Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

aabgcolors (in ete2.treeview.faces)	add_faces() (in _TreeScene)	apply_changes() (in _PropertiesDialog)
aafgcolors (in ete2.treeview.faces)	add_feature() (in TreeNode)	arraytable (in ete2.coretype)
add_branch() (in _TreeScene)	add_feature() (in NewickDialog)	ArrayTable (in ete2.coretype.arraytable)
add_child() (in TreeNode)	add_features() (in TreeNode)	asETE() (in ete2.coretype.tree)
add_childs() (in _NodeItem)	add_scale() (in _TreeScene)	asRphylo() (in ete2.coretype.tree)
add_face_to_node() (in ete2.treeview.faces)	add_sister() (in TreeNode)	AttrFace (in ete2.treeview.faces)

B

back_to_parent_node() (in _NodeItem)	basic() (in ete2.treeview.layouts)

C

CacheMode	cluster_lines() (in ete2.treeview.layouts)	commitAndCloseEditor() (in _TableItem)
CacheMode	clustering (in ete2)	coretype (in ete2)
CacheModeFlag	ClusterNode (in ete2.clustering.clustertree)	count_algs() (in PhylomeDBConnector)
children (in TreeNode)	clustertree (in ete2.clustering)	count_trees() (in PhylomeDBConnector)
cluster_bars() (in ete2.treeview.layouts)	clustvalidation (in ete2.clustering)	createEditor() (in _TableItem)
cluster_cbars() (in ete2.treeview.layouts)	collapse() (in TreeNode)	cut_partition() (in _NodeItem)

D

DEBUG (in ete2.treeview.drawer)	delete_node() (in _NodeItem)	DockOptions
DEFAULT_COMPACT (in ete2.coretype.tree)	describe() (in TreeNode)	DragMode
DEFAULT_DIST (in ete2.parser.newick)	detach() (in TreeNode)	draw() (in _TreeScene)
DEFAULT_NAME (in ete2.parser.newick)	detach_node() (in _NodeItem)	draw_bar_profile() (in ProfileFace)
DEFAULT_SHOWINTERNAL (in ete2.coretype.tree)	deviation (in ClusterNode)	draw_centered_bar_profile() (in ProfileFace)
DEFAULT_SUPPORT (in ete2.parser.newick)	DialogCode	draw_heatmap_profile() (in ProfileFace)
del_feature() (in TreeNode)	displayText() (in _TableItem)	draw_line_profile() (in ProfileFace)
del_feature() (in NewickDialog)	dist (in TreeNode)	drawer (in ete2.treeview)
delete() (in TreeNode)	DockOption

E

EndEditHint	euclidean_dist() (in ete2.clustering.clustvalidation)	expand() (in TreeNode)
ete2	EvolEvent (in ete2.phylo.evolevents)
ete_resources_rc (in ete2.treeview)	evolevents (in ete2.phylo)

F

Face (in ete2.treeview.faces)	fasta (in ete2.parser)	format_node() (in ete2.parser.newick)
faces (in ete2.treeview)	fit_to_scale() (in ProfileFace)

