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| 1 : | olson | 1.2 | # |
| 2 : | golsen | 1.8 | # Copyright (c) 2003-2007 University of Chicago and Fellowship |
| 3 : | olson | 1.2 | # for Interpretations of Genomes. All Rights Reserved. |
| 4 : | # | ||
| 5 : | # This file is part of the SEED Toolkit. | ||
| 6 : | golsen | 1.9 | # |
| 7 : | olson | 1.2 | # The SEED Toolkit is free software. You can redistribute |
| 8 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 9 : | golsen | 1.9 | # Public License. |
| 10 : | olson | 1.2 | # |
| 11 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 12 : | # along with this program; if not write to the University of Chicago | ||
| 13 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 14 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 15 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 16 : | # | ||
| 17 : | |||
| 18 : | golsen | 1.1 | package gjonewicklib; |
| 19 : | |||
| 20 : | #=============================================================================== | ||
| 21 : | # perl functions for dealing with trees | ||
| 22 : | # | ||
| 23 : | # Usage: | ||
| 24 : | # use gjonewicklib | ||
| 25 : | # | ||
| 26 : | # | ||
| 27 : | #=============================================================================== | ||
| 28 : | # Tree data structures: | ||
| 29 : | #=============================================================================== | ||
| 30 : | # | ||
| 31 : | # Elements in newick text file are: | ||
| 32 : | # | ||
| 33 : | # [c1] ( desc_1, desc_2, ... ) [c2] label [c3] : [c4] x [c5] | ||
| 34 : | # | ||
| 35 : | # Note that: | ||
| 36 : | golsen | 1.9 | # |
| 37 : | golsen | 1.1 | # Comment list 1 can exist on any subtree, but its association with |
| 38 : | # tree components can be upset by rerooting | ||
| 39 : | # Comment list 2 cannot exist without a descendant list | ||
| 40 : | # Comment list 3 cannot exist without a label | ||
| 41 : | # Comment lists 4 and 5 cannot exist without a branch length | ||
| 42 : | # | ||
| 43 : | # Elements in perl representation are: | ||
| 44 : | # | ||
| 45 : | # $tree = \@rootnode; | ||
| 46 : | # | ||
| 47 : | overbeek | 1.7 | # $node = [ \@desc, # reference to list of descendants |
| 48 : | golsen | 1.1 | # $label, # node label |
| 49 : | # $x, # branch length | ||
| 50 : | # \@c1, # reference to comment list 1 | ||
| 51 : | # \@c2, # reference to comment list 2 | ||
| 52 : | # \@c3, # reference to comment list 3 | ||
| 53 : | # \@c4, # reference to comment list 4 | ||
| 54 : | # \@c5 # reference to comment list 5 | ||
| 55 : | overbeek | 1.7 | # ] |
| 56 : | golsen | 1.1 | # |
| 57 : | # At present, no routine tests or enforces the length of the list (a single | ||
| 58 : | # element list could be a valid internal node). | ||
| 59 : | # | ||
| 60 : | # All empty lists can be [] or undef | ||
| 61 : | # | ||
| 62 : | # Putting the comments at the end allows a shorter list nearly all the | ||
| 63 : | # time, but is different from the prolog representation. | ||
| 64 : | # | ||
| 65 : | # | ||
| 66 : | overbeek | 1.7 | # Ross Overbeek has a different tree node structure: |
| 67 : | # | ||
| 68 : | # $node = [ Label, | ||
| 69 : | # DistanceToParent, | ||
| 70 : | # [ ParentPointer, ChildPointer1, ... ], | ||
| 71 : | # [ Name1\tVal1, Name2\tVal2, ... ] | ||
