From 75a9cf7ea7e3e91a4cea5d7a0c892c8f9f6bce64 Mon Sep 17 00:00:00 2001 From: jordibc Date: Mon, 27 May 2024 21:28:45 +0000 Subject: [PATCH] deploy: 2fabb2e70a95c2a628979353eac519540be88d73 --- reference/reference_smartview.html | 2 +- searchindex.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html index a5b8a247..38b5708d 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 0x7ff651d234c0> = 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 0x7fa23ab236a0> = 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 418bad7c..db364e13 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1) Layout Tab": [[16, "layout-tab"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "3) Advanced Tab": [[16, "advanced-tab"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "About": [[0, "about"]], "Add legend": [[16, "add-legend"]], "Add legend and title": [[20, "add-legend-and-title"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Advanced traversing": [[19, "advanced-traversing"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "Bar Plot": [[16, "bar-plot"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "Can I control the order in which nodes are visited?": [[1, "can-i-control-the-order-in-which-nodes-are-visited"]], "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"]], "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"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Color Strip": [[16, "color-strip"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Comparing trees": [[19, "comparing-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "contents"]], "Contents:": [[2, null]], "Control Panel": [[16, "control-panel"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Distances between trees": [[19, "distances-between-trees"]], "Domain annotation": [[16, "domain-annotation"]], "Download": [[16, "download"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "EvolEvent": [[7, "evolevent"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Expression search": [[16, "expression-search"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "General": [[1, "general"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Getting taxid information": [[17, "getting-taxid-information"]], "Heatmap": [[16, "heatmap"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "How do I find a leaf by its name?": [[1, "how-do-i-find-a-leaf-by-its-name"]], "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 use ETE?": [[1, "how-do-i-use-ete"]], "How do I visit all nodes within a tree?": [[1, "how-do-i-visit-all-nodes-within-a-tree"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Img faces": [[20, "img-faces"]], "Implementation": [[15, "implementation"]], "Indices and tables": [[2, "indices-and-tables"]], "Interactive sessions": [[16, "interactive-sessions"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Layout functions": [[20, "layout-functions"]], "Layouts": [[9, "layouts"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "NCBITaxa": [[10, "ncbitaxa"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Node Panel": [[16, "node-panel"]], "Node annotation": [[19, "node-annotation"]], "Node backgrounds": [[20, "node-backgrounds"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Node style": [[16, "node-style"], [20, "node-style"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Outside variables": [[18, "outside-variables"]], "Overrall": [[16, "overrall"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "Parsers": [[6, "parsers"]], "PhyloTree": [[7, "phylotree"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Pruning trees": [[19, "pruning-trees"]], "Reading and writing": [[1, "reading-and-writing"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Reference Guide": [[3, "reference-guide"]], "Regular expression search": [[16, "regular-expression-search"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Renderer": [[9, "renderer"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Rotate a tree": [[20, "rotate-a-tree"]], "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"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Shortcuts": [[19, "shortcuts"]], "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"]], "Simple search": [[16, "simple-search"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Standalone scripts": [[16, "standalone-scripts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Topological search": [[16, "topological-search"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree Browsing": [[1, "tree-browsing"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "Tree rooting": [[19, "tree-rooting"]], "Tree style": [[20, "tree-style"]], "Tree visualization": [[1, "tree-visualization"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Trees": [[19, "trees"]], "Trees within trees": [[20, "trees-within-trees"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Verbose mode": [[16, "verbose-mode"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Writing newick trees": [[19, "writing-newick-trees"]], "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, 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"ete4.treematcher.treematcher.TreePattern.__init__", false]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__", false]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade", false]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node", false]], "active (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Active", false]], "active (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.active", false]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face", false]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos", false]], "add_branch_values() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_branch_values", false]], "add_child() (tree method)": [[11, "ete4.Tree.add_child", false]], "add_children() (tree method)": [[11, "ete4.Tree.add_children", false]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face", false]], "add_face() (tree method)": [[11, "ete4.Tree.add_face", false]], "add_face_smartview() (tree method)": [[11, "ete4.Tree.add_face_smartview", false]], "add_face_treeview() (tree method)": [[11, "ete4.Tree.add_face_treeview", false]], "add_feature() (tree method)": [[11, "ete4.Tree.add_feature", false]], "add_features() (tree method)": [[11, "ete4.Tree.add_features", false]], "add_leaf_names() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_leaf_names", false]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend", false]], "add_next_branch() (walker method)": [[5, "ete4.core.operations.Walker.add_next_branch", false]], "add_prop() (tree method)": [[11, "ete4.Tree.add_prop", false]], "add_props() (tree method)": [[11, "ete4.Tree.add_props", false]], "add_sister() (tree method)": [[11, "ete4.Tree.add_sister", false]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree", false]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request", false]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer", false]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header", false]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid", false]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace", false]], "alignmentface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignmentFace", false]], "ancestors() (tree method)": [[11, "ete4.Tree.ancestors", false]], "annotate_gtdb_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_gtdb_taxa", false]], "annotate_ncbi_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_ncbi_taxa", false]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree", false]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree", false]], "apply_translations() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.apply_translations", false]], "arrowface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ArrowFace", false]], "assert_root_consistency() (in module ete4.core.operations)": [[5, "ete4.core.operations.assert_root_consistency", false]], "attrface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AttrFace", false]], "box (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Box", false]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks", false]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions", false]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback", false]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian", false]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name", false]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name", false]], "check_monophyly() (tree method)": [[11, "ete4.Tree.check_monophyly", false]], "children (tree attribute)": [[11, "ete4.Tree.children", false]], "circleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.CircleFace", false]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec", false]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect", false]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades", false]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles", false]], "clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree", false]], "collapse_lineage_specific_expansions() (phylotree method)": [[7, "ete4.PhyloTree.collapse_lineage_specific_expansions", false]], "collapse_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE", false]], "collapsed_faces (tree attribute)": [[11, "ete4.Tree.collapsed_faces", false]], "common_ancestor() (in module ete4.core.operations)": [[5, "ete4.core.operations.common_ancestor", false]], "common_ancestor() (tree method)": [[11, "ete4.Tree.common_ancestor", false]], "compare() (tree method)": [[11, "ete4.Tree.compare", false]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box", false]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box", false]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box", false]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box", false]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box", false]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box", false]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box", false]], "compute_bounding_box() 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"ete4.Tree.copy", false]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style", false]], "create_dichotomic_sister() (in module ete4.core.operations)": [[5, "ete4.core.operations.create_dichotomic_sister", false]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade", false]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node", false]], "del_feature() (tree method)": [[11, "ete4.Tree.del_feature", false]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop", false]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree", false]], "delete() (tree method)": [[11, "ete4.Tree.delete", false]], "descendants() (tree method)": [[11, "ete4.Tree.descendants", false]], "describe() (tree method)": [[11, "ete4.Tree.describe", false]], "detach() (tree