Thanks for all the helpful info Elaine ! As you pointed out - Jalview's
quality score is essentially a sum of pairs calculation for each column
based on Blosum62 and normalised for gapped positions. I've been meaning
to add in a summary score for the annotation row - but until then,
Anton, your students could use the groovy script below:
// Open the Tools->Groovy Console
// paste the following lines in and
// press 'CTRL+R' or 'CMD+R' to execute
// output is sum of quality scores for each alignment
def alf = Jalview.getAlignframes();
print "Title\tQuality sum\n"
def qual;
for (ala in alf)
{
// ala is an jalview.gui.AlignFrame object
print ala.getTitle()+"\t";
// get the conservation object and sum the quality scores
def alcons = ala.viewport.getAlignmentQualityAnnot();
qual=0;
for (q in alcons.annotations)
{
if (q!=null) { qual+=q.value; }
}
print "\t"+qual+"\n";
}
// end of groovy script
ps. for help with groovy - see here:
http://www.jalview.org/help/html/features/groovy.html
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