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Trackster painters: rename y_center variable to y_start to reflect real position.

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This commit is contained in:
Jeremy Goecks
2013-11-18 14:18:10 -05:00
parent e5621a9485
commit d3041bd82e
1 changed files with 51 additions and 51 deletions
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static/scripts/viz/trackster/painters.js
+51 -51
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@@ -466,7 +466,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ),
draw_start = f_start,
draw_end = f_end,
y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width),
y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width),
thickness, y_start, thick_start = null, thick_end = null,
// TODO: is there any reason why block, label color cannot be set at the Painter level?
// For now, assume '.' === '+'
@@ -484,7 +484,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
if (mode === "no_detail") {
// No details for feature, so only one way to display.
ctx.fillStyle = block_color;
ctx.fillRect(f_start, y_center + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT);
ctx.fillRect(f_start, y_start + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT);
}
else { // Mode is either Squish or Pack:
// Feature details.
@@ -517,7 +517,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
if (!feature_blocks) {
// If there are no blocks, treat the feature as one big exon.
ctx.fillStyle = block_color;
ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
ctx.fillRect(f_start, y_start + 1, f_end - f_start, thick_height);
// If strand is specified, draw arrows over feature
if ( feature_strand && full_height ) {
if (feature_strand === "+") {
@@ -525,7 +525,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
} else if (feature_strand === "-") {
ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' );
}
ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
ctx.fillRect(f_start, y_start + 1, f_end - f_start, thick_height);
}
} else {
//
@@ -536,19 +536,19 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// a block, is visible.
//
// Compute y axis center position and height
var cur_y_center, cur_height;
// Compute y axis start position and height
var cur_y_start, cur_height;
if (mode === "Squish" || mode === "Dense") {
cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1;
cur_y_start = y_start + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1;
cur_height = 1;
}
else { // mode === "Pack"
if (feature_strand) {
cur_y_center = y_center;
cur_y_start = y_start;
cur_height = thick_height;
}
else {
cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1;
cur_y_start += (SQUISH_FEATURE_HEIGHT/2) + 1;
cur_height = 1;
}
}
@@ -570,7 +570,7 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
ctx.fillStyle = CONNECTOR_COLOR;
}
}
ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height);
ctx.fillRect(f_start, cur_y_start, f_end - f_start, cur_height);
}
// Draw blocks.
@@ -587,14 +587,14 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// Draw thin block.
ctx.fillStyle = block_color;
ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height);
ctx.fillRect(block_start, y_start + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height);
// If block intersects with thick region, draw block as thick.
// - No thick is sometimes encoded as thick_start == thick_end, so don't draw in that case
if (thick_start !== undefined && feature_te > feature_ts && !(block_start > thick_end || block_end < thick_start) ) {
var block_thick_start = Math.max(block_start, thick_start),
block_thick_end = Math.min(block_end, thick_end);
ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height);
ctx.fillRect(block_thick_start, y_start + 1, block_thick_end - block_thick_start, thick_height);
if ( feature_blocks.length === 1 && mode === "Pack") {
// Exactly one block means we have no introns, but do have a distinct "thick" region,
// draw arrows over it if in pack mode.
@@ -608,12 +608,12 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
block_thick_start += 2;
block_thick_end -= 2;
}
ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height);
ctx.fillRect(block_thick_start, y_start + 1, block_thick_end - block_thick_start, thick_height);
}
}
// Draw individual connectors if required
if ( this.draw_individual_connectors && last_block_start ) {
this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_center );
this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_start );
}
last_block_start = block_start;
last_block_end = block_end;
@@ -632,8 +632,8 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
new_height = Math.ceil(thick_height * hscale_factor),
ws_height = Math.round( (thick_height-new_height)/2 );
if (hscale_factor !== 1) {
ctx.fillRect(f_start, cur_y_center + 1, f_end - f_start, ws_height);
ctx.fillRect(f_start, cur_y_center + thick_height - ws_height + 1, f_end - f_start, ws_height);
ctx.fillRect(f_start, cur_y_start + 1, f_end - f_start, ws_height);
ctx.fillRect(f_start, cur_y_start + thick_height - ws_height + 1, f_end - f_start, ws_height);
}
}
}
@@ -647,11 +647,11 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// FIXME: assumption here that the entire view starts at 0
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8);
ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8);
draw_end += ctx.measureText(feature_name).width + LABEL_SPACING;
} else {
ctx.textAlign = "right";
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8);
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8);
draw_start -= ctx.measureText(feature_name).width + LABEL_SPACING;
}
//ctx.fillStyle = block_color;
@@ -741,7 +741,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
/**
* Draw a single read.
*/
draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
ctx.textAlign = "center";
var tile_region = [tile_low, tile_high],
base_offset = 0,
@@ -793,7 +793,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw read base as rectangle.
ctx.fillStyle = block_color;
ctx.fillRect(s_start,
y_center + (pack_mode ? 1 : 4 ),
y_start + (pack_mode ? 1 : 4 ),
s_end - s_start,
(pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
@@ -824,12 +824,12 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) );
ctx.fillStyle = this.base_color_fn(seq[c]);
if (pack_mode && w_scale > char_width_px) {
ctx.fillText(seq[c], c_start, y_center + 9);
ctx.fillText(seq[c], c_start, y_start + 9);
}
// Require a minimum w_scale so that variants are only drawn when somewhat zoomed in.
