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Download the applet jar file from here.
**NEW FEATURES** in Jalview 2.3
**NEW FEATURES** in Jalview 2.1
- Jalview Applet can read and display JNet secondary structure annotation
directly via the jnetfile parameter.
- Param UserDefinedColour
- specify your own colours for each residue using a semi colon
separated list. Multiple residues can be assigned the same colour
using commas. eg:
<param name="userDefinedColour"
value="D,E=red; K,R,H=0022FF; C=yellow">
- Param showFeatureSettings
- this will display the feature settings window when the applet starts.
- Param Application_URL value="http://www.jalview.org/services/launchApp"
This calls a servlet which creates a JNLP file with the alignment
file, annotations file and features file of the applet as arguments.
If the user has Java installed, the returned JNLP file should start
up the full Jalview Application. BUT this does not currently work
for alignment files added to the applet in a zip file.
- Alignment file can be a series of parameters using eg PFAM format
<param name="sequence1"
value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI">
<param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT">
(All the usual Jalview File formats are valid, however each
new line in an alignment file must be entered as a parameter)
Useful to know!!
- Package all your data files into a single (or multiple) zip / jar
files. This is very useful to reduce download time of large data files.
The applet archive tag can take multiple entries separated by commas,
eg
<applet code="jalview.bin.JalviewLite"
archive="jalviewApplet.jar, mydata.zip">
- Use Jalview for input to a HTML form. For an example of how to
code this using Javascript, click here.
- Embed Jalview into the web page, without the "Start Jalview"
button by setting the embed parameter to true;
<param name="embedded" value="true">
<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"....
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linkUrl_1
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http://us.expasy.org/cgi-bin/
niceprot.pl?$SEQUENCE_ID$
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showFeatureSettings |
true or false |
Shows the feature settings window when starting the applet |
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 |
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