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Added complementary DNA strand, and DNA highlighting URL parameter.
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@rbuels
Ian Davis authored and rbuels committed Mar 7, 2012
1 parent 66c055d commit 94e9db0
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Showing 2 changed files with 143 additions and 45 deletions.
159 changes: 115 additions & 44 deletions js/Browser.js
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Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,10 @@ var Browser = function(params) {
for (var i = 0; i < brwsr.deferredFunctions.length; i++)
brwsr.deferredFunctions[i]();
brwsr.deferredFunctions = [];

if (params.highlight) {
brwsr.highlightRegion(params.highlight);
}
});
};

Expand Down Expand Up @@ -321,7 +325,7 @@ Browser.prototype.addTracks = function(trackList, replace) {
};

/**
* navigate to a given location
* Parse a location string. showTracks and/or startBase may be undefined.
* @example
* gb=dojo.byId("GenomeBrowser").genomeBrowser
* gb.navigateTo("ctgA:100..200")
Expand All @@ -332,10 +336,9 @@ Browser.prototype.addTracks = function(trackList, replace) {
* &lt;center base&gt;<br>
* &lt;feature name/ID&gt;
*/
Browser.prototype.navigateTo = function(loc) {
Browser.prototype.parseLocation = function(loc) {
if (!this.isInitialized) {
var brwsr = this;
this.deferredFunctions.push(function() { brwsr.navigateTo(loc); });
console.log("parseLocation() cannot usefully be deferred!");
return;
}

Expand All @@ -348,60 +351,33 @@ Browser.prototype.navigateTo = function(loc) {
//matches[6] = end base (or center base, if it's the only one)
if (matches) {
if (matches[3]) {
var refName;
for (ref in this.allRefs) {
if ((matches[3].toUpperCase() == ref.toUpperCase())
||
("CHR" + matches[3].toUpperCase() == ref.toUpperCase())
||
(matches[3].toUpperCase() == "CHR" + ref.toUpperCase())) {

refName = ref;
return { refName: ref,
startBase: parseInt(matches[4].replace(/[,.]/g, "")),
endBase: parseInt(matches[6].replace(/[,.]/g, "")) };
}
}
if (refName) {
dojo.cookie(this.container.id + "-refseq", refName, {expires: 60});
if (refName == this.refSeq.name) {
//go to given start, end on current refSeq
this.view.setLocation(this.refSeq,
parseInt(matches[4].replace(/[,.]/g, "")),
parseInt(matches[6].replace(/[,.]/g, "")));
} else {
//new refseq, record open tracks and re-open on new refseq
var curTracks = [];
this.viewDndWidget.forInItems(function(obj, id, map) {
curTracks.push(obj.data);
});

for (var i = 0; i < this.chromList.options.length; i++)
if (this.chromList.options[i].text == refName)
this.chromList.selectedIndex = i;
this.refSeq = this.allRefs[refName];
//go to given refseq, start, end
this.view.setLocation(this.refSeq,
parseInt(matches[4].replace(/[,.]/g, "")),
parseInt(matches[6].replace(/[,.]/g, "")));

this.viewDndWidget.insertNodes(false, curTracks);
this.onVisibleTracksChanged();
}
return;
}
} else if (matches[4]) {
//go to start, end on this refseq
this.view.setLocation(this.refSeq,
parseInt(matches[4].replace(/[,.]/g, "")),
parseInt(matches[6].replace(/[,.]/g, "")));
return;
return { refName: this.refSeq,
startBase: parseInt(matches[4].replace(/[,.]/g, "")),
endBase: parseInt(matches[6].replace(/[,.]/g, "")) };
} else if (matches[6]) {
//center at given base
this.view.centerAtBase(parseInt(matches[6].replace(/[,.]/g, "")));
return;
return { refName: this.refSeq,
endBase: parseInt(matches[6].replace(/[,.]/g, "")) };
}
}
//if we get here, we didn't match any expected location format

var brwsr = this;
var retval;
this.names.exactMatch(loc, function(nameMatches) {
var goingTo;
//first check for exact case match
Expand All @@ -422,13 +398,108 @@ Browser.prototype.navigateTo = function(loc) {
var endbp = goingTo[4];
var flank = Math.round((endbp - startbp) * .2);
//go to location, with some flanking region
brwsr.navigateTo(goingTo[2]
+ ":" + (startbp - flank)
+ ".." + (endbp + flank));
brwsr.showTracks(brwsr.names.extra[nameMatches[0][0]]);
retval = { refName: goingTo[2],
startBase: (startbp - flank),
endBase: (endbp + flank),
showTracks: brwsr.names.extra[nameMatches[0][0]]};
});
return retval;
};