| 72 : | # ] | ||
| 73 : | # | ||
| 74 : | # So: | ||
| 75 : | # | ||
| 76 : | #=============================================================================== | ||
| 77 : | # Tree format interconversion: | ||
| 78 : | #=============================================================================== | ||
| 79 : | # | ||
| 80 : | golsen | 1.9 | # $bool = is_overbeek_tree( $tree ) |
| 81 : | # $bool = is_gjonewick_tree( $tree ) | ||
| 82 : | # | ||
| 83 : | overbeek | 1.7 | # $gjonewick = overbeek_to_gjonewick( $overbeek ) |
| 84 : | # $overbeek = gjonewick_to_overbeek( $gjonewick ) | ||
| 85 : | # | ||
| 86 : | golsen | 1.1 | #=============================================================================== |
| 87 : | # Tree data extraction: | ||
| 88 : | #=============================================================================== | ||
| 89 : | # | ||
| 90 : | # $listref = newick_desc_ref( $noderef ) | ||
| 91 : | # $label = newick_lbl( $noderef ) | ||
| 92 : | # $x = newick_x( $noderef ) | ||
| 93 : | # $listref = newick_c1( $noderef ) | ||
| 94 : | # $listref = newick_c2( $noderef ) | ||
| 95 : | # $listref = newick_c3( $noderef ) | ||
| 96 : | # $listref = newick_c4( $noderef ) | ||
| 97 : | # $listref = newick_c5( $noderef ) | ||
| 98 : | # | ||
| 99 : | # @desclist = newick_desc_list( $noderef ) | ||
| 100 : | # $n = newick_n_desc( $noderef ) | ||
| 101 : | # $descref = newick_desc_i( $noderef, $i ) # 1-based numbering | ||
| 102 : | # $bool = newick_is_tip( $noderef ) | ||
| 103 : | # | ||
| 104 : | # set_newick_desc_ref( $noderef, $listref ) | ||
| 105 : | # set_newick_lbl( $noderef, $label ) | ||
| 106 : | # set_newick_x( $noderef, $x ) | ||
| 107 : | # set_newick_c1( $noderef, $listref ) | ||
| 108 : | # set_newick_c2( $noderef, $listref ) | ||
| 109 : | # set_newick_c3( $noderef, $listref ) | ||
| 110 : | # set_newick_c4( $noderef, $listref ) | ||
| 111 : | # set_newick_c5( $noderef, $listref ) | ||
| 112 : | # set_newick_desc_list( $noderef, @desclist ) | ||
| 113 : | golsen | 1.9 | # set_newick_desc_i( $noderef1, $i, $noderef2 ) # 1-based numbering |
| 114 : | golsen | 1.8 | # |
| 115 : | # $bool = newick_is_valid( $noderef ) # verify that tree is valid | ||
| 116 : | golsen | 1.1 | # |
| 117 : | # $bool = newick_is_rooted( $noderef ) # 2 branches from root | ||
| 118 : | # $bool = newick_is_unrooted( $noderef ) # 3 or more branches from root | ||
| 119 : | # $bool = newick_is_tip_rooted( $noderef ) # 1 branch from root | ||
| 120 : | # $bool = newick_is_bifurcating( $noderef ) | ||
| 121 : | # | ||
| 122 : | # $n = newick_tip_count( $noderef ) | ||
| 123 : | # @tiprefs = newick_tip_ref_list( $noderef ) | ||
| 124 : | golsen | 1.9 | # \@tiprefs = newick_tip_ref_list( $noderef ) |
| 125 : | golsen | 1.1 | # @tips = newick_tip_list( $noderef ) |
| 126 : | golsen | 1.9 | # \@tips = newick_tip_list( $noderef ) |
| 127 : | # | ||
| 128 : | golsen | 1.1 | # $tipref = newick_first_tip_ref( $noderef ) |
| 129 : | # $tip = newick_first_tip( $noderef ) | ||
| 130 : | golsen | 1.9 | # |
| 131 : | golsen | 1.1 | # @tips = newick_duplicated_tips( $noderef ) |
| 132 : | golsen | 1.9 | # \@tips = newick_duplicated_tips( $noderef ) |
| 133 : | # | ||
| 134 : | golsen | 1.1 | # $bool = newick_tip_in_tree( $noderef, $tipname ) |
| 135 : | golsen | 1.9 | # |
