diff --git a/reference/reference_parsers.html b/reference/reference_parsers.html index 85fc3e3c..8fdd14a8 100644 --- a/reference/reference_parsers.html +++ b/reference/reference_parsers.html @@ -114,13 +114,13 @@

Parsers
-read_content(text, pos, endings=',);')
+read_content(unicode text, int pos, endings=u', );')

Return content starting at position pos in text, and where it ends.

-read_nodes(nodes_text, parser, pos=0, tree_class=Tree)
+read_nodes(nodes_text, parser, int pos=0, tree_class=Tree)

Return a list of nodes and the position in the text where they end.

@@ -132,13 +132,13 @@

Parsers
-skip_quoted_name(text, pos)
+skip_quoted_name(unicode text, int pos)

Return the position where a quoted name ends.

-skip_spaces_and_comments(text, pos)
+skip_spaces_and_comments(text, int pos)

Return position in text after pos and all whitespaces and comments.

diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html index d70f945f..9308da2e 100644 --- a/reference/reference_smartview.html +++ b/reference/reference_smartview.html @@ -92,7 +92,7 @@

Smartview (web graphi
-class TreeData(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f3842b42a20> = None, searches: dict = None)[source]
+class TreeData(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7ff480f42a20> = None, searches: dict = None)[source]
__init__(tree: Tree = None, name: str = None, style: TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: namedtuple = None, searches: dict = None) → None
diff --git a/searchindex.js b/searchindex.js index f69af720..d808bf82 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "faqs", "index", "reference/index", "reference/reference_clustering", "reference/reference_operations", "reference/reference_parsers", "reference/reference_phylo", "reference/reference_seqgroup", "reference/reference_smartview", "reference/reference_taxonomy", "reference/reference_tree", "reference/reference_treematcher", "reference/reference_treeview", "tutorial/index", "tutorial/tutorial_phylogeny", "tutorial/tutorial_smartview", "tutorial/tutorial_taxonomy", "tutorial/tutorial_treematcher", "tutorial/tutorial_trees", "tutorial/tutorial_treeview"], "filenames": ["about.rst", "faqs.rst", "index.rst", "reference/index.rst", "reference/reference_clustering.rst", "reference/reference_operations.rst", "reference/reference_parsers.rst", "reference/reference_phylo.rst", "reference/reference_seqgroup.rst", "reference/reference_smartview.rst", "reference/reference_taxonomy.rst", "reference/reference_tree.rst", "reference/reference_treematcher.rst", "reference/reference_treeview.rst", "tutorial/index.rst", "tutorial/tutorial_phylogeny.rst", "tutorial/tutorial_smartview.rst", "tutorial/tutorial_taxonomy.rst", "tutorial/tutorial_treematcher.rst", "tutorial/tutorial_trees.rst", "tutorial/tutorial_treeview.rst"], "titles": ["About", "Frequently Asked Questions", "Welcome to ETE\u2019s documentation!", "Reference Guide", "Clustering", "Tree operations", "Parsers", "Phylogenetic trees", "Multiple Sequence Alignments (SeqGroup)", "Smartview (web graphics)", "Taxonomy databases", "Tree (main class)", "Tree matcher", "Treeview (qt graphics)", "Tutorial", "Phylogenetic trees", "Tree drawing and exploration (web)", "Taxonomy databases", "Tree matcher", "Working with the Tree structure", "Tree drawing (Qt)"], "terms": {"The": [0, 1, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 20], "toolkit": [0, 17, 19, 20], 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"sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"About": [[0, "about"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "contents"]], "General": [[1, "general"]], "How do I use ETE?": [[1, "how-do-i-use-ete"]], "Tree Browsing": [[1, "tree-browsing"]], "How do I find a leaf by its name?": [[1, "how-do-i-find-a-leaf-by-its-name"]], "How do I visit all nodes within a tree?": [[1, "how-do-i-visit-all-nodes-within-a-tree"]], "Can I control the order in which nodes are visited?": [[1, "can-i-control-the-order-in-which-nodes-are-visited"]], "Reading and writing": [[1, "reading-and-writing"]], "How do I load a tree with internal node names or support?": [[1, "how-do-i-load-a-tree-with-internal-node-names-or-support"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "Tree visualization": [[1, "tree-visualization"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "Can the visualization of trees with very unbalanced tree branches be improved?": [[1, "can-the-visualization-of-trees-with-very-unbalanced-tree-branches-be-improved"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Contents:": [[2, null]], "Indices and tables": [[2, "indices-and-tables"]], "Reference Guide": [[3, "reference-guide"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Parsers": [[6, "parsers"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "PhyloTree": [[7, "phylotree"]], "EvolEvent": [[7, "evolevent"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Renderer": [[9, "renderer"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Layouts": [[9, "layouts"]], "context": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "NCBITaxa": [[10, "ncbitaxa"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[15, "implementation"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Standalone scripts": [[16, "standalone-scripts"]], "Interactive sessions": [[16, "interactive-sessions"]], "Verbose mode": [[16, "verbose-mode"]], "Show leaf node names, branch length and branch support": [[16, "show-leaf-node-names-branch-length-and-branch-support"], [20, "show-leaf-node-names-branch-length-and-branch-support"]], "Showing node\u2019s properties in pop up": [[16, "showing-node-s-properties-in-pop-up"]], "Control Panel": [[16, "control-panel"]], "1) Layout Tab": [[16, "layout-tab"]], "Overrall": [[16, "overrall"]], "Download": [[16, "download"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "Simple search": [[16, "simple-search"]], "Regular expression search": [[16, "regular-expression-search"]], "Expression search": [[16, "expression-search"]], "Topological