opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Trackster: add generic functions to convert from chromosome position to drawing position. Use functions in variant painter.

Browse Source
This commit is contained in:
Jeremy Goecks
2014-10-24 15:43:34 -04:00
parent d1eabea652
commit bda44d0daf
3 changed files with 63 additions and 9 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/galaxy/scripts/viz/trackster/painters.js
+31 -4
View File
@@ -137,6 +137,35 @@ Painter.prototype.default_prefs = {};
*/
Painter.prototype.draw = function(ctx, width, height, w_scale) {};
/**
* Get starting drawing position, which is offset a half-base left of coordinate.
*/
Painter.prototype.get_start_draw_pos = function(chrom_pos, w_scale) {
return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, -0.5);
};
/**
* Get end drawing position, which is offset a half-base right of coordinate.
*/
Painter.prototype.get_end_draw_pos = function(chrom_pos, w_scale) {
return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0.5);
};
/**
* Get drawing position.
*/
Painter.prototype.get_draw_pos = function(chrom_pos, w_scale) {
return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0);
};
/**
* Convert chromosome position to drawing position.
*/
Painter.prototype._chrom_pos_to_draw_pos = function(chrom_pos, w_scale, offset) {
return Math.floor( w_scale * ( Math.max(0, chrom_pos - this.view_start) + offset) );
};
var LinePainter = function(data, view_start, view_end, prefs, mode) {
Painter.call( this, data, view_start, view_end, prefs, mode );
if ( this.prefs.min_value === undefined ) {
@@ -1447,7 +1476,6 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
allele_counts,
variant,
draw_x_start,
char_x_start,
draw_y_start,
genotype,
// Always draw variants at least 1 pixel wide.
@@ -1510,8 +1538,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
}
// Compute start for drawing variants marker, text.
draw_x_start = Math.floor( Math.max(-0.5 * w_scale, (pos - this.view_start - 0.5) * w_scale) );
char_x_start = Math.floor( Math.max(0, (pos - this.view_start) * w_scale) );
draw_x_start = this.get_start_draw_pos(pos, w_scale);
// Draw summary.
if (draw_summary) {
@@ -1563,7 +1590,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
var snp = variant.value;
ctx.fillStyle = this.base_color_fn(snp);
if (paint_utils.draw_details) {
ctx.fillText(snp, char_x_start, draw_y_start + row_height);
ctx.fillText(snp, this.get_draw_pos(pos, w_scale), draw_y_start + row_height);
}
else {
ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height);
static/scripts/packed/viz/trackster/painters.js
+1 -1
View File
File diff suppressed because one or more lines are too long
static/scripts/viz/trackster/painters.js
+31 -4
View File
@@ -137,6 +137,35 @@ Painter.prototype.default_prefs = {};
*/
Painter.prototype.draw = function(ctx, width, height, w_scale) {};
/**
* Get starting drawing position, which is offset a half-base left of coordinate.
*/
Painter.prototype.get_start_draw_pos = function(chrom_pos, w_scale) {
return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, -0.5);
};
/**
* Get end drawing position, which is offset a half-base right of coordinate.
*/
Painter.prototype.get_end_draw_pos = function(chrom_pos, w_scale) {
return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0.5);
};
/**
* Get drawing position.
*/
Painter.prototype.get_draw_pos = function(chrom_pos, w_scale) {
return this._chrom_pos_to_draw_pos(chrom_pos, w_scale, 0);
};
/**
* Convert chromosome position to drawing position.
*/
Painter.prototype._chrom_pos_to_draw_pos = function(chrom_pos, w_scale, offset) {
return Math.floor( w_scale * ( Math.max(0, chrom_pos - this.view_start) + offset) );
};
var LinePainter = function(data, view_start, view_end, prefs, mode) {
Painter.call( this, data, view_start, view_end, prefs, mode );
if ( this.prefs.min_value === undefined ) {
@@ -1447,7 +1476,6 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
allele_counts,
variant,
draw_x_start,
char_x_start,
draw_y_start,
genotype,
// Always draw variants at least 1 pixel wide.
@@ -1510,8 +1538,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
}
// Compute start for drawing variants marker, text.
draw_x_start = Math.floor( Math.max(-0.5 * w_scale, (pos - this.view_start - 0.5) * w_scale) );
char_x_start = Math.floor( Math.max(0, (pos - this.view_start) * w_scale) );
draw_x_start = this.get_start_draw_pos(pos, w_scale);
// Draw summary.
if (draw_summary) {
@@ -1563,7 +1590,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
var snp = variant.value;
ctx.fillStyle = this.base_color_fn(snp);
if (paint_utils.draw_details) {
ctx.fillText(snp, char_x_start, draw_y_start + row_height);
ctx.fillText(snp, this.get_draw_pos(pos, w_scale), draw_y_start + row_height);
}
else {
ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height);