<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 or Pairwise Identity |
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"....
|
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 |
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 |