| 136 : | golsen | 1.1 | # @tips = newick_shared_tips( $tree1, $tree2 ) |
| 137 : | golsen | 1.9 | # \@tips = newick_shared_tips( $tree1, $tree2 ) |
| 138 : | golsen | 1.1 | # |
| 139 : | # $length = newick_tree_length( $noderef ) | ||
| 140 : | golsen | 1.9 | # |
| 141 : | # %tip_distances = newick_tip_distances( $noderef ) | ||
| 142 : | # \%tip_distances = newick_tip_distances( $noderef ) | ||
| 143 : | # | ||
| 144 : | golsen | 1.1 | # $xmax = newick_max_X( $noderef ) |
| 145 : | # ( $tipref, $xmax ) = newick_most_distant_tip_ref( $noderef ) | ||
| 146 : | golsen | 1.9 | # ( $tipname, $xmax ) = newick_most_distant_tip_name( $noderef ) |
| 147 : | golsen | 1.1 | # |
| 148 : | golsen | 1.8 | # Tree tip insertion point (tip is on branch of length x that |
| 149 : | # is inserted into branch connecting node1 and node2, a distance | ||
| 150 : | # x1 from node1 and x2 from node2): | ||
| 151 : | # | ||
| 152 : | golsen | 1.9 | # [ $node1, $x1, $node2, $x2, $x ] = newick_tip_insertion_point( $tree, $tip ) |
| 153 : | golsen | 1.8 | # |
| 154 : | # Standardized label for a node in terms of intersection of 3 lowest sorting | ||
| 155 : | # tips (sort is lower case): | ||
| 156 : | # | ||
| 157 : | golsen | 1.9 | # @TipOrTips = std_node_name( $tree, $node ) |
| 158 : | golsen | 1.8 | # |
| 159 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 160 : | # Paths from root of tree: | ||
| 161 : | #------------------------------------------------------------------------------- | ||
| 162 : | # | ||
| 163 : | # Path descriptions are of form: | ||
| 164 : | # ( $node0, $i0, $node1, $i1, $node2, $i2, ..., $nodeN ) | ||
| 165 : | # () is returned upon failure | ||
| 166 : | # | ||
| 167 : | # @path = path_to_tip( $treenode, $tipname ) | ||
| 168 : | # @path = path_to_named_node( $treenode, $nodename ) | ||
| 169 : | # @path = path_to_node_ref( $treenode, $noderef ) | ||
| 170 : | # | ||
| 171 : | # @path = path_to_node( $node, $tip1, $tip2, $tip3 ) # 3 tip names | ||
| 172 : | # @path = path_to_node( $node, [ $tip1, $tip2, $tip3 ] ) # Array of tips | ||
| 173 : | # @path = path_to_node( $node, $tip1 ) # Use path_to_tip | ||
| 174 : | # @path = path_to_node( $node, [ $tip1 ] ) # Use path_to_tip | ||
| 175 : | # | ||
| 176 : | # $distance = newick_path_length( @path ) | ||
| 177 : | # $distance = tip_to_tip_distance( $tree, $tip1, $tip2 ) | ||
| 178 : | # $distance = node_to_node_distance( $tree, $node1, $node2 ) | ||
| 179 : | # | ||
| 180 : | # | ||
| 181 : | #=============================================================================== | ||
| 182 : | # Tree manipulations: | ||
| 183 : | #=============================================================================== | ||
| 184 : | # | ||
| 185 : | overbeek | 1.4 | # $treecopy = copy_newick_tree( $tree ) |
| 186 : | golsen | 1.1 | # |
| 187 : | #------------------------------------------------------------------------------- | ||
| 188 : | golsen | 1.8 | # The following modify the existing tree, and possibly any components of that |
| 189 : | golsen | 1.1 | # tree that are reached by reference. If the old version is still needed, copy |
| 190 : | # before modifying. | ||
| 191 : | #------------------------------------------------------------------------------- | ||
| 192 : | # | ||
| 193 : | # Modify labels: | ||
| 194 : | # | ||