G

get_age() (in PhyloNode)	get_farthest_node() (in TreeNode)	get_raw_alg() (in PhylomeDBConnector)
get_algs() (in PhylomeDBConnector)	get_farthest_oldest_leaf() (in PhyloNode)	get_reconciled_tree() (in ete2.phylo.reconciliation)
get_ascii() (in TreeNode)	get_id_by_external() (in PhylomeDBConnector)	get_row_vector() (in ArrayTable)
get_available_trees() (in PhylomeDBConnector)	get_id_translations() (in PhylomeDBConnector)	get_seed_ids() (in PhylomeDBConnector)
get_available_trees_by_phylome() (in PhylomeDBConnector)	get_leaf_names() (in TreeNode)	get_selected_nodes() (in _SelectorItem)
get_available_trees_in_phylome() (in PhylomeDBConnector)	get_leaf_profiles() (in ClusterNode)	get_seq() (in SeqGroup)
get_average_centroid_linkage_dist() (in ete2.coretype.arraytable)	get_leaves() (in TreeNode)	get_seqid_info() (in PhylomeDBConnector)
get_avg_profile() (in ete2.clustering.clustvalidation)	get_leaves_by_name() (in TreeNode)	get_seqids_in_proteome() (in PhylomeDBConnector)
get_best_tree() (in PhylomeDBConnector)	get_longest_isoform() (in PhylomeDBConnector)	get_seqs_in_proteome() (in PhylomeDBConnector)
get_centroid_dist() (in ete2.coretype.arraytable)	get_max_vector() (in ete2.coretype.arraytable)	get_several_column_vectors() (in ArrayTable)
get_children() (in TreeNode)	get_mean_vector() (in ete2.coretype.arraytable)	get_several_row_vectors() (in ArrayTable)
get_clean_alg() (in PhylomeDBConnector)	get_median_vector() (in ete2.coretype.arraytable)	get_silhouette() (in ClusterNode)
get_collateral_seeds() (in PhylomeDBConnector)	get_midpoint_outgroup() (in TreeNode)	get_silhouette_width() (in ete2.clustering.clustvalidation)
get_color_gradient() (in ProfileFace)	get_min_vector() (in ete2.coretype.arraytable)	get_sisters() (in TreeNode)
get_column_vector() (in ArrayTable)	get_my_evol_events() (in PhyloNode)	get_species() (in PhyloNode)
get_common_ancestor() (in TreeNode)	get_orthologs() (in PhylomeDBConnector)	get_species() (in PhylomeDBConnector)
get_descendant_evol_events() (in PhyloNode)	get_phylome_algs() (in PhylomeDBConnector)	get_species_info() (in PhylomeDBConnector)
get_descendants() (in TreeNode)	get_phylome_info() (in PhylomeDBConnector)	get_text() (in AttrFace)
get_distance() (in TreeNode)	get_phylome_trees() (in PhylomeDBConnector)	get_text() (in TextFace)
get_dunn() (in ClusterNode)	get_phylomes() (in PhylomeDBConnector)	get_tree() (in PhylomeDBConnector)
get_dunn_index() (in ete2.clustering.clustvalidation)	get_prop_table() (in _PropertiesDialog)	get_tree_root() (in TreeNode)
get_entries() (in SeqGroup)	get_props_in_nodes() (in _PropertiesDialog)	GraphicsItemChange
get_evol_events_from_leaf() (in ete2.phylo.spoverlap)	get_proteome_info() (in PhylomeDBConnector)	GraphicsItemFlag
get_evol_events_from_root() (in ete2.phylo.spoverlap)	get_proteomes() (in PhylomeDBConnector)	GraphicsItemFlags
get_farthest_leaf() (in TreeNode)	get_proteomes_in_phylome() (in PhylomeDBConnector)

H

heatmap() (in ete2.treeview.layouts)	hoverEnterEvent() (in _NodeItem)	hoverLeaveEvent() (in _NodeItem)
highlight_node() (in _TreeScene)	hoverEnterEvent() (in _TextItem)	hoverLeaveEvent() (in _TextItem)
hoverEnterEvent() (in _FaceItem)	hoverLeaveEvent() (in _FaceItem)

I

ImgFace (in ete2.treeview.faces)	is_root() (in TreeNode)	iter_leaf_names() (in TreeNode)
initialize_tree_scene() (in _TreeScene)	isActive() (in _SelectorItem)	iter_leaf_profiles() (in ClusterNode)
intercluster_dist (in ClusterNode)	isSupportedType() (in _TableItem)	iter_leaves() (in TreeNode)
intracluster_dist (in ClusterNode)	ItemIndexMethod	iter_search_nodes() (in TreeNode)
is_leaf() (in TreeNode)	iter_descendants() (in TreeNode)	iter_species() (in PhyloNode)
is_monophyletic() (in PhyloNode)	iter_entries() (in SeqGroup)