else if (w_scale > 0.05) {
ctx.fillRect(c_start - gap,
y_center + (pack_mode ? 1 : 4),
y_start + (pack_mode ? 1 : 4),
Math.max( 1, Math.round(w_scale) ),
(pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
}
@@ -843,12 +843,12 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
ctx.fillRect(s_start, y_center + 5, s_end - s_start, 1);
//ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5);
ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1);
//ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5);
base_offset += cig_len;
break;
case "D": // Deletion.
paint_utils.draw_deletion(s_start, y_center, 1);
paint_utils.draw_deletion(s_start, y_start, 1);
base_offset += cig_len;
break;
case "P": // TODO: No good way to draw insertions/padding right now, so ignore
@@ -874,8 +874,8 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) {
// Draw sequence container.
ctx.fillStyle = "yellow";
ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9);
draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]};
ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9);
draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_start + 4, 5]};
ctx.fillStyle = CONNECTOR_COLOR;
// Based on overlap b/t sequence and tile, get sequence to be drawn.
switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) {
@@ -895,21 +895,21 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw sequence.
for (var c = 0, str_len = seq.length; c < str_len; c++) {
var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) );
ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_center);
ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_start);
}
}
else {
// Draw block.
ctx.fillStyle = "yellow";
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
ctx.fillRect(x_center, y_center + (this.mode !== "Dense" ? 2 : 5),
ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT));
}
}
else {
if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) {
// Show insertions with a single number at the insertion point.
draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } );
draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_start + 9] } );
}
else {
// TODO: probably can merge this case with code above.
@@ -955,7 +955,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// -0.5 to put element between bases.
f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ),
y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
label_color = this.prefs.label_color;
@@ -966,7 +966,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw left/forward read.
if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
}
else {
connector = false;
@@ -974,7 +974,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw right/reverse read.
if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) {
this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
}
else {
connector = false;
@@ -989,21 +989,21 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) );
if (connector && b2_start > b1_end) {
ctx.fillStyle = CONNECTOR_COLOR;
dashedLine(ctx, b1_end, y_center + 5, b2_start, y_center + 5);
dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5);
}
} else {
// Read is single.
this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]);
this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]);
}
if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") {
// Draw label.
ctx.fillStyle = this.prefs.label_color;
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8);
ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8);
} else {
ctx.textAlign = "right";
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8);
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8);
}
}
@@ -1024,7 +1024,7 @@ extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
/**
* Draw a single read from reference-based read sequence and cigar.
*/
draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
ctx.textAlign = "center";
var tile_region = [tile_low, tile_high],
base_offset = 0,
@@ -1063,7 +1063,7 @@ extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
// Draw read base as rectangle.
ctx.fillStyle = block_color;
ctx.fillRect(s_start,
y_center + (pack_mode ? 1 : 4 ),
y_start + (pack_mode ? 1 : 4 ),
s_end - s_start,
(pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
}
@@ -1130,12 +1130,12 @@ extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
var c_start = Math.floor( Math.max(0, (start_pos + c - tile_low) * w_scale) );
ctx.fillStyle = this.base_color_fn(cur_seq[c]);
if (pack_mode && w_scale > char_width_px) {
ctx.fillText(cur_seq[c], c_start, y_center + 9);
ctx.fillText(cur_seq[c], c_start, y_start + 9);
}
// Require a minimum w_scale so that variants are only drawn when somewhat zoomed in.
else if (w_scale > 0.05) {
ctx.fillRect(c_start - gap,
y_center + (pack_mode ? 1 : 4),
y_start + (pack_mode ? 1 : 4),
Math.max( 1, Math.round(w_scale) ),
(pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
}
@@ -1150,14 +1150,14 @@ extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
ctx.fillRect(s_start, y_center + 5, s_end - s_start, 1);
//ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5);
ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1);
//ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5);
// No change in seq_offset because sequence not used when skipping.
base_offset += cig_len;
break;
case "D": // Deletion.
ctx.fillStyle = "black";
ctx.fillRect(s_start, y_center + 4, s_end - s_start, 3);
ctx.fillRect(s_start, y_start + 4, s_end - s_start, 3);
base_offset += cig_len;
break;
case "I": // Insertion.
@@ -1180,8 +1180,8 @@ extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) {
// Draw sequence container.
ctx.fillStyle = "yellow";
ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9);
draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]};
ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9);
draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_start + 4, 5]};
ctx.fillStyle = CONNECTOR_COLOR;
// Based on overlap b/t sequence and tile, get sequence to be drawn.
switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) {
@@ -1201,21 +1201,21 @@ extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
// Draw sequence.
for (var c = 0, str_len = seq.length; c < str_len; c++) {
var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) );
ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_center);
ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_start);
}
}
else {
// Draw block.
ctx.fillStyle = "yellow";
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
ctx.fillRect(x_center, y_center + (this.mode !== "Dense" ? 2 : 5),
ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT));
}
}
else {
if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) {
// Show insertions with a single number at the insertion point.
draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } );
draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_start + 9] } );
}
else {
// TODO: probably can merge this case with code above.
@@ -1275,7 +1275,7 @@ extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeatur
return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) );
},
draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_center ) {
draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_start ) {
// Arc drawing -- from closest endpoints
var x_center = ( block1_end + block2_start ) / 2,
radius = block2_start - x_center;
@@ -1283,7 +1283,7 @@ extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeatur
var angle1 = Math.PI, angle2 = 0;
if ( radius > 0 ) {
ctx.beginPath();
ctx.arc( x_center, y_center, block2_start - x_center, Math.PI, 0 );
ctx.arc( x_center, y_start, block2_start - x_center, Math.PI, 0 );
ctx.stroke();
}
}