def __lt__(self, other):
col = self.par.sortColumn()
if col in [TIMEPOINT_COLUMN, REPLICATE_COLUMN]:
left = tfloat(self.text(col))
right = tfloat(other.text(col))
if isinstance(left, float) and isinstance(right, float):
return left < right
return QTreeWidgetItem.__lt__(self, other)
def __lt__(self, other):
col = self.par.sortColumn()
if col in [TIMEPOINT_COLUMN, REPLICATE_COLUMN]:
left = tfloat(self.text(col))
right = tfloat(other.text(col))
if isinstance(left, float) and isinstance(right, float):
return left < right
return QTreeWidgetItem.__lt__(self, other)
def __add__(self, other):
if isinstance(other, QTreeWidgetItem):
self.invisibleRootItem().addChild(other)
elif isinstance(other, str):
item = QTreeWidgetItem(other)
self.invisibleRootItem().addChild(item)
elif isinstance(other, list):
for x in other:
if isinstance(x, str):
item = QTreeWidgetItem(x)
self.invisibleRootItem().addChild(item)
else:
self.invisibleRootItem().addChild(x)
else:
item = QTreeWidgetItem(other)
self.invisibleRootItem().addChild(item)
# self.setFirstColumnSpanned( self.model().rowCount() - 1, self.rootIndex(), True)
return self
def create_child(self, name, parent=None, icon=None):
"""
Create a new child for to the parent item.
If the parent is None it add to the root.
"""
item = QTreeWidgetItem(self, [name]) if (
parent is None) else QTreeWidgetItem(parent, [name])
if icon is not None:
if isinstance(icon, str):
item.setIcon(0, QIcon(icon))
elif isinstance(icon, QIcon):
item.setIcon(0, icon)
return item
def clone_item(self, parent, item, copy_function=None):
new_item = QTreeWidgetItem()
for col_index in range(item.columnCount()):
new_item.setText(col_index, item.text(col_index))
new_item.setIcon(col_index, item.icon(col_index))
if copy_function is not None: copy_function(item, new_item)
parent.addChild(new_item)
for child_index in range(item.childCount()):
child_item = item.child(child_index)
self.clone_item(new_item, child_item, copy_function)
def __init__(self, parent, *args):
QTreeWidgetItem.__init__(self, parent, *args)
self.par = parent
def __init__(self, item):
QTreeWidgetItem.__init__(self, type=QTreeWidgetItem.UserType)
self.item = None
self.setUpdateItem(item)
def fill(col, parent, full=(), org=""):
for key, value in sorted(col.items()):
full_cat = full + (key, )
item = QTreeWidgetItem(parent, [key])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable
| Qt.ItemIsSelectable | Qt.ItemIsEnabled)
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
checked = self.categoriesCheckState.get((full_cat, org),
Qt.Checked)
item.setData(0, Qt.CheckStateRole, checked)
item.setExpanded(True)
item.category = full_cat
item.organism = org
self.groupsWidgetItems[full_cat] = item
fill(value, item, full_cat, org=org)
def setAnnotations(self, gds):
self._annotationsUpdating = True
self.annotationsTree.clear()
annotations = defaultdict(set)
subsetscount = {}
for desc in gds["subsets"]:
annotations[desc["type"]].add(desc["description"])
subsetscount[desc["description"]] = str(len(desc["sample_id"]))
for type, subsets in annotations.items():
key = (gds["dataset_id"], type)
subsetItem = QTreeWidgetItem(self.annotationsTree, [type])
subsetItem.setFlags(subsetItem.flags() | Qt.ItemIsUserCheckable |
Qt.ItemIsTristate)
subsetItem.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked)
)
subsetItem.key = key
for subset in subsets:
key = (gds["dataset_id"], type, subset)
item = QTreeWidgetItem(
subsetItem, [subset, subsetscount.get(subset, "")]
)
item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
item.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked)
)
item.key = key
self._annotationsUpdating = False
self.annotationsTree.expandAll()
for i in range(self.annotationsTree.columnCount()):
self.annotationsTree.resizeColumnToContents(i)
def _set_annotations_widget(self, gds):
self._annotations_updating = True
self.annotations_widget.clear()
annotations = defaultdict(set)
subsets_count = {}
for desc in gds['subsets']:
annotations[desc['type']].add(desc['description'])
subsets_count[desc['description']] = str(len(desc['sample_id']))
for _type, subsets in annotations.items():
key = (gds["name"], _type)
parent = QTreeWidgetItem(self.annotations_widget, [_type])
parent.key = key
for subset in subsets:
key = (gds['name'], _type, subset)
item = QTreeWidgetItem(
parent, [subset, subsets_count.get(subset, '')])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
item.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked))
item.key = key
self._annotations_updating = False
self.annotations_widget.expandAll()
for i in range(self.annotations_widget.columnCount()):
self.annotations_widget.resizeColumnToContents(i)
def __lt__(self, o1):
col = self.par.sortColumn()
if col in [8, 9]: # WARNING: hardcoded column numbers
return tfloat(self.text(col)) < tfloat(o1.text(col))
else:
return QTreeWidgetItem.__lt__(self, o1)
def __init__(self, fs):
""" A QTreeWidgetItem for displaying a FileState.