| 195 : | # $newtree = newick_relabel_nodes( $node, \%new_name ) | ||
| 196 : | # $newtree = newick_relabel_nodes_i( $node, \%new_name ) | ||
| 197 : | # $newtree = newick_relabel_tips( $node, \%new_name ) | ||
| 198 : | # $newtree = newick_relabel_tips_i( $node, \%new_name ) | ||
| 199 : | # | ||
| 200 : | # Modify branches: | ||
| 201 : | # | ||
| 202 : | # $n_changed = newick_set_undefined_branches( $node, $x ) | ||
| 203 : | # $n_changed = newick_set_all_branches( $node, $x ) | ||
| 204 : | golsen | 1.5 | # $n_changed = newick_fix_negative_branches( $tree ) |
| 205 : | overbeek | 1.7 | # $node = newick_rescale_branches( $node, $factor ) |
| 206 : | golsen | 1.1 | # |
| 207 : | golsen | 1.8 | # Modify comments: |
| 208 : | # | ||
| 209 : | # $node = newick_strip_comments( $node ) | ||
| 210 : | # | ||
| 211 : | golsen | 1.1 | # Modify rooting and/or order: |
| 212 : | # | ||
| 213 : | # $nrmtree = normalize_newick_tree( $tree ) | ||
| 214 : | # $revtree = reverse_newick_tree( $tree ) | ||
| 215 : | # $stdtree = std_unrooted_newick( $tree ) | ||
| 216 : | # $newtree = aesthetic_newick_tree( $tree, $direction ) | ||
| 217 : | # $rndtree = random_order_newick_tree( $tree ) | ||
| 218 : | # $newtree = reroot_newick_by_path( @path ) | ||
| 219 : | # $newtree = reroot_newick_to_tip( $tree, $tip ) | ||
| 220 : | # $newtree = reroot_newick_next_to_tip( $tree, $tip ) | ||
| 221 : | # $newtree = reroot_newick_to_node( $tree, @node ) | ||
| 222 : | # $newtree = reroot_newick_to_node_ref( $tree, $noderef ) | ||
| 223 : | golsen | 1.9 | # $newtree = reroot_newick_between_nodes( $tree, $node1, $node2, $fraction ) |
| 224 : | golsen | 1.12 | # $newtree = reroot_newick_to_midpoint( $tree ) # unweighted |
| 225 : | # $newtree = reroot_newick_to_midpoint_w( $tree ) # weight by tips | ||
| 226 : | golsen | 1.5 | # $newtree = reroot_newick_to_approx_midpoint( $tree ) # unweighted |
| 227 : | # $newtree = reroot_newick_to_approx_midpoint_w( $tree ) # weight by tips | ||
| 228 : | golsen | 1.1 | # $newtree = uproot_tip_rooted_newick( $tree ) |
| 229 : | # $newtree = uproot_newick( $tree ) | ||
| 230 : | # | ||
| 231 : | # $newtree = prune_from_newick( $tree, $tip ) | ||
| 232 : | golsen | 1.12 | # $newtree = rooted_newick_subtree( $tree, @tips ) |
| 233 : | # $newtree = rooted_newick_subtree( $tree, \@tips ) | ||
| 234 : | golsen | 1.1 | # $newtree = newick_subtree( $tree, @tips ) |
| 235 : | # $newtree = newick_subtree( $tree, \@tips ) | ||
| 236 : | golsen | 1.12 | # $newtree = newick_covering_subtree( $tree, @tips ) |
| 237 : | # $newtree = newick_covering_subtree( $tree, \@tips ) | ||
| 238 : | golsen | 1.1 | # |
| 239 : | golsen | 1.5 | # $newtree = collapse_zero_length_branches( $tree ) |
| 240 : | # | ||
| 241 : | golsen | 1.8 | # $node = newick_insert_at_node( $node, $subtree ) |
| 242 : | # $tree = newick_insert_between_nodes( $tree, $subtree, $node1, $node2, $fraction ) | ||
| 243 : | # | ||
| 244 : | golsen | 1.1 | #=============================================================================== |
| 245 : | golsen | 1.9 | # Tree neighborhood: subtree of n tips to represent a larger tree. |
| 246 : | #=============================================================================== | ||
| 247 : | # | ||
| 248 : | # Focus around root: | ||
| 249 : | # | ||