search": [[16, "topological-search"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "3) Advanced Tab": [[16, "advanced-tab"]], "Node Panel": [[16, "node-panel"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Add legend": [[16, "add-legend"]], "Node style": [[16, "node-style"], [20, "node-style"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Color Strip": [[16, "color-strip"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Bar Plot": [[16, "bar-plot"]], "Heatmap": [[16, "heatmap"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Domain annotation": [[16, "domain-annotation"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Getting taxid information": [[17, "getting-taxid-information"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "Outside variables": [[18, "outside-variables"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Trees": [[19, "trees"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Writing newick trees": [[19, "writing-newick-trees"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Advanced traversing": [[19, "advanced-traversing"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Search all nodes matching a given criteria": [[19, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria": [[19, "search-nodes-matching-a-given-criteria"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Shortcuts": [[19, "shortcuts"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[19, "node-annotation"]], "Comparing trees": [[19, "comparing-trees"]], "Distances between trees": [[19, "distances-between-trees"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[19, "pruning-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Tree rooting": [[19, "tree-rooting"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Tree style": [[20, "tree-style"]], "Change branch length scale (zoom in x)": [[20, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[20, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[20, "rotate-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Add legend and title": [[20, "add-legend-and-title"]], "Layout functions": [[20, "layout-functions"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Node backgrounds": [[20, "node-backgrounds"]], "Img faces": [[20, "img-faces"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Trees within trees": [[20, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]]}, "indexentries": {"clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree"]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__"]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation"]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree"]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn"]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette"]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist"]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist"]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles"]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable"]], "module": [[4, "module-ete4.clustering.clustertree"], [5, "module-ete4.core.operations"], [6, "module-ete4.parser.newick"], [6, "module-ete4.parser.nexus"], [8, "module-ete4.core.seqgroup"], [9, "module-ete4.smartview.gui.server"], [9, "module-ete4.smartview.renderer.draw_helpers"], [9, "module-ete4.smartview.renderer.drawer"], [9, "module-ete4.smartview.renderer.face_positions"], [9, "module-ete4.smartview.renderer.faces"], [9, "module-ete4.smartview.renderer.layouts.context_layouts"], [9, "module-ete4.smartview.renderer.layouts.default_layouts"], [9, "module-ete4.smartview.renderer.layouts.domain_layouts"], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [9, "module-ete4.smartview.renderer.layouts.seq_layouts"], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [9, "module-ete4.smartview.renderer.layouts.staple_layouts"], [9, "module-ete4.smartview.renderer.nodestyle"], [9, "module-ete4.smartview.renderer.treelayout"], [9, "module-ete4.smartview.renderer.treestyle"], [12, "module-ete4.treematcher.treematcher"], [13, "module-treeview"]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile"]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function"]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette"]], "walker (class in ete4.core.operations)": [[5, "ete4.core.operations.Walker"]], "add_branch_values() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_branch_values"]], "add_leaf_names() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_leaf_names"]], "add_next_branch() (walker method)": [[5, "ete4.core.operations.Walker.add_next_branch"]], "assert_root_consistency() (in module ete4.core.operations)": [[5, "ete4.core.operations.assert_root_consistency"]], "common_ancestor() (in module ete4.core.operations)": [[5, "ete4.core.operations.common_ancestor"]], "create_dichotomic_sister() (in module ete4.core.operations)": [[5, "ete4.core.operations.create_dichotomic_sister"]], "ete4.core.operations": [[5, "module-ete4.core.operations"]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest"]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant"]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit"]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back"]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches"]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate"]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references"]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch"]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize"]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name"]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint"]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move"]], "node (walker property)": [[5, "ete4.core.operations.Walker.node"]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id"]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate"]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform"]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule"]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang"]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove"]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy"]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at"]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup"]], "set_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_outgroup"]], "sort() (in