From: gmungoc Date: Thu, 27 Aug 2015 11:33:55 +0000 (+0100) Subject: JAL-1701 help page for Split Frame view linked in X-Git-Tag: Jalview_2_9~10^2~10 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=023d23abaad346f745b93fced2407d7342ab7171;p=jalview.git JAL-1701 help page for Split Frame view linked in --- diff --git a/help/help.jhm b/help/help.jhm index 2cfe8d8..a450473 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -74,6 +74,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 345cb51..4ce9892 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -29,6 +29,7 @@ + diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html index c9ce093..16d6c10 100644 --- a/help/html/features/splitView.html +++ b/help/html/features/splitView.html @@ -43,7 +43,8 @@ This consensus may reveal variation in nucleotides coding for conserved protein

Add Sequences

If you add (coding) DNA sequences to an open peptide alignment, or vice versa, and at least one DNA sequence translates to one of the peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron) -sequence.

+sequence.
+If more than one cDNA variant is present in the alignment, Jalview will first try to match these to protein sequences based on any retrieved cross-references, and failing that, pairwise as they are ordered in the alignments.

This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox). The additional options below apply to Jalview Desktop only.

@@ -56,7 +57,7 @@ calculated protein product in a Split Frame view.

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 Split View

+

Realign a Split View

If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new Split Frame.

    @@ -69,6 +70,6 @@ Split Frame.

-

Split Frame Views were introduced in Jalview 2.?.?

+

Split Frame Views were introduced in Jalview 2.9