Skip to content

Commit

Permalink
Merge branch 'peter' into devel
Browse files Browse the repository at this point in the history
  • Loading branch information
@PeterFCKeen
PeterFCKeen committed Apr 5, 2016
2 parents 75c60de + 156a232 commit f7d0216
Show file tree
Hide file tree
Showing 5 changed files with 210 additions and 120 deletions.
4 changes: 2 additions & 2 deletions lib/LIMS2/WebApp/Controller/PublicAPI.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ sub trace_data_GET{
}

my $data = $self->_extract_region( \%scf, $match->{start} - $context, $match->{end} + $context, $params->{reverse} );

$DB::single=1;
return $self->status_ok( $c, entity => $data );
}

Expand Down Expand Up @@ -179,7 +179,7 @@ sub _extract_region {
};
}

return { labels => \@labels, series => \@series, length => $length };
return { labels => \@labels, series => \@series, length => $length, bases => \%sample_to_base };
}

=head1 NAME
Expand Down
6 changes: 3 additions & 3 deletions root/lib/crispr_qc_alignment.tt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
</span><br/>
</div>
<div id="seqs[% qc.well_name %]" class="alignment_inner">
<span id="f[% qc.well_name %]" class="seq seq_a">
<span id="f" class="seq seq_a">
[% IF qc.alignment.no_forward_read %]
No Read
[% ELSIF qc.alignment.no_forward_alignment %]
Expand All @@ -15,15 +15,15 @@
[% END %]
</span>(F)
<span style="display: block">
<span id="r[% qc.well_name %]" class="seq seq_b">
<div id="r" class="seq seq_b">
[% IF qc.alignment.no_reverse_read %]
No Read
[% ELSIF qc.alignment.no_reverse_alignment %]
No alignment to target region
[% ELSE %]
<div class="rev">[% qc.alignment.reverse %]</div>
[% END %]
</span>(R)
</div>(R)
</span>
</div>
</div>
Expand Down
183 changes: 122 additions & 61 deletions root/site/user/crisprqc/crispr_es_qc_run.tt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -181,122 +181,183 @@ $(document).ready(function() {

var focusTrace;
var wellTrace;
var click;
var wellName;
var parent;


$(document).click(function(event) {
var click = $(event.target);
var dir = click.children();
var wellName = click.parents('tr[class^="well_tr"]').attr('id');
if (typeof(dir.attr('id')) != "undefined") {
traceviewers.forEach( function(trace) {
if (trace.well == wellName) {
wellTrace = trace;
}
});
click = $(event.target);
children = click.children();
parent = click.parent()[0].getElementsByTagName('span');
well = click.parents('tr[class^="well_tr"]');
wellName = well.attr('id');
var id;
for (var pos = 0; pos < parent.length; pos++) {
if (parent[pos].id != "") {
id = parent[pos].id;
console.log(parent[pos].id);
}
}
traceviewers.forEach( function(trace) {
if (trace.well == wellName) {
wellTrace = trace;
}
});

console.log(id);
if (id) {
if (wellTrace) {
focusTrace = wellTrace[dir.attr('id') + "_plot"];
adjustPane(dir, dir.text());
console.log(id + "_plot");
focusTrace = wellTrace[id + "_plot"];
adjustPane(children, id, click);
}
else {
console.log(wellName + dir.attr('id') + " not found");
console.log(wellName + children.attr('id') + " not found");
}
}
else {
var reads = ['forward_full','reverse_full'];
var plots = ['fwd','rev'];
var query = click.text();
for (var count = 0; count < reads.length; count++) {
var read = well[0].getElementsByClassName(reads[count])[0].innerText;
var result = read.search(query.toUpperCase());
if (result != -1) {
console.log(plots[count]+ "_plot");
focusTrace = wellTrace[plots[count] + "_plot"];
adjustPane(children, plots[count], click);

}
}
}
});


var test;
var result;
var test3;
var test2;

function adjustPane(text, dir) {
function adjustPane(text, dir, target) {
console.log("adjustPane");
var selection = window.getSelection();