module ete4.core.operations)": [[5, "ete4.core.operations.sort"]], "swap_props() (in module ete4.core.operations)": [[5, "ete4.core.operations.swap_props"]], "to_dendrogram() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_dendrogram"]], "to_ultrametric() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_ultrametric"]], "traverse() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse"]], "traverse_bfs() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse_bfs"]], "unroot() (in module ete4.core.operations)": [[5, "ete4.core.operations.unroot"]], "update_size() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_size"]], "update_sizes_all() (in module ete4.core.operations)": [[5, 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"ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName.__init__"]], "__init__() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.__init__"]], "__init__() (layoutsmartdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains.__init__"]], "__init__() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.__init__"]], "__init__() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__"]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__"]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__"]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__"]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__"]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__"]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__"]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__"]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__"]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__"]], "__init__() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.__init__"]], "__init__() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.__init__"]], "__init__() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.__init__"]], "__init__() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.__init__"]], "__init__() (treedata method)": [[9, "ete4.smartview.gui.server.TreeData.__init__"]], "__init__() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.__init__"]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__"]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade"]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node"]], "active (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.active"]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face"]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos"]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face"]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend"]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree"]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request"]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer"]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header"]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks"]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions"]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback"]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian"]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name"]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name"]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box"]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box"]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box"]], "compute_bounding_box() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box"]], "compute_bounding_box() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box"]], "compute_bounding_box() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches"]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected"]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection"]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get"]], "tree (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.tree"]], "ultrametric (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.ultrametric"]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa"]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa"]], "__init__() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.__init__"]], "__init__() (ncbitaxa method)": [[10, "ete4.NCBITaxa.__init__"]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree"]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree"]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches"]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches"]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names"]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names"]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa"]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage"]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage"]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator"]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator"]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage"]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator"]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator"]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank"]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank"]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator"]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator"]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology"]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology"]], "translate_to_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.translate_to_names"]], "translate_to_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.update_taxonomy_database"]], "update_taxonomy_database() (ncbitaxa method)": [[10, "ete4.NCBITaxa.update_taxonomy_database"]], "tree (class in ete4)": [[11, "ete4.Tree"]], "__init__() (tree method)": [[11, "ete4.Tree.