K

keyPressEvent() (in _MainView)

L

large() (in ete2.treeview.layouts)	link_to_alignment() (in PhyloNode)	logger() (in ete2.treeview.drawer)
layout_functions (in ete2.treeview.layouts)	link_to_arraytable() (in ClusterNode)
layouts (in ete2.treeview)	load_pixmap_from_file() (in Face)

M

merge_columns() (in ArrayTable)	mousePressEvent() (in _NodeItem)	mouseReleaseEvent() (in _NodeItem)
mouseDoubleClickEvent() (in _TreeScene)	mousePressEvent() (in _TextItem)	mouseReleaseEvent() (in _TextItem)
mouseMoveEvent() (in _TreeScene)	mousePressEvent() (in _TreeScene)	mouseReleaseEvent() (in _TreeScene)
mousePressEvent() (in _FaceItem)	mouseReleaseEvent() (in _FaceItem)

N

newick (in ete2.parser)	node2internalformat() (in ete2.parser.newick)	ntfgcolors (in ete2.treeview.faces)
NewickDialog (in ete2.treeview.drawer)	node2leafformat() (in ete2.parser.newick)	NW_FORMAT (in ete2.parser.newick)
NewickError (in ete2.parser.newick)	ntbgcolors (in ete2.treeview.faces)

O

on_actionBranchLength_triggered() (in _MainApp)	on_actionPaste_newick_triggered() (in _MainApp)	on_actionZoomIn_triggered() (in _MainApp)
on_actionChange_orientation_triggered() (in _MainApp)	on_actionRender_selected_region_triggered() (in _MainApp)	on_actionZoomInX_triggered() (in _MainApp)
on_actionClear_search_triggered() (in _MainApp)	on_actionRenderPDF_triggered() (in _MainApp)	on_actionZoomInY_triggered() (in _MainApp)
on_actionETE_triggered() (in _MainApp)	on_actionSave_newick_triggered() (in _MainApp)	on_actionZoomOut_triggered() (in _MainApp)
on_actionFit2region_triggered() (in _MainApp)	on_actionSearchNode_triggered() (in _MainApp)	on_actionZoomOutX_triggered() (in _MainApp)
on_actionFit2tree_triggered() (in _MainApp)	on_actionShow_newick_triggered() (in _MainApp)	on_actionZoomOutY_triggered() (in _MainApp)
on_actionForceTopology_triggered() (in _MainApp)	on_actionShow_phenogram_triggered() (in _MainApp)	OptimizationFlag
on_actionOpen_triggered() (in _MainApp)	on_actionShowCladogram_triggered() (in _MainApp)	OptimizationFlags

P

paint() (in _HighlighterItem)	phylip (in ete2.parser)	populate() (in TreeNode)
paint() (in _NodeItem)	phylo (in ete2)	populate_partition() (in _NodeItem)
paint() (in _SelectorItem)	phylogeny() (in ete2.treeview.layouts)	print_supported_formats() (in ete2.parser.newick)
paint() (in _TableItem)	phylomedb (in ete2)	profile (in ClusterNode)
PaintDeviceMetric	phylomeDB (in ete2.phylomedb)	ProfileFace (in ete2.treeview.faces)
parser (in ete2)	PhylomeDBConnector (in ete2.phylomedb.phylomeDB)	prune() (in TreeNode)
paste_partition() (in _NodeItem)	PhyloNode (in ete2.phylo.phylotree)
pearson_dist() (in ete2.clustering.clustvalidation)	phylotree (in ete2.phylo)

Q

qCleanupResources() (in ete2.treeview.ete_resources_rc)	qt_resource_data (in ete2.treeview.ete_resources_rc)	qt_resource_struct (in ete2.treeview.ete_resources_rc)
qInitResources() (in ete2.treeview.ete_resources_rc)	qt_resource_name (in ete2.treeview.ete_resources_rc)

