information for the alignment can be included.
The draw-back is that it can only be included in web-pages, but not in office documents or e-mails.
A minimal html-page including the web link for the selected proteins is generated on pressing 
.
For testing it is loaded into the web browser upon pressing 
.
From this html code the text between the opening and closing and <body> tags can be used in any html-page.
An overview of the STRAP scripting commands is given in http://3d-alignment.eu/web/strap_script.html.
The following commands are available:
DAS_features ,STRAP_to_front,aa_sequence ,accession_id ,add_annotation ,add_xref ,align ,below_row ,box ,cds ,close ,close_wire ,cursor ,deiconify,delete ,gaps ,hide ,icon ,iconify,jalview ,load ,load_from_databases ,mseconds,new_aminoacid_selection ,new_nucleotide_selection ,plugin ,project_coordinates ,remove_xref ,rotate_translate ,scroll_to ,select ,seqvista ,set_annotation ,source_code ,spice ,superimpose ,to_row ,to_structure_viewer ,tree ,unhide ,unselect ,wire
;){kind=link}