__init__"]], "add_child() (tree method)": [[11, "ete4.Tree.add_child"]], "add_children() (tree method)": [[11, "ete4.Tree.add_children"]], "add_face() (tree method)": [[11, "ete4.Tree.add_face"]], "add_face_smartview() (tree method)": [[11, "ete4.Tree.add_face_smartview"]], "add_face_treeview() (tree method)": [[11, "ete4.Tree.add_face_treeview"]], "add_feature() (tree method)": [[11, "ete4.Tree.add_feature"]], "add_features() (tree method)": [[11, "ete4.Tree.add_features"]], "add_prop() (tree method)": [[11, "ete4.Tree.add_prop"]], "add_props() (tree method)": [[11, "ete4.Tree.add_props"]], "add_sister() (tree method)": [[11, "ete4.Tree.add_sister"]], "ancestors() (tree method)": [[11, "ete4.Tree.ancestors"]], "check_monophyly() (tree method)": [[11, "ete4.Tree.check_monophyly"]], "children (tree attribute)": [[11, "ete4.Tree.children"]], "collapsed_faces (tree attribute)": [[11, "ete4.Tree.collapsed_faces"]], "common_ancestor() (tree method)": [[11, "ete4.Tree.common_ancestor"]], "compare() (tree method)": [[11, "ete4.Tree.compare"]], "cophenetic_matrix() (tree method)": [[11, "ete4.Tree.cophenetic_matrix"]], "copy() (tree method)": [[11, "ete4.Tree.copy"]], "del_feature() (tree method)": [[11, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop"]], "delete() (tree method)": [[11, "ete4.Tree.delete"]], "descendants() (tree method)": [[11, "ete4.Tree.descendants"]], "describe() (tree method)": [[11, "ete4.Tree.describe"]], "detach() (tree method)": [[11, "ete4.Tree.detach"]], "dist (tree attribute)": [[11, "ete4.Tree.dist"]], "edges() (tree method)": [[11, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[11, 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"sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"About": [[0, "about"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "contents"]], "General": [[1, "general"]], "How do I use ETE?": [[1, "how-do-i-use-ete"]], "Tree Browsing": [[1, "tree-browsing"]], "How do I find a leaf by its name?": [[1, "how-do-i-find-a-leaf-by-its-name"]], "How do I visit all nodes within a tree?": [[1, "how-do-i-visit-all-nodes-within-a-tree"]], "Can I control the order in which nodes are visited?": [[1, "can-i-control-the-order-in-which-nodes-are-visited"]], "Reading and writing": [[1, "reading-and-writing"]], "How do I load a tree with internal node names or support?": [[1, "how-do-i-load-a-tree-with-internal-node-names-or-support"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "Tree visualization": [[1, "tree-visualization"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "Can the visualization of trees with very unbalanced tree branches be improved?": [[1, "can-the-visualization-of-trees-with-very-unbalanced-tree-branches-be-improved"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Contents:": [[2, null]], "Indices and tables": [[2, "indices-and-tables"]], "Reference Guide": [[3, "reference-guide"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Parsers": [[6, "parsers"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "PhyloTree": [[7, "phylotree"]], "EvolEvent": [[7, "evolevent"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Renderer": [[9, "renderer"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Layouts": [[9, "layouts"]], "context": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "NCBITaxa": [[10, "ncbitaxa"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[15, "implementation"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Standalone scripts": [[16, "standalone-scripts"]], "Interactive sessions": [[16, "interactive-sessions"]], "Verbose mode": [[16, "verbose-mode"]], "Show leaf node names, branch length and branch support": [[16, "show-leaf-node-names-branch-length-and-branch-support"], [20, "show-leaf-node-names-branch-length-and-branch-support"]], "Showing node\u2019s properties in pop up": [[16, "showing-node-s-properties-in-pop-up"]], "Control Panel": [[16, "control-panel"]], "1) Layout Tab": [[16, "layout-tab"]], "Overrall": [[16, "overrall"]], "Download": [[16, "download"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "Simple search": [[16, "simple-search"]], "Regular expression search": [[16, "regular-expression-search"]], "Expression search": [[16, "expression-search"]], "Topological search": [[16, "topological-search"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "3) Advanced Tab": [[16, "advanced-tab"]], "Node Panel": [[16, "node-panel"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Add legend": [[16, "add-legend"]], "Node style": [[16, "node-style"], [20, "node-style"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Color Strip": [[16, "color-strip"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Bar Plot": [[16, "bar-plot"]], "Heatmap": [[16, "heatmap"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Domain annotation": [[16, "domain-annotation"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Getting taxid information": [[17, "getting-taxid-information"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "Outside variables": [[18, "outside-variables"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Trees": [[19, "trees"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Writing newick trees": [[19, "writing-newick-trees"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Advanced traversing": [[19, "advanced-traversing"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Search all nodes matching a given criteria": [[19, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria": [[19, "search-nodes-matching-a-given-criteria"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Shortcuts": [[19, "shortcuts"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[19, "node-annotation"]], "Comparing trees": [[19, "comparing-trees"]], "Distances between trees": [[19, "distances-between-trees"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[19, "pruning-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Tree rooting": [[19, "tree-rooting"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Tree style": [[20, "tree-style"]], "Change branch length scale (zoom