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Merge pull request #960 from UC-Davis-molecular-computing/959-display…
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…-dna-sequence-on-extension-in-order-5-to-3

fixes #959: display DNA sequence on extension in order 5' to 3'
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@dave-doty
dave-doty authored Dec 22, 2023
2 parents 5d4cc56 + 35f4e9f commit 3e68f72
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Showing 2 changed files with 38 additions and 12 deletions.
44 changes: 32 additions & 12 deletions lib/src/view/design_main_strand_extension.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -89,21 +89,35 @@ class DesignMainExtensionComponent extends UiComponent2<DesignMainExtensionProps

// To ensure that the extension name displays right-side up, we always draw from the
// left point to the right point, regardless of which is the free end and which is attached.
var left_svg = extension_free_end_svg;
var right_svg = extension_attached_end_svg;
if (left_svg.x > right_svg.x) {
var swap = left_svg;
left_svg = right_svg;
right_svg = swap;
//NOTE: this causes the DNA to appear backwards in cases when the 3' end appears to the left
// of the 5' end. For now we will ditch this and draw the extension path from 5' to 3'
// (see svg_5p and svg_3p below), and figure out later how to display the name properly.
// Leaving this code here to help with that later.
// var left_svg = extension_free_end_svg;
// var right_svg = extension_attached_end_svg;
// if (left_svg.x > right_svg.x) {
// var swap = left_svg;
// left_svg = right_svg;
// right_svg = swap;
// }

var svg_5p = extension_free_end_svg;
var svg_3p = extension_attached_end_svg;
if (!ext.is_5p) {
var swap = svg_5p;
svg_5p = svg_3p;
svg_3p = swap;
}

var color = ext.color ?? props.strand_color;

// This is just a straight line, but for some reason, for displaying the extension name,
// it only works to attach a textPath to it if it is a path, not a line.
// So we use Dom.path() instead of Dom.line()
var path_d = 'M ${left_svg.x} ${left_svg.y} '
'L ${right_svg.x} ${right_svg.y}';
// var path_d = 'M ${left_svg.x} ${left_svg.y} '
// 'L ${right_svg.x} ${right_svg.y}';
var path_d = 'M ${svg_5p.x} ${svg_5p.y} '
'L ${svg_3p.x} ${svg_3p.y}';
return (Dom.path()
..className = classname
..onPointerDown = handle_click_down
Expand Down Expand Up @@ -241,10 +255,16 @@ class DesignMainExtensionComponent extends UiComponent2<DesignMainExtensionProps
if (results == null) return;

String name = (results[name_idx] as DialogText).value;
app.dispatch(actions.BatchAction(
app.state.ui_state.selectables_store.selected_extensions
.map((e) => actions.SubstrandNameSet(name: name, substrand: e)),
"set extension names"));
var selected_exts = app.state.ui_state.selectables_store.selected_extensions;
var action;
if (selected_exts.length > 1) {
action = actions.BatchAction(
selected_exts.map((e) => actions.SubstrandNameSet(name: name, substrand: e)),
"set extension names");
} else {
action = actions.SubstrandNameSet(name: name, substrand: props.ext);
}
app.dispatch(action);
}

extension_display_length_and_angle_change() =>
Expand Down
6 changes: 6 additions & 0 deletions lib/src/view/design_main_strand_paths.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,7 @@ class DesignMainStrandPathsComponent extends UiComponent2<DesignMainStrandPathsP
..helices = {helix.idx: helix}.build()
..groups = {helix.group: props.groups[helix.group]}.build()
..geometry = props.geometry
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
..strand_tooltip = props.strand_tooltip
..helix_svg_position = props.helix_idx_to_svg_position_map[helix.idx]
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
Expand All @@ -139,6 +140,7 @@ class DesignMainStrandPathsComponent extends UiComponent2<DesignMainStrandPathsP
..is_scaffold = props.strand.is_scaffold
..selected = end_selected
..strand = strand
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
..context_menu_strand = props.context_menu_strand
..moving_this_dna_end = props.moving_dna_ends && end_selected
..drawing_potential_crossover = props.drawing_potential_crossover
Expand Down Expand Up @@ -171,6 +173,7 @@ class DesignMainStrandPathsComponent extends UiComponent2<DesignMainStrandPathsP
..next_domain = next_dom
..prev_helix = prev_helix
..next_helix = next_helix
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
..prev_helix_svg_position_y = props.helix_idx_to_svg_position_map[prev_helix.idx].y
..next_helix_svg_position_y = props.helix_idx_to_svg_position_map[next_helix.idx].y
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
Expand All @@ -194,6 +197,7 @@ class DesignMainStrandPathsComponent extends UiComponent2<DesignMainStrandPathsP
..strand_color = strand.color
..transform = transform_of_helix(adj_helix.idx)
..selected = props.selected_extensions_in_strand.contains(ext)
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
..adjacent_domain = adj_dom
..adjacent_helix = adj_helix
..strand_tooltip = props.strand_tooltip
Expand All @@ -216,6 +220,7 @@ class DesignMainStrandPathsComponent extends UiComponent2<DesignMainStrandPathsP
..is_scaffold = props.strand.is_scaffold
..selected = end_selected
..strand = strand
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
..context_menu_strand = props.context_menu_strand
..moving_this_dna_end = props.moving_dna_ends && end_selected
..drawing_potential_crossover = props.drawing_potential_crossover
Expand Down Expand Up @@ -246,6 +251,7 @@ class DesignMainStrandPathsComponent extends UiComponent2<DesignMainStrandPathsP
..prev_domain = prev_ss
..next_domain = next_ss
..geometry = props.geometry
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
..prev_domain_helix_svg_position_y = props.helix_idx_to_svg_position_map[prev_ss.helix].y
..next_domain_helix_svg_position_y = props.helix_idx_to_svg_position_map[next_ss.helix].y
..retain_strand_color_on_selection = props.retain_strand_color_on_selection
Expand Down

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