R

read_arraytable() (in ete2.parser.text_arraytable)	remove_sister() (in TreeNode)	retranslateUi() (in Ui_MainWindow)
read_fasta() (in ete2.parser.fasta)	render() (in TreeNode)	retranslateUi() (in Ui_OpenNewick)
read_newick() (in ete2.parser.newick)	render_node() (in _TreeScene)	retranslateUi() (in Ui_Dialog)
read_phylip() (in ete2.parser.phylip)	render_tree() (in ete2.treeview.drawer)	retranslateUi() (in Ui_Newick)
reconcile() (in PhyloNode)	RenderFlag	ROOTED_PHYLOMES (in ete2)
reconciliation (in ete2.phylo)	RenderFlags	ROOTED_PHYLOMES (in ete2.phylomedb.phylomeDB)
remove_child() (in TreeNode)	resizeEvent() (in _MainView)	rotate_node() (in _TreeScene)
remove_column() (in ArrayTable)	retranslateUi() (in Ui_About)

S

safe_mean() (in ete2.clustering.clustvalidation)	set_custom_features() (in NewickDialog)	ShapeMode
safe_mean() (in ete2.coretype.arraytable)	set_distance_function() (in ClusterNode)	show() (in TreeNode)
safe_mean_vector() (in ete2.clustering.clustvalidation)	set_outgroup() (in TreeNode)	show_newick() (in _NodeItem)
safe_mean_vector() (in ete2.coretype.arraytable)	set_species_naming_function() (in PhyloNode)	show_tree() (in ete2.treeview.drawer)
safe_scale() (in _MainView)	set_start_node() (in _NodeItem)	showActionPopup() (in _NodeItem)
save() (in _TreeScene)	set_style_from() (in _TreeScene)	silhouette (in ClusterNode)
save_by_chunks() (in _TreeScene)	setActive() (in _SelectorItem)	spearman_dist() (in ete2.clustering.clustvalidation)
SceneLayer	setEditorData() (in _TableItem)	species (in PhyloNode)
SceneLayers	setupUi() (in Ui_About)	species_ages (in ete2.phylomedb)
search_id() (in PhylomeDBConnector)	setupUi() (in Ui_MainWindow)	spoverlap (in ete2.phylo)
search_nodes() (in TreeNode)	setupUi() (in Ui_OpenNewick)	square_euclidean_dist() (in ete2.clustering.clustvalidation)
seqgroup (in ete2.coretype)	setupUi() (in Ui_Dialog)	StyleMask
SeqGroup (in ete2.coretype.seqgroup)	setupUi() (in Ui_Newick)	support (in TreeNode)
SequenceFace (in ete2.treeview.faces)	Shadow	swap_branches() (in _NodeItem)
set_as_outgroup() (in _NodeItem)	Shape	swap_childs() (in TreeNode)

T

text_arraytable (in ete2.parser)	traverse() (in TreeNode)	TreeNode (in ete2.coretype.tree)
TextFace (in ete2.treeview.faces)	tree (in ete2.coretype)	treeview (in ete2)
toggle_collapse() (in _NodeItem)	TreeError (in ete2.coretype.tree)
transpose() (in ArrayTable)	TreeImageProperties (in ete2.treeview.drawer)

U

Ui_About (in ete2.treeview._about)	unroot() (in TreeNode)	update_pixmap() (in ProfileFace)
Ui_Dialog (in ete2.treeview._search_dialog)	up (in TreeNode)	update_pixmap() (in SequenceFace)
Ui_MainWindow (in ete2.treeview._mainwindow)	update_newick() (in NewickDialog)	update_pixmap() (in ValidationFace)
Ui_Newick (in ete2.treeview._show_newick)	update_node_areas() (in _TreeScene)	update_properties() (in _PropertiesDialog)
Ui_OpenNewick (in ete2.treeview._open_newick)	update_pixmap() (in Face)	USE_GL (in ete2.treeview.drawer)
unhighlight_node() (in _TreeScene)	update_pixmap() (in ImgFace)