in x)": [[20, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[20, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[20, "rotate-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Add legend and title": [[20, "add-legend-and-title"]], "Layout functions": [[20, "layout-functions"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Node backgrounds": [[20, "node-backgrounds"]], "Img faces": [[20, "img-faces"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Trees within trees": [[20, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]]}, "indexentries": {"clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree"]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__"]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation"]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree"]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn"]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette"]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist"]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist"]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles"]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable"]], "module": [[4, "module-ete4.clustering.clustertree"], [5, "module-ete4.core.operations"], [6, "module-ete4.parser.newick"], [6, "module-ete4.parser.nexus"], [8, "module-ete4.core.seqgroup"], [9, "module-ete4.smartview.gui.server"], [9, "module-ete4.smartview.renderer.draw_helpers"], [9, "module-ete4.smartview.renderer.drawer"], [9, "module-ete4.smartview.renderer.face_positions"], [9, "module-ete4.smartview.renderer.faces"], [9, "module-ete4.smartview.renderer.layouts.context_layouts"], [9, "module-ete4.smartview.renderer.layouts.default_layouts"], [9, "module-ete4.smartview.renderer.layouts.domain_layouts"], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [9, "module-ete4.smartview.renderer.layouts.seq_layouts"], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [9, "module-ete4.smartview.renderer.layouts.staple_layouts"], [9, "module-ete4.smartview.renderer.nodestyle"], [9, "module-ete4.smartview.renderer.treelayout"], [9, "module-ete4.smartview.renderer.treestyle"], [12, "module-ete4.treematcher.treematcher"], [13, "module-treeview"]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile"]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function"]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette"]], "walker (class in ete4.core.operations)": [[5, "ete4.core.operations.Walker"]], "add_branch_values() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_branch_values"]], "add_leaf_names() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_leaf_names"]], "add_next_branch() (walker method)": [[5, "ete4.core.operations.Walker.add_next_branch"]], "assert_root_consistency() (in module ete4.core.operations)": [[5, "ete4.core.operations.assert_root_consistency"]], "common_ancestor() (in module ete4.core.operations)": [[5, "ete4.core.operations.common_ancestor"]], "create_dichotomic_sister() (in module ete4.core.operations)": [[5, "ete4.core.operations.create_dichotomic_sister"]], "ete4.core.operations": [[5, "module-ete4.core.operations"]], "farthest() (in module ete4.core.operations)": 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"move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move"]], "node (walker property)": [[5, "ete4.core.operations.Walker.node"]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id"]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate"]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform"]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule"]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang"]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove"]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy"]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at"]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup"]], "set_outgroup() (in 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"ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule.__init__"]], "__init__() (layoutkeggnumber method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber.__init__"]], "__init__() (layoutkeggpathway method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway.__init__"]], "__init__() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.__init__"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.__init__"]], "__init__() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.__init__"]], "__init__() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.__init__"]], "__init__() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.__init__"]], "__init__() (layoutpdb method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb.__init__"]], "__init__() (layoutpfamdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains.__init__"]], "__init__() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.__init__"]], "__init__() (layoutproteinname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName.__init__"]], "__init__() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.__init__"]], "__init__() (layoutscientificname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName.__init__"]], "__init__() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.__init__"]], "__init__() (layoutsmartdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains.__init__"]], "__init__() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.__init__"]], "__init__() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__"]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__"]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__"]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__"]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__"]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__"]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__"]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__"]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__"]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__"]], "__init__() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.