From cb231b238443611effe9ed859f1e9d4370882f9b Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 2 Sep 2015 12:10:01 +0100 Subject: [PATCH] JAL-1619 additions, standardised menu item symbols --- help/html/features/splitView.html | 26 ++++++++++++++++++++------ 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html index 16d6c10..5b48ec3 100644 --- a/help/html/features/splitView.html +++ b/help/html/features/splitView.html @@ -27,13 +27,17 @@

Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are linked, with these features supported:

An alignment annotation row on the protein alignment shows the cDNA consensus for each peptide column.
This consensus may reveal variation in nucleotides coding for conserved protein residues.

@@ -50,11 +54,11 @@ If more than one cDNA variant is present in the alignment, Jalview will first tr The additional options below apply to Jalview Desktop only.

Translate as cDNA

-

Menu option "Calculate | Translate as cDNA" is available for a nucleotide alignment. Selecting this option shows the DNA and its +

Menu option "Calculate→Translate as cDNA" is available for a nucleotide alignment. Selecting this option shows the DNA and its calculated protein product in a Split Frame view.

Get Cross-References

-

Menu option "Calculate | Get Cross-References" is available for fetched sequences which have cross-references to other databases. +

Menu option "Calculate→Get Cross-References" is available for fetched sequences which have cross-references to other databases. On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.

Realign a Split View

@@ -68,7 +72,17 @@ Split Frame.

- + +

Applet

+

To see a split frame view in the Jalview applet, provide these applet parameters: + + + + + +
ParameterValueDescription
filepath to an alignment filea cDNA (or protein) alignment
filepath to an alignment filea protein (or cDNA) alignment
enableSplitFrametrueto enable the Split Frame feature
+

If compatible sequences are present in the input alignments, Jalview will open a Split Frame view.
+If not, only the first alignment will be opened (an error message is written to the Java console).

Split Frame Views were introduced in Jalview 2.9

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