V

ValidationFace (in ete2.treeview.faces)	ViewportUpdateMode
ViewportAnchor	void() (in _NodeItem)

W

wheelEvent() (in _MainView)	write() (in TreeNode)	write_newick() (in ete2.parser.newick)
write() (in ArrayTable)	write_arraytable() (in ete2.parser.text_arraytable)	write_phylip() (in ete2.parser.phylip)
write() (in SeqGroup)	write_fasta() (in ete2.parser.fasta)

_

__add__() (in TreeNode)	__package__ (in ete2.phylomedb)	_get_expected_topology() (in ete2.phylo.reconciliation)
__and__() (in TreeNode)	__package__ (in ete2.phylomedb.phylomeDB)	_get_features_string() (in ete2.parser.newick)
__contains__() (in SeqGroup)	__package__ (in ete2.treeview)	_get_inter() (in ClusterNode)
__contains__() (in TreeNode)	__package__ (in ete2.treeview._about)	_get_intra() (in ClusterNode)
__init__() (in ClusterNode)	__package__ (in ete2.treeview._mainwindow)	_get_prof() (in ClusterNode)
__init__() (in ArrayTable)	__package__ (in ete2.treeview._open_newick)	_get_silh() (in ClusterNode)
__init__() (in SeqGroup)	__package__ (in ete2.treeview._search_dialog)	_get_species() (in PhyloNode)
__init__() (in TreeError)	__package__ (in ete2.treeview._show_newick)	_get_species_on_TOL() (in ete2.phylo.reconciliation)
__init__() (in TreeNode)	__package__ (in ete2.treeview.drawer)	_get_std() (in ClusterNode)
__init__() (in EvolEvent)	__package__ (in ete2.treeview.ete_resources_rc)	_get_support() (in TreeNode)
__init__() (in PhyloNode)	__package__ (in ete2.treeview.faces)	_get_up() (in TreeNode)
__init__() (in PhylomeDBConnector)	__package__ (in ete2.treeview.layouts)	_height() (in Face)
__init__() (in NewickDialog)	__str__() (in ArrayTable)	_height() (in TextFace)
__init__() (in TreeImageProperties)	__str__() (in SeqGroup)	_HighlighterItem (in ete2.treeview.drawer)
__init__() (in _FaceItem)	__str__() (in TreeError)	_humanv1 (in ete2.phylomedb)
__init__() (in _HighlighterItem)	__str__() (in TreeNode)	_ILEGAL_NEWICK_CHARS (in ete2.parser.newick)
__init__() (in _MainApp)	__VERSION__ (in ete2)	_iter_descendants_postorder() (in TreeNode)
__init__() (in _MainView)	__VERSION__ (in ete2.clustering)	_iter_descendants_preorder() (in TreeNode)
__init__() (in _NodeItem)	__VERSION__ (in ete2.clustering.clustertree)	_link_names2matrix() (in ArrayTable)
__init__() (in _PropModeChooser)	__VERSION__ (in ete2.clustering.clustvalidation)	_MainApp (in ete2.treeview.drawer)
__init__() (in _PropertiesDialog)	__VERSION__ (in ete2.coretype)	_MainView (in ete2.treeview.drawer)
__init__() (in _SelectorItem)	__VERSION__ (in ete2.coretype.arraytable)	_mainwindow (in ete2.treeview)
__init__() (in _TableItem)	__VERSION__ (in ete2.coretype.seqgroup)	_MIN_NODE_STYLE (in ete2.treeview.drawer)
__init__() (in _TextItem)	__VERSION__ (in ete2.coretype.tree)	_NAME_RE (in ete2.parser.newick)
__init__() (in _TreeScene)	__VERSION__ (in ete2.parser)	_NHX_RE (in ete2.parser.newick)
__init__() (in AttrFace)	__VERSION__ (in ete2.parser.fasta)	_NodeItem (in ete2.treeview.drawer)
