X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FsplitView.html;fp=help%2Fhtml%2Ffeatures%2FsplitView.html;h=5b48ec33145d082deab24f6e5fc35bbca93f2df5;hb=81dc22411a15b2afb62ef80124db37479c5e764f;hp=16d6c10b031072c036bd10a6b99b40ba828636fc;hpb=02615f4ca92570e571d166aeb8d9c0bf6531424d;p=jalview.git 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.
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: +
Parameter | Value | Description | +
---|---|---|
file | path to an alignment file | a cDNA (or protein) alignment | +
file | path to an alignment file | a protein (or cDNA) alignment | +
enableSplitFrame | true | to enable the Split Frame feature | +
Split Frame Views were introduced in Jalview 2.9