| 250 : | # $subtree = root_neighborhood_representative_tree( $tree, $n, \%tip_priority ) | ||
| 251 : | # $subtree = root_neighborhood_representative_tree( $tree, $n ) | ||
| 252 : | # @tips = root_neighborhood_representative_tips( $tree, $n, \%tip_priority ) | ||
| 253 : | # @tips = root_neighborhood_representative_tips( $tree, $n ) | ||
| 254 : | # \@tips = root_neighborhood_representative_tips( $tree, $n, \%tip_priority ) | ||
| 255 : | # \@tips = root_neighborhood_representative_tips( $tree, $n ) | ||
| 256 : | # | ||
| 257 : | # Focus around a tip insertion point (the tip is not in the subtree): | ||
| 258 : | # | ||
| 259 : | # $subtree = tip_neighborhood_representative_tree( $tree, $tip, $n, \%tip_priority ) | ||
| 260 : | # $subtree = tip_neighborhood_representative_tree( $tree, $tip, $n ) | ||
| 261 : | # @tips = tip_neighborhood_representative_tips( $tree, $tip, $n, \%tip_priority ) | ||
| 262 : | # @tips = tip_neighborhood_representative_tips( $tree, $tip, $n ) | ||
| 263 : | # \@tips = tip_neighborhood_representative_tips( $tree, $tip, $n, \%tip_priority ) | ||
| 264 : | # \@tips = tip_neighborhood_representative_tips( $tree, $tip, $n ) | ||
| 265 : | # | ||
| 266 : | #=============================================================================== | ||
| 267 : | golsen | 1.1 | # Tree reading and writing: |
| 268 : | #=============================================================================== | ||
| 269 : | golsen | 1.9 | # Write machine-readable trees: |
| 270 : | golsen | 1.1 | # |
| 271 : | # writeNewickTree( $tree ) | ||
| 272 : | # writeNewickTree( $tree, $file ) | ||
| 273 : | overbeek | 1.7 | # writeNewickTree( $tree, \*FH ) |
| 274 : | # fwriteNewickTree( $file, $tree ) # Matches the C arg list for f... I/O | ||
| 275 : | golsen | 1.1 | # $treestring = swriteNewickTree( $tree ) |
| 276 : | # $treestring = formatNewickTree( $tree ) | ||
| 277 : | golsen | 1.9 | # |
| 278 : | # Write human-readable trees: | ||
| 279 : | # | ||
| 280 : | golsen | 1.1 | # @textlines = text_plot_newick( $node, $width, $min_dx, $dy ) |
| 281 : | # printer_plot_newick( $node, $file, $width, $min_dx, $dy ) | ||
| 282 : | # | ||
| 283 : | golsen | 1.9 | # Read trees: |
| 284 : | # | ||
| 285 : | overbeek | 1.7 | # $tree = read_newick_tree( $file ) # reads to a semicolon |
| 286 : | # @trees = read_newick_trees( $file ) # reads to end of file | ||
| 287 : | # $tree = parse_newick_tree_str( $string ) | ||
| 288 : | golsen | 1.1 | # |
| 289 : | #=============================================================================== | ||
| 290 : | |||
| 291 : | |||
| 292 : | golsen | 1.8 | use Carp; |
| 293 : | use Data::Dumper; | ||
| 294 : | golsen | 1.9 | use strict; |
| 295 : | golsen | 1.8 | |
| 296 : | golsen | 1.1 | require Exporter; |
| 297 : | |||
| 298 : | our @ISA = qw(Exporter); | ||
| 299 : | our @EXPORT = qw( | ||
| 300 : | golsen | 1.9 | is_overbeek_tree |
| 301 : | is_gjonewick_tree | ||
| 302 : | overbeek | 1.7 | overbeek_to_gjonewick |
| 303 : | gjonewick_to_overbeek | ||
| 304 : | golsen | 1.8 | newick_is_valid |
| 305 : | golsen | 1.1 | newick_is_rooted |
| 306 : | newick_is_unrooted | ||
| 307 : | tree_rooted_on_tip | ||
| 308 : | newick_is_bifurcating | ||
| 309 : | newick_tip_count | ||
| 310 : | golsen | 1.9 | newick_tip_ref_list |
| 311 : | golsen | 1.1 | newick_tip_list |