//Using Jquery mouse target $(event.target)

var tr = text.closest("tr");
var tr = target.closest("tr");
test = tr[0];
var well_name = tr.attr('id');
//Get table row nearest to mouse location
var alignmentInner = tr[0];


tr = tr[0].getElementsByTagName('div');
tr = alignmentInner.getElementsByTagName('div');

var div;
for (var counter = 0; counter < tr.length; counter++) {
if (tr[counter].id == "seqs" + well_name && tr[counter].className == "alignment_inner") {
div = tr[counter];
}
}
//HTMLcollection must not be iterated through by foreach
//Find the div inside the HTMLcollection containing the two sequences

test3 = div;
div = $(div).text();
//Remove HTML tags
div = div.replace(/-/g,'N');

var regex = /[ACTGNn]+/g;

var match;
result = div.match(regex);
var result = sanitise(div);
test2 = result;
//Remove everything not relating to the sequence
var customSelection = selection.toString();
var referencePoint = focusTrace._pos;

for (var index = 0; index < result.length; index++) {
if (result[index].search(focusTrace._read) != -1) {
dir = index;
}
console.log("Read " + focusTrace._read);
console.log("Dir " + dir);
if (dir == 'fwd') {
dir = 0;
} else {
dir = 1;
}
console.log("Dir " + dir);
if (focusTrace._reduced != 1 && [% truncate %] == 0) {
console.log("reach");
cleanseReference(result[dir], alignmentInner, dir);
focusTrace._reduced = 1;
}

var loc = findCoords(result, referencePoint, selection, dir);
wellTrace.moveToPoint(focusTrace, loc[0], loc[1]);
}

function getSliderOffset(seq){
var read = focusTrace._read;
return seq.search(read);
function sanitise(text) {
text = text.replace(/-/g,'N');

var regex = /[ACTGNn]+/g;

var match;
result = text.match(regex);
return result;
}

function cleanseReference(userString, row, dir) {
var read;
if (dir == 0) {
read = 'forward_full';
} else {
read = 'reverse_full';
}
var fullSeq = row.getElementsByClassName(read)[0].innerText;
console.log(fullSeq);
console.log(userString.slice(0,10));
var offset = fullSeq.search(userString.slice(0,10));
console.log("Start: " + offset);
focusTrace._ref.splice(0,offset);
console.log(fullSeq.slice(offset, fullSeq.length));
}
var test4;
function getMouseOffset(seq, selection){
var offset;
console.log(seq);
test4 = selection;
if (selection.toString().length > 1) {
return seq.search(selection.toString());
offset = seq.search(selection.toString());
} else {
return seq.search(selection.focusNode.data) + selection.focusOffset;
offset = seq.search(selection.focusNode.data) + selection.focusOffset;
}
console.log("Offset: " + offset);

return offset;
}


function findCoords(seqs, point, selection, dir) {
var traceSeq = seqs[dir]; //Dir: 0 -> Fwd seq | 1 -> Rev seq

var target = selection.toString();
var mouseOffset = getMouseOffset(traceSeq, selection); //Must be done before any update to the traceviewer
console.log(mouseOffset);
var ends = [];

//Init position is outside of the boundaries
if (getSliderOffset(traceSeq) == -1) {
focusTrace._initPos = focusTrace._pos;
if (target.length < 5) {
if ([% truncate %] == 0) {
mouseOffset += 10;
}
ends.push(mouseOffset - 10);
ends.push(mouseOffset + 10);
if (ends[0] < 0) {
ends[0] = 0;
}
if (ends[1] > traceSeq.length){
ends[1] = traceSeq.length;
}
}

//Allow for an average
if (focusTrace._pos == focusTrace._initPos) {
forceUpdate();
else {
ends.push(mouseOffset);
ends.push(mouseOffset + target.length);
}

var loc = [];

var sliderOffset = getSliderOffset(traceSeq); //Position of traceviewer slider in the seq
var positionDiff = Math.round(focusTrace._pos - focusTrace._initPos);
var rate = Math.round( positionDiff / sliderOffset * 100) / 100; //Get rate to 2 decimal places

var cost = (mouseOffset - sliderOffset) * rate;
//Hueristic to mouse point

if (target.length < 5) {
return [cost + focusTrace._pos - 125, cost + focusTrace._pos + 125];
} else {
var endCost = cost + (target.length * rate);
return [cost + focusTrace._pos, endCost + focusTrace._pos];
for (var point = 0; point < ends.length; point++){
loc.push(focusTrace._ref[ends[point]]);
}
}

function forceUpdate() {
var newPos = focusTrace._pos + 300;
wellTrace.moveToPoint(focusTrace, newPos - 125, newPos + 125);
//Move the traceviewer to allow for an average of the spacing between bases

return loc;
}

</script>
Expand Down
Loading

0 comments on commit f7d0216

Please sign in to comment.