method)": [[11, "ete4.Tree.detach", false]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation", false]], "dist (tree attribute)": [[11, "ete4.Tree.dist", false]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist", false]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw", false]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw", false]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw", false]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw", false]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw", false]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw", false]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw", false]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw", false]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw", false]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw", false]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw", false]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw", false]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw", false]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw", false]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw", false]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw", false]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers", false]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc", false]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array", false]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow", false]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline", false]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline", false]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle", false]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed", false]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed", false]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed", false]], "draw_collapsed() 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false]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline", false]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect", false]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus", false]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice", false]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text", false]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle", false]], "drawer (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Drawer", false]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces", false]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces", false]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc", false]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces", false]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRect", false]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces", false]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size", false]], "dump() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dump", false]], "dumps() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dumps", false]], "dx (box attribute)": [[9, 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[[9, "module-ete4.smartview.renderer.drawer", false]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions", false]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces", false]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts", false]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts", false]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts", false]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false]], 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[[9, "module-ete4.smartview.renderer.treestyle", false]], "ete4.treematcher.treematcher": [[12, "module-ete4.treematcher.treematcher", false]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent", false]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props", false]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies", false]], "explore() (tree method)": [[11, "ete4.Tree.explore", false]], "face (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.Face", false]], "faces (tree attribute)": [[11, "ete4.Tree.faces", false]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest", false]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant", false]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node", false]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value", false]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit", false]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits", false]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits", false]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits", false]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits", false]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits", false]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline", false]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline", false]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table", false]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio", false]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children", false]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade", false]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades", false]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age", false]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup", false]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec", false]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box", false]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box", false]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box", false]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box", false]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box", false]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches", false]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches", false]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content", false]], "get_children() (tree method)": [[11, "ete4.Tree.get_children", false]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf", false]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node", false]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color", false]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search", false]], "get_commands() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_commands", false]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names", false]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names", false]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content", false]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content", false]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context", false]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events", false]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa", false]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa", false]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance", false]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer", false]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers", false]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn", false]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active", false]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries", false]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search", false]], "get_extended_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_extended_props", false]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf", false]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node", false]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf", false]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node", false]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation", false]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype", false]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames", false]], "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", false]], "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", false]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname", false]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts", false]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters", false]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend", false]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type", false]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage", false]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage", false]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator", false]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator", false]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup", false]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic", false]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events", false]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage", false]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator", false]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator", false]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick", false]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port", false]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info", false]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline", false]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents", false]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser", false]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props", false]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop", false]], "get_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_props", false]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank", false]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank", false]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect", false]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function", false]], "get_section() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_section", false]], "get_sections() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_sections", false]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children", false]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info", false]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections", false]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq", false]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq", false]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq", false]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette", false]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters", false]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees", false]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species", false]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats", false]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator", false]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator", false]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid", false]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip", false]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search", false]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology", false]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology", false]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id", false]], "get_trees() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_trees", false]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file", false]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form", false]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick", false]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs", false]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys", false]], "globalstuff (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.GlobalStuff", false]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back", false]], "grid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.Grid", false]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa", false]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches", false]], "htmlface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.HTMLFace", false]], "id (tree attribute)": [[11, "ete4.Tree.id", false]], "img_style (tree property)": [[11, "ete4.Tree.img_style", false]], "imgface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ImgFace", false]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport", false]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport", false]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport", false]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props", false]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init", false]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete", false]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick", false]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize", false]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style", false]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized", false]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate", false]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references", false]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist", false]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles", false]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box", false]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment", false]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist", false]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed", false]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed", false]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized", false]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf", false]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic", false]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root", false]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small", false]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small", false]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries", false]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder", false]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species", false]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch", false]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error", false]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize", false]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize", false]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment", false]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName", false]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot", false]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName", false]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg", false]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength", false]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport", false]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard", false]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy", false]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName", false]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance", false]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.evol_events_layouts)": [[9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents", false]], "layoutgenomiccontext (class in ete4.smartview.renderer.layouts.context_layouts)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext", false]], "layouthumanogs (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs", false]], "layoutkeggenzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme", false]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule", false]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber", false]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor", false]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName", false]], "layoutnumberleaves (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves", false]], "layoutoutline (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline", false]], "layoutpdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains", false]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName", false]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName", false]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts", false]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName", false]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName", false]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains", false]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC", false]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans", false]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names", false]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles", false]], "leaves() (tree method)": [[11, "ete4.Tree.leaves", false]], "legendface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.LegendFace", false]], "level (tree attribute)": [[11, "ete4.Tree.level", false]], "lineage() (tree method)": [[11, "ete4.Tree.lineage", false]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment", false]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable", false]], "load() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.load", false]], "load() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.load", false]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree", false]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick", false]], "loads() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.loads", false]], "loads() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.loads", false]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance", false]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box", false]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces", false]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name", false]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name", false]], "make_parser() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.make_parser", false]], "match() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.match", false]], "match() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.match", false]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint", false]], "min_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE", false]], "module": [[4, "module-ete4.clustering.clustertree", false], [5, "module-ete4.core.operations", false], [6, "module-ete4.parser.newick", false], [6, "module-ete4.parser.nexus", false], [8, "module-ete4.core.seqgroup", false], [9, "module-ete4.smartview.gui.server", false], [9, "module-ete4.smartview.renderer.draw_helpers", false], [9, "module-ete4.smartview.renderer.drawer", false], [9, "module-ete4.smartview.renderer.face_positions", false], [9, "module-ete4.smartview.renderer.faces", false], [9, "module-ete4.smartview.renderer.layouts.context_layouts", false], [9, "module-ete4.smartview.renderer.layouts.default_layouts", false], [9, "module-ete4.smartview.renderer.layouts.domain_layouts", false], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false], [9, "module-ete4.smartview.renderer.layouts.seq_layouts", false], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false], [9, "module-ete4.smartview.renderer.layouts.staple_layouts", false], [9, "module-ete4.smartview.renderer.nodestyle", false], [9, "module-ete4.smartview.renderer.treelayout", false], [9, "module-ete4.smartview.renderer.treestyle", false], [12, "module-ete4.treematcher.treematcher", false], [13, "module-treeview", false]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move", false]], "name (tree attribute)": [[11, "ete4.Tree.name", false]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name", false]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare", false]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa", false]], "newickerror": [[6, "ete4.parser.newick.NewickError", false]], "nexuserror": [[6, "ete4.parser.nexus.NexusError", false]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html", false]], "node (walker property)": [[5, "ete4.core.operations.Walker.node", false]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id", false]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size", false]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size", false]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes", false]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle", false]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles", false]], "npanels (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.NPANELS", false]], "npanels (draweraligncircfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS", false]], "npanels (draweralignrectfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS", false]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit", false]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit", false]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window", false]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation", false]], "outlineface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.OutlineFace", false]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Padding", false]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents", false]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree", false]], "piechartface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.PieChartFace", false]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child", false]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate", false]], "populate() (tree method)": [[11, "ete4.Tree.populate", false]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform", false]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule", false]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile", false]], "prop_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.prop_repr", false]], "props (tree attribute)": [[11, "ete4.Tree.props", false]], "prune() (tree method)": [[11, "ete4.Tree.prune", false]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection", false]], "quote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.quote", false]], "read_content() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_content", false]], "read_nodes() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_nodes", false]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile", false]], "rectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.RectFace", false]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang", false]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove", false]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active", false]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade", false]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child", false]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children", false]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search", false]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection", false]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister", false]], "render() (tree method)": [[11, "ete4.Tree.render", false]], "repr_short() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.repr_short", false]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json", false]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy", false]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy", false]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results", false]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts", false]], "retrieve_tree_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data", false]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children", false]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds", false]], "root (tree attribute)": [[11, "ete4.Tree.root", false]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at", false]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview", false]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string", false]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval", false]], "safer_eval() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.safer_eval", false]], "scaleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ScaleFace", false]], "search() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.search", false]], "search() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.search", false]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors", false]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants", false]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name", false]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes", false]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection", false]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches", false]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected", false]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face", false]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos", false]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace", false]], "selectedface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedFace", false]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace", false]], "seqface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqFace", false]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup", false]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace", false]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function", false]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup", false]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style", false]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style", false]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style", false]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style", false]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style", false]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style", false]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style", false]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style", false]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style", false]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style", false]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style", false]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style", false]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style", false]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style", false]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style", false]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style", false]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style", false]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style", false]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style", false]], "set_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_outgroup", false]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup", false]], "set_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.set_seq", false]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function", false]], "set_style() (tree method)": [[11, "ete4.Tree.set_style", false]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style", false]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style", false]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style", false]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style", false]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style", false]], "show() (tree method)": [[11, "ete4.Tree.show", false]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette", false]], "size (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Size", false]], "size (tree attribute)": [[11, "ete4.Tree.size", false]], "skip_quoted_name() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_quoted_name", false]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_spaces_and_comments", false]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style", false]], "sort() (in module ete4.core.operations)": [[5, "ete4.core.operations.sort", false]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort", false]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants", false]], "species (phylotree property)": [[7, "ete4.PhyloTree.species", false]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups", false]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis", false]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack", false]], "stackedbarface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.StackedBarFace", false]], "standardize() (tree method)": [[11, "ete4.Tree.standardize", false]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active", false]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search", false]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection", false]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style", false]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary", false]], "support (tree attribute)": [[11, "ete4.Tree.support", false]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children", false]], "swap_props() (in module ete4.core.operations)": [[5, "ete4.core.operations.swap_props", false]], "textface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.TextFace", false]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer", false]], "to_dendrogram() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_dendrogram", false]], "to_str() (tree method)": [[11, "ete4.Tree.to_str", false]], "to_ultrametric() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_ultrametric", false]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric", false]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, 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(in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle", false]], "drawer (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Drawer", false]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces", false]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces", false]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc", false]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces", false]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRect", false]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces", false]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size", false]], "dump() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dump", false]], "dumps() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dumps", false]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx", false]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx", false]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy", false]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy", false]], "edges() (tree method)": [[11, "ete4.Tree.edges", false]], "error() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.error", false]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree", false]], "ete4.core.operations": [[5, "module-ete4.core.operations", false]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup", false]], "ete4.parser.newick": [[6, "module-ete4.parser.newick", false]], "ete4.parser.nexus": [[6, "module-ete4.parser.nexus", false]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server", false]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers", false]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer", false]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions", false]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces", false]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts", false]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts", false]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts", false]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts", false]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts", false]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle", false]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout", false]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle", false]], "ete4.treematcher.treematcher": [[12, "module-ete4.treematcher.treematcher", false]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent", false]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props", false]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies", false]], "explore() (tree method)": [[11, "ete4.Tree.explore", false]], "face (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.Face", false]], "faces (tree