Hi Julie - thanks for your questions. I'll answer them in reverse :)
On 10/11/2014 14:11, Julie Lee-Yaw wrote:
> Also as an aside, this is my first time using the list serve. I didn't
> see a way to search old archives other than to click on the digest
> month by month and manually read through the list of headings. Can
> someone please tell me how to search for particular topics so I can
> avoid posting redundant questions?
Great question. Google indexes our mailing list, so I just created a
custom search link:
https://www.google.co.uk/cse/publicurl?cx=005718409729431308369:evyfdt8zyyq
I'll add a search box to the web site when I get a moment !
On 10/11/2014 14:11, Julie Lee-Yaw wrote:
> I am a new user of jalview. I am using the program to inspect/edit a
> nucleotide alignment of about 188000 bp. The sequences that I'm
> inspecting are all at the intraspecific level so most of my alignment
> is identical. I wish to inspect those residues for which there is some
> evidence of variation. Is there a way to view only those residues with
> a consensus score less than a certain threshold.
You've discovered something that really needs to be included in Jalview,
but we haven't actually done yet :)
I'm hoping we'll add the 'mark unconserved' function in a future
release, but until then, you could use this groovy script:
// hides columns above a certain percentage identity threshold
// Open the Tools->Groovy Console
// paste the following lines in and
// press 'CTRL+R' or 'CMD+R' to execute
// percentage below which columns will be marked
def consThresh = 50f;
def alf = Jalview.getAlignframes();
for (ala in alf)
{
// ala is an jalview.gui.AlignFrame object
// get the alignment consensus annotation
def alcons = ala.viewport.getAlignmentConsensusAnnotation();
// and mark columns in a column selection object
jalview.datamodel.ColumnSelection cs = ala.viewport.getColumnSelection();
if (cs == null) {
cs = new jalview.datamodel.ColumnSelection();
ala.viewport.setColumnSelection(cs);
} else {
cs.clear();
}
int p=0;
for (q in alcons.annotations)
{
if (q!=null && q.value<consThresh) { cs.addElement(p); }
p++
}
// lastly simulate a 'SHIFT+CTRL+H' to hide unmarked regions
ala.hideAllButSelection_actionPerformed(null);
}
// end of groovy script
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