- Quick Links: -
-Additional applet deployment notes are below.
+JalviewLite Applet Parameter Documentation
++The JalviewLite applet is configured through a series of applet parameters, +which are described below. Once initialised, +the applet can be interacted with via its +Javascript API. +
Issues arising from tightening of Java Security default settings
JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings.
For additional deployment notes, see below.
Applet Parameters
The applet takes the following initialisation parameters.
| fileName | The file to open, must be on same server as the applet. | ||
| file2 | +fileName | +A second file to open and show linked in a Split Frame + view. If one file is nucleotide and the other peptide, and at + least one peptide sequence matches the translation of one of the + nucleotide sequences, then gaps will be inserted into the + sequences in this file to match the aligned columns for + corresponding positions in the primary alignment file. This + parameter is ignored if enableSplitFrame is set to false (since + 2.9). + | +|
| enableSplitFrame | +true or false (default true) | +Enable or disable the display of linked cDNA and Protein alignments in a split frame (since 2.9). | +|
| sequence1, sequence2, @@ -237,10 +114,18 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr | defaultColour | One of: Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide |
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices
Default is no colour. |
| defaultColourNuc | +A colour scheme (from the list above) to apply to Nucleotide alignments | This overrides defaultColour if it is specified. | +|
| defaultColourProt | +A colour scheme (from the list above) to apply to Peptide alignments | This overrides defaultColour if it is specified. | +|
| userDefinedColour | Example: |
@@ -394,11 +279,14 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
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. (since 2.5.1) |
| scaleProteinAsCdna | true or false (default is false) | +Set true to shown protein residues the same width as their encoding codons. + For use with parameter file2 when showing a split frame of cDNA and protein. (since 2.9) | |
| centrecolumnlabels | -true of false (default is false) | +true or false (default is false) | When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (since 2.4) |
| showUnconserved | -true of false (default is false) | +true or false (default is false) | When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (since 2.5) |
| upperCase | @@ -406,29 +294,29 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trIndicate a text style to apply to uppercase sequence symbols. Currently, only bold is supported. | ||
| automaticScrolling | -true of false (default is true) | +true or false (default is true) | When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (since 2.6) |
| showGroupConsensus | -true of false (default is false) | +true or false (default is false) | When true, shows consensus annotation row for any groups on the alignment. (since 2.7) |
| showGroupConservation | -true of false (default is false) | +true or false (default is false) | When true, shows amino-acid property conservation annotation row for any groups on the alignment. (since 2.7) |
| showConsensusHistogram | -true of false (default is true) | +true or false (default is true) | When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (since 2.7) |
| showSequenceLogo | -true of false (default is false) | +true or false (default is false) | When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (since 2.7) |
| normaliseSequenceLogo | -true of false (default is false) | +true or false (default is false) | When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (since 2.8) |
| oninit | @@ -479,7 +367,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr archive="jalviewApplet.jar, mydata.zip">