"""
QTreeWidgetItem.__init__(self, type=QTreeWidgetItem.UserType)
self.update_data(fs)
self._update_tool_tip(fs)
def fill(col, parent, full=(), org=""):
for key, value in sorted(col.items()):
full_cat = full + (key,)
item = QTreeWidgetItem(parent, [key])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable |
Qt.ItemIsSelectable | Qt.ItemIsEnabled)
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
checked = self.categoriesCheckState.get(
(full_cat, org), Qt.Checked)
item.setData(0, Qt.CheckStateRole, checked)
item.setExpanded(True)
item.category = full_cat
item.organism = org
self.groupsWidgetItems[full_cat] = item
fill(value, item, full_cat, org=org)
def set_hierarchy_model(self, tree_widget, sets):
def beautify_displayed_text(text):
if '_' in text:
return text.replace('_', ' ').title()
else:
return text
# TODO: maybe optimize this code?
for key, value in sets.items():
item = QTreeWidgetItem(tree_widget, [beautify_displayed_text(key)])
item.setFlags(item.flags()
& (Qt.ItemIsUserCheckable | Qt.ItemIsSelectable
| Qt.ItemIsEnabled))
item.setExpanded(True)
item.hierarchy = key
if value:
item.setFlags(item.flags() | Qt.ItemIsTristate)
self.set_hierarchy_model(item, value)
else:
if item.parent():
item.hierarchy = (item.parent().hierarchy, key)
if not item.childCount() and not item.parent():
item.hierarchy = (key, )
def _walkCreate(koEntry, lvItem):
item = QTreeWidgetItem(lvItem)
id = "path:" + org_code + koEntry.title[:5]
if koEntry.title[:5] in path_ids:
p = kegg_pathways.get_entry(id)
if p is None:
# In case the genesets still have obsolete entries
name = koEntry.title
else:
name = p.name
genes, p_value, ref = self.pathways[id]
item.setText(0, name)
item.setText(1, "%.5f" % p_value)
item.setText(2, "%i of %i" % (len(genes), len(self.genes)))
item.setText(3, "%i of %i" % (ref, len(self.referenceGenes)))
item.pathway_id = id if p is not None else None
else:
if id in allPathways:
text = kegg_pathways.get_entry(id).name
else:
text = koEntry.title
item.setText(0, text)
if id in allPathways:
item.pathway_id = id
elif "path:map" + koEntry.title[:5] in allRefPathways:
item.pathway_id = "path:map" + koEntry.title[:5]
else:
item.pathway_id = None
for child in koEntry.entries:
if child in allClasses:
_walkCreate(child, item)
def UpdateListView(self):
self.bestPValueItem = None
self.listView.clear()
if not self.data:
return
allPathways = self.org.pathways()
allRefPathways = kegg.pathways("map")
items = []
kegg_pathways = kegg.KEGGPathways()
org_code = self.organismCodes[min(self.organismIndex, len(self.organismCodes) - 1)]
if self.showOrthology:
self.koOrthology = kegg.KEGGBrite("ko00001")
self.listView.setRootIsDecorated(True)
path_ids = set([s[-5:] for s in self.pathways.keys()])
def _walkCollect(koEntry):
num = koEntry.title[:5] if koEntry.title else None
if num in path_ids:
return [koEntry] + reduce(
lambda li, c: li + _walkCollect(c), [child for child in koEntry.entries], []
)
else:
c = reduce(lambda li, c: li + _walkCollect(c), [child for child in koEntry.entries], [])
return c + (c and [koEntry] or [])
allClasses = reduce(lambda li1, li2: li1 + li2, [_walkCollect(c) for c in self.koOrthology], [])
def _walkCreate(koEntry, lvItem):
item = QTreeWidgetItem(lvItem)
id = "path:" + org_code + koEntry.title[:5]
if koEntry.title[:5] in path_ids:
p = kegg_pathways.get_entry(id)
