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James Taylor
2011-03-31 14:08:00 -04:00
parent 955acd87e1 2a96970ef3
commit 8b9c1c4627
2 changed files with 23 additions and 21 deletions
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lib/galaxy/web/api/workflows.py
+1 -1
View File
@@ -57,7 +57,7 @@ class WorkflowsAPIController(BaseController):
inputs = {}
for step in latest_workflow.steps:
if step.type == 'data_input':
inputs[step.id] = {'label':"Input Dataset", 'value':""}
inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
else:
pass
# Eventually, allow regular tool parameters to be inserted and modified at runtime.
static/scripts/trackster.js
+22 -20
View File
@@ -2298,7 +2298,8 @@ $.extend(FeatureTrack.prototype, TiledTrack.prototype, {
// Create painter, and canvas of sufficient size to contain all features
// HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument
var painter = new (this.painter)( filtered, tile_low, tile_high, this.prefs, mode, ref_seq );
var required_height = painter.get_required_height( slots_required );
// FIXME: ERROR_PADDING is an ugly gap most of the time
var required_height = painter.get_required_height( slots_required ) + ERROR_PADDING;
var canvas = this.view.canvas_manager.new_canvas();
canvas.width = width + left_offset;
@@ -2336,7 +2337,7 @@ $.extend(FeatureTrack.prototype, TiledTrack.prototype, {
this.example_feature = (result.data.length ? result.data[0] : undefined);
// Draw features
ctx.translate( left_offset, 0 );
ctx.translate( left_offset, ERROR_PADDING );
painter.draw( ctx, width, required_height, slots );
return canvas;
@@ -2772,7 +2773,8 @@ extend( FeaturePainter.prototype, {
// Calculate new slots incrementally for this new chunk of data and update height if necessary.
required_height = rows_required * y_scale;
}
return required_height;
// Pad bottom by half a row
return required_height + Math.round( y_scale / 2 );
},
draw: function( ctx, width, height, slots ) {
@@ -2846,11 +2848,11 @@ extend( LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
feature_name = feature[3],
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
y_center = ERROR_PADDING + (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
thickness, y_start, thick_start = null, thick_end = null,
block_color = this.prefs.block_color,
label_color = this.prefs.label_color;
// Dense mode displays the same for all data.
if (mode === "Dense") {
ctx.fillStyle = block_color;
@@ -2989,7 +2991,7 @@ extend( VariantPainter.prototype, FeaturePainter.prototype, {
// All features need a start, end, and vertical center.
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
y_center = ERROR_PADDING + (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
thickness, y_start, thick_start = null, thick_end = null;
if (no_label) {
@@ -3052,7 +3054,7 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
}
else { // mode === "Pack"
y_scale = PACK_TRACK_HEIGHT;
if (this.track_config.values.show_insertions) {
if (this.prefs.show_insertions) {
y_scale *= 2;
}
}
@@ -3109,12 +3111,12 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
var seq = orig_seq.slice(seq_offset, seq_offset + cig_len);
if (gap > 0) {
ctx.fillStyle = this.prefs.block_color;
ctx.fillRect(s_start + this.left_offset - gap, y_center + 1, s_end - s_start, 9);
ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9);
ctx.fillStyle = CONNECTOR_COLOR;
// 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.track_config.values.show_differences && ref_seq) {
if (this.prefs.show_differences && ref_seq) {
var ref_char = ref_seq[seq_start - tile_low + c];
if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) {
continue;
@@ -3122,13 +3124,13 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
}
if (seq_start + c >= tile_low && seq_start + c <= tile_high) {
var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) );
ctx.fillText(seq[c], c_start + this.left_offset, y_center + 9);
ctx.fillText(seq[c], c_start, y_center + 9);
}
}
} else {
ctx.fillStyle = this.prefs.block_color;
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
ctx.fillRect(s_start + this.left_offset,
ctx.fillRect(s_start,
y_center + (this.mode !== "Dense" ? 4 : 5),
s_end - s_start,
(mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT) );
@@ -3139,14 +3141,14 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
break;
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
ctx.fillRect(s_start + this.left_offset - gap, y_center + 5, s_end - s_start, 1);
ctx.fillRect(s_start - gap, 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);
// No change in seq_offset because sequence not used when skipping.
base_offset += cig_len;
break;
case "D": // Deletion.
ctx.fillStyle = "red";
ctx.fillRect(s_start + this.left_offset - gap, y_center + 4, s_end - s_start, 3);
ctx.fillRect(s_start - gap, y_center + 4, s_end - s_start, 3);
// TODO: is this true? No change in seq_offset because sequence not used when skipping.
base_offset += cig_len;
break;
@@ -3158,20 +3160,20 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
// the sequence region and the tile region.
var
seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region),
insert_x_coord = this.left_offset + s_start - gap;
insert_x_coord = s_start - gap;
if (seq_tile_overlap !== NO_OVERLAP) {
var seq = orig_seq.slice(seq_offset, seq_offset + cig_len);
// Insertion point is between the sequence start and the previous base: (-gap) moves
// back from sequence start to insertion point.
if (this.track_config.values.show_insertions) {
if (this.prefs.show_insertions) {
//
// Show inserted sequence above, centered on insertion point.
//
// Draw sequence.
// X center is offset + start - <half_sequence_length>
var x_center = this.left_offset + s_start - (s_end - s_start)/2;
var x_center = s_start - (s_end - s_start)/2;
if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) {
// Draw sequence container.
ctx.fillStyle = "yellow";
@@ -3196,7 +3198,7 @@ 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 + this.left_offset - (s_end - s_start)/2, y_center);
ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_center);
}
}
else {
@@ -3288,7 +3290,7 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
// Draw connector.
if (b2_start > b1_end) {
ctx.fillStyle = CONNECTOR_COLOR;
ctx.dashedLine(b1_end + left_offset - gap, y_center + 5, left_offset + b2_start - gap, y_center + 5);
ctx.dashedLine(b1_end - gap, y_center + 5, b2_start - gap, y_center + 5);
}
} else {
// Read is single.
@@ -3302,10 +3304,10 @@ extend( ReadPainter.prototype, FeaturePainter.prototype, {
var tile_index = 1;
if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING - gap, y_center + 8);
ctx.fillText(feature_name, f_end + LABEL_SPACING - gap, y_center + 8);
} else {
ctx.textAlign = "right";
ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING - gap, y_center + 8);
ctx.fillText(feature_name, f_start - LABEL_SPACING - gap, y_center + 8);
}
ctx.fillStyle = block_color;
}