| 312 : | golsen | 1.9 | |
| 313 : | golsen | 1.1 | newick_first_tip |
| 314 : | newick_duplicated_tips | ||
| 315 : | newick_tip_in_tree | ||
| 316 : | newick_shared_tips | ||
| 317 : | |||
| 318 : | newick_tree_length | ||
| 319 : | golsen | 1.9 | newick_tip_distances |
| 320 : | golsen | 1.1 | newick_max_X |
| 321 : | newick_most_distant_tip_ref | ||
| 322 : | newick_most_distant_tip_name | ||
| 323 : | golsen | 1.9 | |
| 324 : | newick_tip_insertion_point | ||
| 325 : | |||
| 326 : | golsen | 1.1 | std_newick_name |
| 327 : | |||
| 328 : | path_to_tip | ||
| 329 : | path_to_named_node | ||
| 330 : | path_to_node_ref | ||
| 331 : | path_to_node | ||
| 332 : | |||
| 333 : | newick_path_length | ||
| 334 : | tip_to_tip_distance | ||
| 335 : | node_to_node_distance | ||
| 336 : | |||
| 337 : | overbeek | 1.4 | copy_newick_tree |
| 338 : | golsen | 1.1 | |
| 339 : | newick_relabel_nodes | ||
| 340 : | newick_relabel_nodes_i | ||
| 341 : | newick_relabel_tips | ||
| 342 : | newick_relabel_tips_i | ||
| 343 : | |||
| 344 : | newick_set_undefined_branches | ||
| 345 : | newick_set_all_branches | ||
| 346 : | golsen | 1.5 | newick_fix_negative_branches |
| 347 : | overbeek | 1.7 | newick_rescale_branches |
| 348 : | golsen | 1.1 | |
| 349 : | golsen | 1.8 | newick_strip_comments |
| 350 : | |||
| 351 : | golsen | 1.1 | normalize_newick_tree |
| 352 : | reverse_newick_tree | ||
| 353 : | std_unrooted_newick | ||
| 354 : | aesthetic_newick_tree | ||
| 355 : | unaesthetic_newick_tree | ||
| 356 : | random_order_newick_tree | ||
| 357 : | |||
| 358 : | reroot_newick_by_path | ||
| 359 : | reroot_newick_to_tip | ||
| 360 : | reroot_newick_next_to_tip | ||
| 361 : | reroot_newick_to_node | ||
| 362 : | reroot_newick_to_node_ref | ||
| 363 : | golsen | 1.9 | reroot_newick_between_nodes |
| 364 : | golsen | 1.12 | reroot_newick_to_midpoint |
| 365 : | reroot_newick_to_midpoint_w | ||
| 366 : | golsen | 1.1 | reroot_newick_to_approx_midpoint |
| 367 : | golsen | 1.5 | reroot_newick_to_approx_midpoint_w |
| 368 : | golsen | 1.1 | uproot_tip_rooted_newick |
| 369 : | uproot_newick | ||
| 370 : | |||
| 371 : | prune_from_newick | ||
| 372 : | golsen | 1.12 | rooted_newick_subtree |
| 373 : | golsen | 1.1 | newick_subtree |
| 374 : | golsen | 1.12 | newick_covering_subtree |
| 375 : | golsen | 1.5 | collapse_zero_length_branches |
| 376 : | golsen | 1.1 | |
| 377 : | golsen | 1.8 | newick_insert_at_node |
| 378 : | newick_insert_between_nodes | ||
| 379 : | |||
| 380 : | golsen | 1.9 | root_neighborhood_representative_tree |
| 381 : | root_neighborhood_representative_tips | ||
| 382 : | tip_neighborhood_representative_tree | ||
| 383 : | tip_neighborhood_representative_tips | ||
| 384 : | |||
| 385 : | golsen | 1.1 | writeNewickTree |
| 386 : | fwriteNewickTree | ||
| 387 : | strNewickTree | ||
| 388 : | formatNewickTree | ||
| 389 : | overbeek | 1.7 | |
| 390 : | read_newick_tree | ||
| 391 : | read_newick_trees | ||
| 392 : | golsen | 1.1 | parse_newick_tree_str |
| 393 : | |||
| 394 : | printer_plot_newick | ||
| 395 : | text_plot_newick | ||
| 396 : | ); | ||
| 397 : | |||
| 398 : | our @EXPORT_OK = qw( | ||
| 399 : | newick_desc_ref | ||
| 400 : | newick_lbl | ||
| 401 : | newick_x | ||
| 402 : | newick_c1 | ||
| 403 : | newick_c2 | ||
| 404 : | newick_c3 | ||
