"""
Parts Workshop — mRNA assembly from parts library.
Users select multiple parts from each category (5'UTR, Kozak, CDS, 3'UTR, PolyA)
and generate all combinatorial assemblies. Make mode only.
"""
from __future__ import annotations
import itertools
import logging
from typing import TYPE_CHECKING, Dict, List, Optional
import panel as pn
import param
from core.models.sequence import mRNASequence
if TYPE_CHECKING:
from ui.state import AppState
from core.models.parts import SequencePart
logger = logging.getLogger(__name__)
class PlasmidView(param.Parameterized):
"""Parts Workshop panel for mRNA assembly."""
def __init__(self, state: "AppState", **params: object) -> None:
super().__init__(**params)
self._state = state
# Selected parts
self._selected_5utr: Optional[SequencePart] = None
self._selected_kozak: Optional[SequencePart] = None
self._selected_cds: Optional[SequencePart] = None
self._selected_3utr: Optional[SequencePart] = None
self._selected_polya: Optional[SequencePart] = None
# UI widgets
self._utr5_select: Optional[pn.widgets.Select] = None
self._kozak_select: Optional[pn.widgets.Select] = None
self._cds_select: Optional[pn.widgets.Select] = None
self._utr3_select: Optional[pn.widgets.Select] = None
self._polya_select: Optional[pn.widgets.Select] = None
self._result_pane = pn.pane.HTML("")
self._sequence_name = pn.widgets.TextInput(
name="Sequence Name",
placeholder="e.g., custom_mrna_001",
value="",
width=300,
)
def _build_part_selector(
self, part_type: str, label: str, color: str
) -> pn.Column:
"""Build a multi-select widget for a specific part type."""
parts = self._state.parts_by_type(part_type)
if not parts:
options_list = []
disabled = True
else:
options_list = parts
disabled = False
selector = pn.widgets.MultiSelect(
name=label,
options={p.name: p for p in options_list},
value=[],
size=5,
width=300,
disabled=disabled,
)
# Store reference
if part_type == "5_utr":
self._utr5_select = selector
elif part_type == "kozak":
self._kozak_select = selector
elif part_type == "cds":
self._cds_select = selector
elif part_type == "3_utr":
self._utr3_select = selector
elif part_type == "polya":
self._polya_select = selector
# Info display
@param.depends(selector.param.value)
def part_info(selected_parts):
if not selected_parts:
return pn.pane.HTML(
f''\
f'No parts selected
'
)
return pn.pane.HTML(
f''\
f'{len(selected_parts)} part(s) selected
'
)
return pn.Column(
pn.pane.HTML(
f'{label} (multi-select)
'
),
selector,
pn.panel(part_info),
sizing_mode="stretch_width",
styles={"background": "#F8FAFC", "padding": "12px", "border-radius": "6px"},
)
@param.depends("_state.parts_library")
def panel(self) -> pn.Column:
"""Main panel layout."""
# Header
header = pn.pane.HTML(
''\
'Parts Workshop
'\
''\
f'Select parts from the library ({len(self._state.parts_library)} parts available) '\
'to assemble a new mRNA sequence.
'
)
# Part selectors in a grid
selectors = pn.GridBox(
self._build_part_selector("5_utr", "5' UTR", "#0284C7"),
self._build_part_selector("kozak", "Kozak", "#D97706"),
self._build_part_selector("cds", "CDS", "#059669"),
self._build_part_selector("3_utr", "3' UTR", "#7C3AED"),
self._build_part_selector("polya", "Poly-A", "#DC2626"),
ncols=3,
sizing_mode="stretch_width",
)
# Assembly controls
assemble_btn = pn.widgets.Button(
name="Preview Combinations",
button_type="primary",
width=180,
margin=(12, 4),
)
assemble_btn.on_click(self._on_assemble)
self._combo_count_pane = pn.pane.HTML("", margin=(12, 4))
controls = pn.Row(
self._combo_count_pane,
pn.layout.HSpacer(),
assemble_btn,
sizing_mode="stretch_width",
)
# Add to worklist section (shown after preview)
self._worklist_name_input = pn.widgets.TextInput(
name="Worklist Name",
placeholder="e.g. Combinatorial Batch 1",
width=250,
)
add_to_worklist_btn = pn.widgets.Button(
name="＋ Generate & Add to Worklist",
button_type="success",
width=240,
margin=(20, 4, 4, 4),
)
self._add_to_worklist_btn = add_to_worklist_btn
add_to_worklist_btn.on_click(self._on_add_to_worklist)
self._add_to_wl_section = pn.Column(
pn.pane.HTML(
''
'Save to Worklist
'
''
'Create a new worklist from the generated combinations.
'
),
pn.Row(self._worklist_name_input, add_to_worklist_btn),
sizing_mode="stretch_width",
styles={"background": "#F8FAFC", "padding": "12px", "border-radius": "6px",
"border": "1px solid #E2E8F0", "margin-top": "8px"},
visible=False,
)
# Result display
result_section = pn.Column(
pn.layout.Divider(),
self._result_pane,
self._add_to_wl_section,
sizing_mode="stretch_width",
)
return pn.Column(
header,
selectors,
controls,
result_section,
sizing_mode="stretch_width",
styles={"padding": "8px 16px"},
)
def _on_assemble(self, event: object) -> None:
"""Preview combinatorial assemblies."""
logger.info("Preview combinations button clicked")
# Collect selected parts for each category
part_groups = []
part_labels = []
if self._utr5_select and self._utr5_select.value:
part_groups.append([("5' UTR", p) for p in self._utr5_select.value])
part_labels.append("5'UTR")
if self._kozak_select and self._kozak_select.value:
part_groups.append([("Kozak", p) for p in self._kozak_select.value])
part_labels.append("Kozak")
if self._cds_select and self._cds_select.value:
part_groups.append([("CDS", p) for p in self._cds_select.value])
part_labels.append("CDS")
if self._utr3_select and self._utr3_select.value:
part_groups.append([("3' UTR", p) for p in self._utr3_select.value])
part_labels.append("3'UTR")
if self._polya_select and self._polya_select.value:
part_groups.append([("Poly-A", p) for p in self._polya_select.value])
part_labels.append("PolyA")
if not part_groups:
self._result_pane.object = (
''\
'Please select at least one part to assemble.
'
)
self._add_to_wl_section.visible = False
self._combo_count_pane.object = ""
return
# Calculate number of combinations
combo_count = 1
for group in part_groups:
combo_count *= len(group)
logger.info(f"Generating {combo_count} combinatorial assemblies")
# Show summary
selection_summary = " × ".join([
f"{len(group)} {part_labels[i]}"
for i, group in enumerate(part_groups)
])
# Show first few combinations as preview
combinations = list(itertools.product(*part_groups))[:5]
preview_html = ""
for i, combo in enumerate(combinations, 1):
combo_parts = [f"{label}: {part.name}" for label, part in combo]
preview_html += f''\
f'Example {i}: {" + ".join(combo_parts)}
'
if combo_count > 5:
preview_html += f''\
f'... and {combo_count - 5} more combinations
'
self._combo_count_pane.object = (
f''\
f'{combo_count} sequences will be generated
'\
f'({selection_summary})
'
)
self._result_pane.object = (
f''\
f'
'\
f'Combination Preview ({combo_count} sequences)
'\
f'
'\
f'{preview_html}'\
f'