__init__"]], "__init__() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.__init__"]], "__init__() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.__init__"]], "__init__() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.__init__"]], "__init__() (treedata method)": [[9, "ete4.smartview.gui.server.TreeData.__init__"]], "__init__() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.__init__"]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__"]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade"]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node"]], "active (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.active"]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face"]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos"]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face"]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend"]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree"]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request"]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer"]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header"]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks"]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions"]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback"]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian"]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name"]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name"]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box"]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box"]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box"]], "compute_bounding_box() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box"]], "compute_bounding_box() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box"]], "compute_bounding_box() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches"]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected"]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection"]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get"]], "tree (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.tree"]], "ultrametric (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.ultrametric"]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa"]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa"]], "__init__() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.__init__"]], "__init__() (ncbitaxa method)": [[10, "ete4.NCBITaxa.__init__"]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree"]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree"]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches"]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches"]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names"]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names"]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa"]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage"]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage"]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator"]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator"]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage"]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator"]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator"]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank"]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank"]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator"]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator"]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology"]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology"]], "translate_to_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.translate_to_names"]], "translate_to_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.update_taxonomy_database"]], "update_taxonomy_database() (ncbitaxa method)": [[10, "ete4.NCBITaxa.update_taxonomy_database"]], "tree (class in ete4)": [[11, "ete4.Tree"]], "__init__() (tree method)": [[11, "ete4.Tree.__init__"]], "add_child() (tree method)": [[11, "ete4.Tree.add_child"]], "add_children() (tree method)": [[11, "ete4.Tree.add_children"]], "add_face() (tree method)": [[11, "ete4.Tree.add_face"]], "add_face_smartview() (tree method)": [[11, "ete4.Tree.add_face_smartview"]], "add_face_treeview() (tree method)": [[11, "ete4.Tree.add_face_treeview"]], "add_feature() (tree method)": [[11, "ete4.Tree.add_feature"]], "add_features() (tree method)": [[11, "ete4.Tree.add_features"]], "add_prop() (tree method)": [[11, "ete4.Tree.add_prop"]], "add_props() (tree method)": [[11, "ete4.Tree.add_props"]], "add_sister() (tree method)": [[11, "ete4.Tree.add_sister"]], "ancestors() (tree method)": [[11, "ete4.Tree.ancestors"]], "check_monophyly() (tree method)": [[11, "ete4.Tree.check_monophyly"]], "children (tree attribute)": [[11, "ete4.Tree.children"]], "collapsed_faces (tree attribute)": [[11, "ete4.Tree.collapsed_faces"]], "common_ancestor() (tree method)": [[11, "ete4.Tree.common_ancestor"]], "compare() (tree method)": [[11, "ete4.Tree.compare"]], "cophenetic_matrix() (tree method)": [[11, "ete4.Tree.cophenetic_matrix"]], "copy() (tree method)": [[11, "ete4.Tree.copy"]], "del_feature() (tree method)": [[11, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop"]], "delete() (tree method)": [[11, "ete4.Tree.delete"]], "descendants() (tree method)": [[11, "ete4.Tree.descendants"]], "describe() (tree method)": [[11, "ete4.Tree.describe"]], "detach() (tree method)": [[11, "ete4.Tree.detach"]], "dist (tree attribute)": [[11, "ete4.Tree.dist"]], "edges() (tree method)": [[11, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies"]], "explore() (tree method)": [[11, "ete4.Tree.explore"]], "faces (tree attribute)": [[11, "ete4.Tree.faces"]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table"]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio"]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content"]], "get_children() (tree method)": 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