attribute)": [[11, "ete4.Tree.faces", false]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest", false]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant", false]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node", false]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value", false]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit", false]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits", false]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits", false]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits", false]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits", false]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits", false]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline", false]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline", false]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table", false]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio", false]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children", false]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade", false]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades", false]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age", false]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup", false]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec", false]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box", false]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box", false]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box", false]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box", false]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box", false]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches", false]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches", false]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content", false]], "get_children() (tree method)": [[11, "ete4.Tree.get_children", false]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf", false]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node", false]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color", false]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search", false]], "get_commands() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_commands", false]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names", false]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names", false]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content", false]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content", false]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context", false]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events", false]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa", false]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa", false]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance", false]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer", false]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers", false]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn", false]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active", false]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries", false]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search", false]], "get_extended_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_extended_props", false]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf", false]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node", false]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf", false]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node", false]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation", false]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype", false]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames", false]], "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", false]], "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", false]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname", false]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts", false]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters", false]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend", false]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type", false]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage", false]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage", false]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator", false]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator", false]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup", false]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic", false]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events", false]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage", false]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator", false]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator", false]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick", false]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port", false]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info", false]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline", false]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents", false]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser", false]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props", false]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop", false]], "get_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_props", false]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank", false]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank", false]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect", false]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function", false]], "get_section() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_section", false]], "get_sections() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_sections", false]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children", false]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info", false]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections", false]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq", false]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq", false]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq", false]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette", false]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters", false]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees", false]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species", false]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats", false]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator", false]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator", false]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid", false]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip", false]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search", false]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology", false]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology", false]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id", false]], "get_trees() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_trees", false]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file", false]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form", false]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick", false]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs", false]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys", false]], "globalstuff (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.GlobalStuff", false]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back", false]], "grid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.Grid", false]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa", false]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches", false]], "htmlface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.HTMLFace", false]], "id (tree attribute)": [[11, "ete4.Tree.id", false]], "img_style (tree property)": [[11, "ete4.Tree.img_style", false]], "imgface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ImgFace", false]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport", false]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport", false]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport", false]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props", false]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init", false]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete", false]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick", false]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize", false]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style", false]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized", false]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate", false]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references", false]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist", false]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles", false]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box", false]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment", false]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist", false]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed", false]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed", false]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized", false]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf", false]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic", false]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root", false]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small", false]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small", false]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries", false]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder", false]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species", false]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch", false]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error", false]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize", false]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize", false]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment", false]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName", false]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot", false]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName", false]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg", false]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength", false]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport", false]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard", false]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy", false]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName", false]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance", false]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.evol_events_layouts)": [[9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents", false]], "layoutgenomiccontext (class in ete4.smartview.renderer.layouts.context_layouts)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext", false]], "layouthumanogs (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs", false]], "layoutkeggenzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme", false]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule", false]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber", false]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor", false]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName", false]], "layoutnumberleaves (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves", false]], "layoutoutline (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline", false]], "layoutpdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains", false]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName", false]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName", false]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts", false]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName", false]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName", false]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains", false]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC", false]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans", false]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names", false]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles", false]], "leaves() (tree method)": [[11, "ete4.Tree.leaves", false]], "legendface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.LegendFace", false]], "level (tree attribute)": [[11, "ete4.Tree.level", false]], "lineage() (tree method)": [[11, "ete4.Tree.lineage", false]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment", false]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable", false]], "load() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.load", false]], "load() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.load", false]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree", false]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick", false]], "loads() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.loads", false]], "loads() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.loads", false]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance", false]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box", false]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces", false]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name", false]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name", false]], "make_parser() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.make_parser", false]], "match() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.match", false]], "match() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.match", false]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint", false]], "min_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE", false]], "module": [[4, "module-ete4.clustering.clustertree", false], [5, "module-ete4.core.operations", false], [6, "module-ete4.parser.newick", false], [6, "module-ete4.parser.nexus", false], [8, "module-ete4.core.seqgroup", false], [9, "module-ete4.smartview.gui.server", false], [9, "module-ete4.smartview.renderer.draw_helpers", false], [9, "module-ete4.smartview.renderer.drawer", false], [9, "module-ete4.smartview.renderer.face_positions", false], [9, "module-ete4.smartview.renderer.faces", false], [9, "module-ete4.smartview.renderer.layouts.context_layouts", false], [9, "module-ete4.smartview.renderer.layouts.default_layouts", false], [9, "module-ete4.smartview.renderer.layouts.domain_layouts", false], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false], [9, "module-ete4.smartview.renderer.layouts.seq_layouts", false], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false], [9, "module-ete4.smartview.renderer.layouts.staple_layouts", false], [9, "module-ete4.smartview.renderer.nodestyle", false], [9, "module-ete4.smartview.renderer.treelayout", false], [9, "module-ete4.smartview.renderer.treestyle", false], [12, "module-ete4.treematcher.treematcher", false], [13, "module-treeview", false]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move", false]], "name (tree attribute)": [[11, "ete4.Tree.name", false]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name", false]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare", false]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa", false]], "newickerror": [[6, "ete4.parser.newick.NewickError", false]], "nexuserror": [[6, "ete4.parser.nexus.NexusError", false]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html", false]], "node (walker property)": [[5, "ete4.core.operations.Walker.node", false]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id", false]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size", false]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size", false]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes", false]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle", false]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles", false]], "npanels (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.NPANELS", false]], "npanels (draweraligncircfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS", false]], "npanels (draweralignrectfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS", false]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit", false]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit", false]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window", false]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation", false]], "outlineface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.OutlineFace", false]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Padding", false]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents", false]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree", false]], "piechartface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.PieChartFace", false]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child", false]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate", false]], "populate() (tree method)": [[11, "ete4.Tree.populate", false]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform", false]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule", false]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile", false]], "prop_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.prop_repr", false]], "props (tree attribute)": [[11, "ete4.Tree.props", false]], "prune() (tree method)": [[11, "ete4.Tree.prune", false]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection", false]], "quote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.quote", false]], "read_content() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_content", false]], "read_nodes() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_nodes", false]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile", false]], "rectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.RectFace", false]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang", false]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove", false]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active", false]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade", false]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child", false]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children", false]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search", false]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection", false]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister", false]], "render() (tree method)": [[11, "ete4.Tree.render", false]], "repr_short() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.repr_short", false]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json", false]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy", false]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy", false]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results", false]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts", false]], "retrieve_tree_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data", false]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children", false]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds", false]], "root (tree attribute)": [[11, "ete4.Tree.root", false]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at", false]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview", false]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string", false]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval", false]], "safer_eval() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.safer_eval", false]], "scaleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ScaleFace", false]], "search() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.search", false]], "search() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.search", false]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors", false]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants", false]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name", false]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes", false]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection", false]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches", false]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected", false]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face", false]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos", false]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace", false]], "selectedface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedFace", false]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace", false]], "seqface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqFace", false]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup", false]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace", false]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function", false]], 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(layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style", false]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style", false]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style", false]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style", false]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style", false]], "set_node_style() (layoutnumberleaves method)": [[9, 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