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moved add modification code from design_main_strand.dart to design_ma…
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…in_strand_modification.dart to keep similar code together
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@dave-doty
dave-doty committed Aug 26, 2023
1 parent 1117e88 commit ff1b027
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Showing 2 changed files with 288 additions and 286 deletions.
177 changes: 3 additions & 174 deletions lib/src/view/design_main_strand.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ import 'package:react/react.dart' as react;

import 'design_main_strand_and_domain_texts.dart';
import 'design_main_strand_dna_end.dart';
import 'design_main_strand_modification.dart';
import 'transform_by_helix_group.dart';
import '../state/idt_fields.dart';
import '../state/modification_type.dart';
Expand Down Expand Up @@ -264,7 +265,8 @@ class DesignMainStrandComponent extends UiComponent2<DesignMainStrandProps>
}

add_modification(Substrand substrand, Address address, ModificationType type) =>
app.disable_keyboard_shortcuts_while(() => ask_for_add_modification(substrand, address, type));
app.disable_keyboard_shortcuts_while(
() => ask_for_add_modification(props.strand, substrand, address, type));

assign_scale_purification_fields() =>
app.disable_keyboard_shortcuts_while(ask_for_assign_scale_purification_fields);
Expand Down Expand Up @@ -887,179 +889,6 @@ PAGEHPLC : Dual PAGE & HPLC
}
}

Future<void> ask_for_add_modification(Substrand substrand, Address address,
[ModificationType type = ModificationType.internal]) async {
/*
substrand - selected substrand (domain or extension)
address - address of DNA base (nullable if substrand is an extension)
type - type of modification: five_prime, three_prime, internal (default)
*/
if (address == null) {
assert(substrand is Extension);
}
int selected_index = 2;

if (type == ModificationType.five_prime) {
selected_index = 1;
} else if (type == ModificationType.three_prime) {
selected_index = 0;
}

// if they clicked on a domain, get the address; if an extension, just default to 0
int strand_dna_idx = address != null ? clicked_strand_dna_idx(substrand, address, props.strand) : 0;

int modification_type_idx = 0;
int display_text_idx = 1;
int idt_text_idx = 2;
int connector_length_idx = 3;
int index_of_dna_base_idx = 4;
int attached_to_base_idx = 5;
int allowed_bases_idx = 6;
var items = List<DialogItem>.filled(7, null);
items[modification_type_idx] = DialogRadio(
label: 'modification type', options: {"3'", "5'", "internal"}, selected_idx: selected_index);

String initial_display_text = "";
String initial_idt_text = "";
int initial_connector_length = constants.default_modification_connector_length;
// String initial_id = "";

// if there is a last mod of this type, it auto-populates the dialog inputs
Modification last_mod;
if (selected_index == 0) {
// 3' mod
last_mod = app.state.ui_state.last_mod_3p;
} else if (selected_index == 1) {
// 5' mod
last_mod = app.state.ui_state.last_mod_5p;
} else if (selected_index == 2) {
// internal mod
last_mod = app.state.ui_state.last_mod_int;
} else {
throw AssertionError('should be unreachable');
}
if (last_mod != null) {
initial_display_text = last_mod.display_text;
initial_idt_text = last_mod.idt_text;
initial_connector_length = last_mod.connector_length;
// initial_id = last_mod.id;
}

items[display_text_idx] = DialogText(label: 'display text', value: initial_display_text);
items[idt_text_idx] = DialogText(label: 'idt text', value: initial_idt_text);
items[connector_length_idx] = DialogInteger(label: 'connector length', value: initial_connector_length);
// items[id_idx] = DialogText(label: 'id', value: initial_id);

items[index_of_dna_base_idx] = DialogInteger(label: 'index of DNA base', value: strand_dna_idx);

items[attached_to_base_idx] =
DialogCheckbox(label: 'attached to base?', value: true, tooltip: tooltip_attached_to_base_checkbox);

items[allowed_bases_idx] =
DialogText(label: 'allowed bases', value: 'ACGT', tooltip: tooltip_allowed_bases_textfield);