if p is None:
# In case the genesets still have obsolete entries
name = koEntry.title
else:
name = p.name
genes, p_value, ref = self.pathways[id]
item.setText(0, name)
item.setText(1, "%.5f" % p_value)
item.setText(2, "%i of %i" % (len(genes), len(self.genes)))
item.setText(3, "%i of %i" % (ref, len(self.referenceGenes)))
item.pathway_id = id if p is not None else None
else:
if id in allPathways:
text = kegg_pathways.get_entry(id).name
else:
text = koEntry.title
item.setText(0, text)
if id in allPathways:
item.pathway_id = id
elif "path:map" + koEntry.title[:5] in allRefPathways:
item.pathway_id = "path:map" + koEntry.title[:5]
else:
item.pathway_id = None
for child in koEntry.entries:
if child in allClasses:
_walkCreate(child, item)
for koEntry in self.koOrthology:
if koEntry in allClasses:
_walkCreate(koEntry, self.listView)
self.listView.update()
else:
self.listView.setRootIsDecorated(False)
pathways = self.pathways.items()
pathways = sorted(pathways, key=lambda item: item[1][1])
for id, (genes, p_value, ref) in pathways:
item = QTreeWidgetItem(self.listView)
item.setText(0, kegg_pathways.get_entry(id).name)
item.setText(1, "%.5f" % p_value)
item.setText(2, "%i of %i" % (len(genes), len(self.genes)))
item.setText(3, "%i of %i" % (ref, len(self.referenceGenes)))
item.pathway_id = id
items.append(item)
self.bestPValueItem = items and items[0] or None
self.listView.expandAll()
for i in range(4):
self.listView.resizeColumnToContents(i)
if self.bestPValueItem:
index = self.listView.indexFromItem(self.bestPValueItem)
self.listView.selectionModel().select(index, QItemSelectionModel.ClearAndSelect)
def setAnnotations(self, gds):
self._annotationsUpdating = True
self.annotationsTree.clear()
annotations = defaultdict(set)
subsetscount = {}
for desc in gds["subsets"]:
annotations[desc["type"]].add(desc["description"])
subsetscount[desc["description"]] = str(len(desc["sample_id"]))
for type, subsets in annotations.items():
key = (gds["dataset_id"], type)
subsetItem = QTreeWidgetItem(self.annotationsTree, [type])
subsetItem.setFlags(subsetItem.flags() | Qt.ItemIsUserCheckable
| Qt.ItemIsTristate)
subsetItem.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked))
subsetItem.key = key
for subset in subsets:
key = (gds["dataset_id"], type, subset)
item = QTreeWidgetItem(
subsetItem, [subset, subsetscount.get(subset, "")])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
item.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked))
item.key = key
self._annotationsUpdating = False
self.annotationsTree.expandAll()
for i in range(self.annotationsTree.columnCount()):
self.annotationsTree.resizeColumnToContents(i)
def UpdateListView(self):
self.bestPValueItem = None
self.listView.clear()
if not self.data:
return
allPathways = self.org.pathways()
allRefPathways = kegg.pathways("map")
items = []
kegg_pathways = kegg.KEGGPathways()
org_code = self.org.org_code
if self.showOrthology:
self.koOrthology = kegg.KEGGBrite("ko00001")
self.listView.setRootIsDecorated(True)
path_ids = {s[-5:] for s in self.pathways.keys()}
def _walkCollect(koEntry):
num = koEntry.title[:5] if koEntry.title else None
if num in path_ids:
return [koEntry] + reduce(
lambda li, c: li + _walkCollect(c),
[child for child in koEntry.entries], [])
else:
c = reduce(lambda li, c: li + _walkCollect(c),