__init__() (in Face)	__VERSION__ (in ete2.parser.newick)	_open_newick (in ete2.treeview)
__init__() (in ImgFace)	__VERSION__ (in ete2.parser.phylip)	_parse_extra_features() (in ete2.parser.newick)
__init__() (in ProfileFace)	__VERSION__ (in ete2.parser.text_arraytable)	_parse_species() (in ete2.phylo.phylotree)
__init__() (in SequenceFace)	__VERSION__ (in ete2.phylo)	_PropertiesDialog (in ete2.treeview.drawer)
__init__() (in TextFace)	__VERSION__ (in ete2.phylo.evolevents)	_PropModeChooser (in ete2.treeview.drawer)
__init__() (in ValidationFace)	__VERSION__ (in ete2.phylo.phylotree)	_QApp (in ete2.treeview.drawer)
__iter__() (in SeqGroup)	__VERSION__ (in ete2.phylo.reconciliation)	_read_newick_from_string() (in ete2.parser.newick)
__iter__() (in TreeNode)	__VERSION__ (in ete2.phylo.spoverlap)	_read_node_data() (in ete2.parser.newick)
__len__() (in SeqGroup)	__VERSION__ (in ete2.phylomedb)	_replace_on_template() (in ete2.phylo.reconciliation)
__len__() (in TreeNode)	__VERSION__ (in ete2.phylomedb.phylomeDB)	_search_dialog (in ete2.treeview)
__package__ (in ete2)	__VERSION__ (in ete2.treeview)	_SelectorItem (in ete2.treeview.drawer)
__package__ (in ete2.clustering)	__VERSION__ (in ete2.treeview._about)	_seq2str() (in ete2.parser.fasta)
__package__ (in ete2.clustering.clustertree)	__VERSION__ (in ete2.treeview._mainwindow)	_set_children() (in TreeNode)
__package__ (in ete2.clustering.clustvalidation)	__VERSION__ (in ete2.treeview._open_newick)	_set_dist() (in TreeNode)
__package__ (in ete2.coretype)	__VERSION__ (in ete2.treeview._search_dialog)	_set_forbidden() (in ClusterNode)
__package__ (in ete2.coretype.arraytable)	__VERSION__ (in ete2.treeview._show_newick)	_set_profile() (in ClusterNode)
__package__ (in ete2.coretype.seqgroup)	__VERSION__ (in ete2.treeview.drawer)	_set_species() (in PhyloNode)
__package__ (in ete2.coretype.tree)	__VERSION__ (in ete2.treeview.ete_resources_rc)	_set_support() (in TreeNode)
__package__ (in ete2.parser)	__VERSION__ (in ete2.treeview.faces)	_set_up() (in TreeNode)
__package__ (in ete2.parser.fasta)	__VERSION__ (in ete2.treeview.layouts)	_show_newick (in ete2.treeview)
__package__ (in ete2.parser.newick)	_about (in ete2.treeview)	_size() (in Face)
__package__ (in ete2.parser.phylip)	_asciiArt() (in TreeNode)	_TableItem (in ete2.treeview.drawer)
__package__ (in ete2.parser.text_arraytable)	_calculate_avg_profile() (in ClusterNode)	_TextItem (in ete2.treeview.drawer)
__package__ (in ete2.phylo)	_execute_block() (in PhylomeDBConnector)	_translate_nodes() (in ete2.coretype.tree)
__package__ (in ete2.phylo.evolevents)	_FaceItem (in ete2.treeview.drawer)	_TreeScene (in ete2.treeview.drawer)
__package__ (in ete2.phylo.phylotree)	_FLOAT_RE (in ete2.parser.newick)	_width() (in AttrFace)
__package__ (in ete2.phylo.reconciliation)	_get_children() (in TreeNode)	_width() (in Face)
__package__ (in ete2.phylo.spoverlap)	_get_dist() (in TreeNode)	_width() (in TextFace)