<param name="" |
value=""> |
Description |
file |
fileName |
The file to open, must be on same server as the applet. |
sequence1,
sequence2,
sequence3 |
sequence in (preferably) PFAM or Fasta format |
The alignment can be added as a series of sequences instead of
from a file. |
tree |
fileName |
Tree file in Newick format |
features |
fileName |
Jalview Features file to be applied to the alignment |
annotations |
fileName |
Jalview Annotation file will be added to the alignment |
jnetfile |
fileName |
Secondary structure predictions from a Jnet Concise
file will be added to the first sequence in the alignment. |
PDBfile(x) |
fileName seq1 seq2 seq3
or
fileName A=seq1 B=seq2 C=seq3 |
PDB file which is to be associated with a sequence, followed by
space separated list of alignment sequence ids. PDB chains can be
specifed to map to particular sequence by using A=SeqA notation |
PDBSeq
*Not needed post Jalview 2.3, use PDBFile instead |
SequenceId |
The sequence to associate a PDB file with. Note the value is case
sensitive. |
defaultColour |
One of:
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide |
Default is no colour. |
userDefinedColour |
Example:
D,E=red; K,R,H=0022FF; c=yellow |
Define residue colours |
showFullId |
true or false |
if true displays start and end residue at the end of sequence
Id. |
showAnnotation |
true or false |
If true shows the annotation panel below the alignment. |
showConservation |
true or false |
Default is true. |
showQuality |
true or false |
Default is true. |
showConsensus |
true or false |
Default is true. |
sortBy |
Id , Pairwise Identity, or Length |
Sorts the alignment on startup |
RGB |
colour as hex string |
Background colour for applet button - purely cosmetic to blend
in with your web page. For orange, enter the value FF6600 |
embedded |
true or false |
The applet is embedded in the web page, the "Start Jalview"
button is not displayed. |
windowWidth |
value |
frame width |
windowHeight |
value |
frame height |
label |
label text |
Change text for the Launch Jalview Button |
wrap |
true or false |
Opens new windows in wrapped mode |
linkLabel_1 |
Uniprot |
Right click on sequence id to see list of available
links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
value. For multiple links, increment the label and url name by
1. ie
<param name="linkLabel_2" ...,
<param name="linkUrl_2"....
Regular expressions may also be used (since Jalview 2.4) to process the ID string inserted into the URL:
$SEQUENCE_ID=/<regex to extract ID>/=$ Use the debug flag to check parsing and make sure that special symbols are properly escaped (particularly when generating applet tags from CGI scripts).
Regex URL links are also applied to the description line (since Jalview 2.4.+). |
linkUrl_1
|
http://us.expasy.org/cgi-bin/
niceprot.pl?$SEQUENCE_ID$
|
showFeatureSettings |
true or false |
Shows the feature settings window when starting the applet |
showfeaturegroups |
separator separated list of feature groups |
Display the features in the given groups on the alignment |
hidefeaturegroups |
separator separated list of feature groups |
Hide the features in the given groups on the alignment
(will be overridden by showfeaturegroups for group names
found in both lists) |
application_url |
URL of dynamic JNLP servlet,
http://www.jalview.org/services/launchApp |
Launches full application with original alignment, features and
annotations files used in applet |
separator |
non-empty separator string default: | |
string used to separate fields in list parameters (such as showfeaturegroups) |
debug |
true |
Instruct the applet to output additional debug messages to the java console |
nojmol |
false |
When set, do not try to find Jmol classes. Set this to supress URL not found errors appearing
in server logs when Jmol is not available.
|
showbutton |
true |
Show the jalview button on the page. When false, JalviewLite will open immediately. |
sortByTree |
true or false (default is false) |
automatically sort the associated alignment view by the tree when a new tree is opened. |
showTreeBootstraps | true or false (default is true) | show or hide branch bootstraps |
showTreeDistances | true or false (default is true) | show or hide branch lengths |
showUnlinkedTreeNodes | true or false (default is false) | indicate if unassociated nodes should be highlighted in the tree view |
heightScale |
1.0 or greater |
Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. |
widthScale |
1.0 or greater |
Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. |