| 405 : | newick_c4 | ||
| 406 : | newick_c5 | ||
| 407 : | newick_desc_list | ||
| 408 : | newick_n_desc | ||
| 409 : | newick_desc_i | ||
| 410 : | newick_is_tip | ||
| 411 : | newick_is_valid | ||
| 412 : | |||
| 413 : | set_newick_desc_ref | ||
| 414 : | set_newick_lbl | ||
| 415 : | set_newick_x | ||
| 416 : | set_newick_c1 | ||
| 417 : | set_newick_c2 | ||
| 418 : | set_newick_c3 | ||
| 419 : | set_newick_c4 | ||
| 420 : | set_newick_c5 | ||
| 421 : | |||
| 422 : | set_newick_desc_list | ||
| 423 : | set_newick_desc_i | ||
| 424 : | |||
| 425 : | add_to_newick_branch | ||
| 426 : | dump_tree | ||
| 427 : | ); | ||
| 428 : | |||
| 429 : | |||
| 430 : | #------------------------------------------------------------------------------- | ||
| 431 : | # Internally used definitions | ||
| 432 : | #------------------------------------------------------------------------------- | ||
| 433 : | |||
| 434 : | sub array_ref { ref( $_[0] ) eq "ARRAY" } | ||
| 435 : | sub hash_ref { ref( $_[0] ) eq "HASH" } | ||
| 436 : | |||
| 437 : | |||
| 438 : | #=============================================================================== | ||
| 439 : | golsen | 1.9 | # Interconvert overbeek and gjonewick trees: |
| 440 : | overbeek | 1.7 | #=============================================================================== |
| 441 : | |||
| 442 : | golsen | 1.9 | sub is_overbeek_tree { array_ref( $_[0] ) && array_ref( $_[0]->[2] ) } |
| 443 : | |||
| 444 : | sub is_gjonewick_tree { array_ref( $_[0] ) && array_ref( $_[0]->[0] ) } | ||
| 445 : | |||
| 446 : | overbeek | 1.7 | sub overbeek_to_gjonewick |
| 447 : | { | ||
| 448 : | return () unless ref( $_[0] ) eq 'ARRAY'; | ||
| 449 : | my ( $lbl, $x, $desc ) = @{ $_[0] }; | ||
| 450 : | my ( undef, @desc ) = ( $desc && ref( $desc ) eq 'ARRAY' ) ? @$desc : (); | ||
| 451 : | [ [ map { overbeek_to_gjonewick( $_ ) } @desc ], $lbl, $x ] | ||
| 452 : | } | ||
| 453 : | |||
| 454 : | sub gjonewick_to_overbeek | ||
| 455 : | { | ||
| 456 : | return () unless ref( $_[0] ) eq 'ARRAY'; | ||
| 457 : | my ( $desc, $lbl, $x ) = @{ $_[0] }; | ||
| 458 : | my @desc = ( $desc && ref( $desc ) eq 'ARRAY' ) ? @$desc : (); | ||
| 459 : | my $parent = $_[1]; | ||
| 460 : | my $node = [ $lbl, $x, undef, [] ]; | ||
| 461 : | $node->[2] = [ $parent, map { gjonewick_to_overbeek( $_, $node ) } @desc ]; | ||
| 462 : | return $node; | ||
| 463 : | } | ||
| 464 : | |||
| 465 : | golsen | 1.9 | |
| 466 : | overbeek | 1.7 | #=============================================================================== |
| 467 : | golsen | 1.1 | # Extract tree structure values: |
| 468 : | #=============================================================================== | ||
| 469 : | # | ||
| 470 : | # $listref = newick_desc_ref( $noderef ) | ||
| 471 : | # $string = newick_lbl( $noderef ) | ||
| 472 : | # $real = newick_x( $noderef ) | ||
| 473 : | # $listref = newick_c1( $noderef ) | ||
| 474 : | # $listref = newick_c2( $noderef ) | ||
| 475 : | # $listref = newick_c3( $noderef ) | ||
| 476 : | # $listref = newick_c4( $noderef ) | ||
| 477 : | # $listref = newick_c5( $noderef ) | ||
| 478 : | # @list = newick_desc_list( $noderef ) | ||
| 479 : | # $int = newick_n_desc( $noderef ) | ||
| 480 : | # $listref = newick_desc_i( $noderef ) | ||
| 481 : | # $bool = node_is_tip( $noderef ) | ||