// don't allow to modify index of DNA base when 3' or 5' is selected
var dialog = Dialog(
title: 'add modification',
type: DialogType.add_modification,
items: items,
// so that where they click influences which type of modification (5'/3'/internal) is automatically
// selected for them instead of being whatever the previous dialog used
use_saved_response: false,
disable_when_any_radio_button_selected: {
index_of_dna_base_idx: {
modification_type_idx: ["3'", "5'"]
},
attached_to_base_idx: {
modification_type_idx: ["3'", "5'"]
},
allowed_bases_idx: {
modification_type_idx: ["3'", "5'"]
},
},
disable_when_any_checkboxes_off: {
allowed_bases_idx: [attached_to_base_idx]
},
);

List<DialogItem> results = await util.dialog(dialog);
if (results == null) return;
String modification_type = (results[modification_type_idx] as DialogRadio).value;
String display_text = (results[display_text_idx] as DialogText).value;
// String id = (results[id_idx] as DialogText).value;
String idt_text = (results[idt_text_idx] as DialogText).value;
int connector_length = (results[connector_length_idx] as DialogInteger).value;
int index_of_dna_base = (results[index_of_dna_base_idx] as DialogInteger).value;
bool attached_to_base = (results[attached_to_base_idx] as DialogCheckbox).value;
String allowed_bases_str = (results[allowed_bases_idx] as DialogText).value;

Modification mod;
if (modification_type == "3'") {
mod = Modification3Prime(
//id: id,
display_text: display_text,
idt_text: idt_text,
connector_length: connector_length,
);
} else if (modification_type == "5'") {
mod = Modification5Prime(
//id: id,
display_text: display_text,
idt_text: idt_text,
connector_length: connector_length,
);
} else {
var allowed_bases = null;
if (attached_to_base) {
allowed_bases_str = allowed_bases_str.replaceAll(RegExp(r'[^(A|C|G|T|a|c|g|t)]'), '');
allowed_bases =
{for (int i = 0; i < allowed_bases_str.length; i++) allowed_bases_str[i].toUpperCase()}.build();
}
mod = ModificationInternal(
// id: id,
display_text: display_text,
idt_text: idt_text,
connector_length: connector_length,
allowed_bases: allowed_bases,
);
}

// if modification type is 5' or 3' and many such ends are selected, add modifications to all of them
actions.UndoableAction action;
if (mod is ModificationInternal) {
action =
actions.ModificationAdd(strand: props.strand, modification: mod, strand_dna_idx: index_of_dna_base);
} else {
List<DNAEnd> ends_selected = app.state.ui_state.selectables_store.selected_dna_ends.toList();

if (mod is Modification5Prime && !ends_selected.contains(props.strand.dnaend_5p)) {
ends_selected.add(props.strand.dnaend_5p);
} else if (mod is Modification3Prime && !ends_selected.contains(props.strand.dnaend_3p)) {
ends_selected.add(props.strand.dnaend_3p);
}

if (ends_selected.length == 1) {
action = actions.ModificationAdd(
strand: props.strand, modification: mod, strand_dna_idx: index_of_dna_base);
} else if (ends_selected.length > 1) {
// safe to batch this action since it's only for 5' or 3', so each strand will only be modified once
List<actions.ModificationAdd> all_actions = [];
for (var end_selected in ends_selected) {
var strand_of_end_selected = app.state.design.end_to_strand(end_selected);
var new_action = actions.ModificationAdd(
strand: strand_of_end_selected, modification: mod, strand_dna_idx: null);
all_actions.add(new_action);
}
action = actions.BatchAction(all_actions, "add modifications");
} else {
print('WARNING: selectable_mods should have at least one element in it by this line');
return;
}
}

app.dispatch(action);
}

Future<void> ask_for_strand_name() async {
int name_idx = 0;
var items = List<DialogItem>.filled(1, null);
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