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Better handling of reference data in Trackster read tracks.

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This commit is contained in:
Jeremy Goecks
2011-10-17 19:57:54 -04:00
parent 98da2311bb
commit 1e2ae076d6
1 changed files with 4 additions and 5 deletions
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static/scripts/trackster.js
+4 -5
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@@ -4375,7 +4375,7 @@ extend(VariantPainter.prototype, FeaturePainter.prototype, {
var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) {
FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
this.ref_seq = ref_seq;
this.ref_seq = (ref_seq ? ref_seq.data : null);
};
ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false });
@@ -4410,8 +4410,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
tile_region = [tile_low, tile_high],
base_offset = 0,
seq_offset = 0,
gap = 0
ref_seq = this.ref_seq.data,
gap = 0,
char_width_px = ctx.canvas.manager.char_width_px;
// Keep list of items that need to be drawn on top of initial drawing layer.
@@ -4465,8 +4464,8 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// TODO: this can be made much more efficient by computing the complete sequence
// to draw and then drawing it.
for (var c = 0, str_len = seq.length; c < str_len; c++) {
if (this.prefs.show_differences && ref_seq) {
var ref_char = ref_seq[seq_start - tile_low + c];
if (this.prefs.show_differences && this.ref_seq) {
var ref_char = this.ref_seq[seq_start - tile_low + c];
if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) {
continue;
}