/**
* navigate to a given location
* @example
* gb=dojo.byId("GenomeBrowser").genomeBrowser
* gb.navigateTo("ctgA:100..200")
* gb.navigateTo("f14")
* @param loc can be either:<br>
* &lt;chromosome&gt;:&lt;start&gt; .. &lt;end&gt;<br>
* &lt;start&gt; .. &lt;end&gt;<br>
* &lt;center base&gt;<br>
* &lt;feature name/ID&gt;
*/
Browser.prototype.navigateTo = function(loc) {
if (!this.isInitialized) {
var brwsr = this;
this.deferredFunctions.push(function() { brwsr.navigateTo(loc); });
return;
}

loc = this.parseLocation(loc);
if (loc === undefined) {
return; // oops -- parsing failed
} else if (loc.refName) {
dojo.cookie(this.container.id + "-refseq", loc.refName, {expires: 60});
if (loc.refName == this.refSeq.name) {
//go to given start, end on current refSeq
this.view.setLocation(this.refSeq, loc.startBase, loc.endBase);
} else {
//new refseq, record open tracks and re-open on new refseq
var curTracks = [];
this.viewDndWidget.forInItems(function(obj, id, map) {
curTracks.push(obj.data);
});
for (var i = 0; i < this.chromList.options.length; i++)
if (this.chromList.options[i].text == loc.refName)
this.chromList.selectedIndex = i;
this.refSeq = this.allRefs[loc.refName];
//go to given refseq, start, end
this.view.setLocation(this.refSeq, loc.startBase, loc.endBase);
this.viewDndWidget.insertNodes(false, curTracks);
this.onVisibleTracksChanged();
}
if (loc.showTracks) {
// We matched a feature name instead of a "chromosome:start..end"
this.showTracks(loc.showTracks);
}
//return;
} else if (loc.startBase) {
//go to start, end on this refseq
this.view.setLocation(this.refSeq, loc.startBase, loc.endBase);
//return;
} else if (loc.endBase) {
//center at given base
this.view.centerAtBase(loc.endBase);
//return;
}
};

/**
* highlight a given location
* @example
* gb=dojo.byId("GenomeBrowser").genomeBrowser
* gb.navigateTo("ctgA:100..200")
* gb.navigateTo("f14")
* @param loc can be either:<br>
* &lt;chromosome&gt;:&lt;start&gt; .. &lt;end&gt;<br>
* &lt;start&gt; .. &lt;end&gt;<br>
* &lt;center base&gt;<br>
* &lt;feature name/ID&gt;
*/
Browser.prototype.highlightRegion = function(loc) {
if (!this.isInitialized) {
var brwsr = this;
this.deferredFunctions.push(function() { brwsr.highlightRegion(loc); });
return;
}
// Capture location for highlighting DNA sequence.
// Tracks are initialized by one of the deferred functions!
var loc = this.parseLocation(loc);
if(!loc || !loc.refName || loc.startBase === undefined || loc.endBase === undefined) return;

// Convert from "natural" numbering to interbase:
loc.startBase -= 1;
for(var i = 0; i < this.view.tracks.length; i++) {
var track = this.view.tracks[i];
if(track.name == "DNA") {
track.hilightLoc = loc;
track.clear();
}
}
this.view.showVisibleBlocks(true);
// Calls to .clear() and .showVisibleBlocks() required to refresh the view...
}

/**
* load and display the given tracks
* @example
Expand Down
29 changes: 28 additions & 1 deletion js/SequenceTrack.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,13 @@ function SequenceTrack(trackMeta, url, refSeq, browserParams) {
Track.call(this, trackMeta.label, trackMeta.key,
false, browserParams.changeCallback);
this.browserParams = browserParams;
this.refSeq = refSeq;
this.trackMeta = trackMeta;
this.setLoaded();
this.chunks = [];
this.chunkSize = trackMeta.args.chunkSize;
this.baseUrl = (browserParams.baseUrl ? browserParams.baseUrl : "") + url;
this.hilightLoc = {refName: null, startBase:-1, endBase:-1};
}

SequenceTrack.prototype = new Track("");
Expand Down Expand Up @@ -57,13 +59,38 @@ SequenceTrack.prototype.fillBlock = function(blockIndex, block,
leftBase, rightBase,
scale, stripeWidth,
containerStart, containerEnd) {
var compl_rx = /[ACGT]/g;
var compl_tbl = {'A':'G', 'C':'T', 'G':'A', 'T':'C'};
var compl_fn = function(m) { return compl_tbl[m] || m; }
var hloc = this.hilightLoc;
var rseq = this.refSeq;
function hilighted_seq(start, end, seq) {
// start, end coords are interbase (half-open intervals)
if(hloc.refName == rseq.name & hloc.startBase < end & hloc.endBase > start) {
var hseq_start = Math.max(0, hloc.startBase - start);
var hseq_end = Math.min(seq.length, hloc.endBase - start);
var spanOuter = document.createElement("span");
var spanInner = document.createElement("span");
spanInner.style.cssText = "background: #ff0;";
spanOuter.appendChild(document.createTextNode(seq.substring(0, hseq_start)));
spanInner.appendChild(document.createTextNode(seq.substring(hseq_start, hseq_end)));
spanOuter.appendChild(spanInner);
spanOuter.appendChild(document.createTextNode(seq.substring(hseq_end, seq.length)));
return spanOuter;
} else {
return document.createTextNode(seq);
}
}
if (this.shown) {
this.getRange(leftBase, rightBase,
function(start, end, seq) {
//console.log("adding seq from %d to %d: %s", start, end, seq);
var seqNode = document.createElement("div");
seqNode.className = "sequence";
seqNode.appendChild(document.createTextNode(seq));
seqNode.appendChild(hilighted_seq(start, end, seq));
// IWD: add complement!
seqNode.appendChild(document.createElement("br"));
seqNode.appendChild(hilighted_seq(start, end, seq.replace(compl_rx, compl_fn)));
seqNode.style.cssText = "top: 0px;";
block.appendChild(seqNode);
});
Expand Down

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