X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=1e45aae5d5483f661652d5c9a2ea7494bfe9e275;hb=df7802fdd54e7d3b12bda12ac55e6057c985bdf2;hp=d6c4edd6624837bfb4445cff3bcd34a398285efb;hpb=3eddf87cb1eb8046d191c65ec69d83264a3c41c0;p=jalview.git
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index d6c4edd..1e45aae 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -17,6 +17,9 @@
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
+
+
Click here to view decorated page
+
JalviewLite Applet Parameter Documentation
@@ -43,11 +46,23 @@ the applet can be interacted with via its
fileName |
The file to open, must be on same server as the applet. |
-
- file2 |
- fileName |
- A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
- is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (since 2.8.3). |
+
+ 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,
@@ -103,6 +118,14 @@ the applet can be interacted with via its
| 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:
D,E=red; K,R,H=0022FF; c=yellow |
@@ -258,7 +281,7 @@ the applet can be interacted with via its
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 2.8.3) |
+ For use with parameter file2 when showing a split frame of cDNA and protein. (since 2.9)
centrecolumnlabels |
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) |
@@ -352,6 +375,13 @@ the applet can be interacted with via its
<param name="embedded"
value="true">
+
+ **NEW FEATURES** in Jalview 2.9
+
+ - Split Views for cDNA and Protein alignments
Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
+
+
+
**NEW FEATURES** in Jalview 2.8
- Normalised sequence logo display
@@ -456,4 +486,4 @@ the applet can be interacted with via its
(All the usual Jalview File formats are valid, however each
new line in an alignment file must be entered as a parameter)
-
\ No newline at end of file
+