[child for child in koEntry.entries], [])
return c + (c and [koEntry] or [])
allClasses = reduce(lambda li1, li2: li1 + li2,
[_walkCollect(c) for c in self.koOrthology],
[])
def _walkCreate(koEntry, lvItem):
item = QTreeWidgetItem(lvItem)
id = "path:" + org_code + koEntry.title[:5]
if koEntry.title[:5] in path_ids:
p = kegg_pathways.get_entry(id)
if p is None:
# In case the genesets still have obsolete entries
name = koEntry.title
else:
name = p.name
genes, p_value, ref = self.pathways[id]
item.setText(0, name)
item.setText(1, "%.5f" % p_value)
item.setText(
2, "%i of %i" % (len(genes), len(self.input_genes)))
item.setText(3, "%i of %i" % (ref, len(self.ref_genes)))
item.pathway_id = id if p is not None else None
else:
if id in allPathways:
text = kegg_pathways.get_entry(id).name
else:
text = koEntry.title
item.setText(0, text)
if id in allPathways:
item.pathway_id = id
elif "path:map" + koEntry.title[:5] in allRefPathways:
item.pathway_id = "path:map" + koEntry.title[:5]
else:
item.pathway_id = None
for child in koEntry.entries:
if child in allClasses:
_walkCreate(child, item)
for koEntry in self.koOrthology:
if koEntry in allClasses:
_walkCreate(koEntry, self.listView)
self.listView.update()
else:
self.listView.setRootIsDecorated(False)
pathways = self.pathways.items()
pathways = sorted(pathways, key=lambda item: item[1][1])
for id, (genes, p_value, ref) in pathways:
item = QTreeWidgetItem(self.listView)
item.setText(0, kegg_pathways.get_entry(id).name)
item.setText(1, "%.5f" % p_value)
item.setText(2,
"%i of %i" % (len(genes), len(self.input_genes)))
item.setText(3, "%i of %i" % (ref, len(self.ref_genes)))
item.pathway_id = id
items.append(item)
self.bestPValueItem = items and items[0] or None
self.listView.expandAll()
for i in range(4):
self.listView.resizeColumnToContents(i)
if self.bestPValueItem:
index = self.listView.indexFromItem(self.bestPValueItem)
self.listView.selectionModel().select(
index, QItemSelectionModel.ClearAndSelect)
def __init__(self, parent, *args):
QTreeWidgetItem.__init__(self, parent, *args)
self.par = parent
def _walkCreate(koEntry, lvItem):
item = QTreeWidgetItem(lvItem)
id = "path:" + org_code + koEntry.title[:5]
if koEntry.title[:5] in path_ids:
p = kegg_pathways.get_entry(id)
if p is None:
# In case the genesets still have obsolete entries
name = koEntry.title
else:
name = p.name
genes, p_value, ref = self.pathways[id]
item.setText(0, name)
item.setText(1, "%.5f" % p_value)
item.setText(
2, "%i of %i" % (len(genes), len(self.input_genes)))
item.setText(3, "%i of %i" % (ref, len(self.ref_genes)))
item.pathway_id = id if p is not None else None
else:
if id in allPathways:
text = kegg_pathways.get_entry(id).name
else:
text = koEntry.title
item.setText(0, text)
if id in allPathways:
item.pathway_id = id
elif "path:map" + koEntry.title[:5] in allRefPathways:
item.pathway_id = "path:map" + koEntry.title[:5]
else:
item.pathway_id = None
for child in koEntry.entries:
if child in allClasses:
_walkCreate(child, item)
def __init__(self, item):
QTreeWidgetItem.__init__(self, type=QTreeWidgetItem.UserType)
self.item = None
self.setUpdateItem(item)
def __lt__(self, o1):
col = self.par.sortColumn()
if col in [8, 9]: # WARNING: hardcoded column numbers
return tfloat(self.text(col)) < tfloat(o1.text(col))
else:
return QTreeWidgetItem.__lt__(self, o1)