| 482 : | # $bool = node_is_valid( $noderef ) | ||
| 483 : | # | ||
| 484 : | #------------------------------------------------------------------------------- | ||
| 485 : | |||
| 486 : | golsen | 1.12 | sub newick_desc_ref { ref($_[0]) ? $_[0]->[0] : Carp::confess() } # = ${$_[0]}[0] |
| 487 : | golsen | 1.8 | sub newick_lbl { ref($_[0]) ? $_[0]->[1] : Carp::confess() } |
| 488 : | golsen | 1.12 | sub newick_x { ref($_[0]) ? $_[0]->[2] : Carp::confess() } |
| 489 : | golsen | 1.10 | sub newick_c1 { ref($_[0]) ? $_[0]->[3] : Carp::confess() } |
| 490 : | golsen | 1.12 | sub newick_c2 { ref($_[0]) ? $_[0]->[4] : Carp::confess() } |
| 491 : | sub newick_c3 { ref($_[0]) ? $_[0]->[5] : Carp::confess() } | ||
| 492 : | sub newick_c4 { ref($_[0]) ? $_[0]->[6] : Carp::confess() } | ||
| 493 : | sub newick_c5 { ref($_[0]) ? $_[0]->[7] : Carp::confess() } | ||
| 494 : | golsen | 1.1 | |
| 495 : | sub newick_desc_list { | ||
| 496 : | my $node = $_[0]; | ||
| 497 : | ! array_ref( $node ) ? undef : | ||
| 498 : | array_ref( $node->[0] ) ? @{ $node->[0] } : | ||
| 499 : | () ; | ||
| 500 : | } | ||
| 501 : | |||
| 502 : | sub newick_n_desc { | ||
| 503 : | my $node = $_[0]; | ||
| 504 : | ! array_ref( $node ) ? undef : | ||
| 505 : | array_ref( $node->[0] ) ? scalar @{ $node->[0] } : | ||
| 506 : | 0 ; | ||
| 507 : | } | ||
| 508 : | |||
| 509 : | sub newick_desc_i { | ||
| 510 : | my ( $node, $i ) = @_; | ||
| 511 : | ! array_ref( $node ) ? undef : | ||
| 512 : | array_ref( $node->[0] ) ? $node->[0]->[$i-1] : | ||
| 513 : | undef ; | ||
| 514 : | } | ||
| 515 : | |||
| 516 : | sub node_is_tip { | ||
| 517 : | my $node = $_[0]; | ||
| 518 : | ! array_ref( $node ) ? undef : # Not a node ref | ||
| 519 : | array_ref( $node->[0] ) ? @{ $node->[0] } == 0 : # Empty descend list? | ||
| 520 : | 1 ; # No descend list | ||
| 521 : | } | ||
| 522 : | |||
| 523 : | sub node_is_valid { # An array ref with nonempty descend list or a label | ||
| 524 : | my $node = $_[0]; | ||
| 525 : | array_ref( $node ) && ( array_ref( $node->[0] ) && @{ $node->[0] } | ||
| 526 : | || defined( $node->[1] ) | ||
| 527 : | ) | ||
| 528 : | } | ||
| 529 : | |||
| 530 : | |||
| 531 : | #------------------------------------------------------------------------------- | ||
| 532 : | # Set tree structure values | ||
| 533 : | #------------------------------------------------------------------------------- | ||
| 534 : | |||
| 535 : | sub set_newick_desc_ref { $_[0]->[0] = $_[1] } | ||
| 536 : | sub set_newick_lbl { $_[0]->[1] = $_[1] } | ||
| 537 : | sub set_newick_x { $_[0]->[2] = $_[1] } | ||
| 538 : | sub set_newick_c1 { $_[0]->[3] = $_[1] } | ||
| 539 : | sub set_newick_c2 { $_[0]->[4] = $_[1] } | ||
| 540 : | sub set_newick_c3 { $_[0]->[5] = $_[1] } | ||
| 541 : | sub set_newick_c4 { $_[0]->[6] = $_[1] } | ||
| 542 : | sub set_newick_c5 { $_[0]->[7] = $_[1] } | ||
| 543 : | |||
| 544 : | sub set_newick_desc_list { | ||
| 545 : | my $node = shift; | ||
| 546 : | array_ref( $node ) || return; | ||
| 547 : | if ( array_ref( $node->[0] ) ) { @{ $node->[0] } = @_ } | ||
| 548 : | else { $node->[0] = [ @_ ] } | ||
| 549 : | } | ||
| 550 : | |||
| 551 : | sub set_newick_desc_i { | ||
| 552 : | my ( $node1, $i, $node2 ) = @_; | ||
| 553 : | array_ref( $node1 ) && array_ref( $node2 ) || return; | ||
| 554 : | if ( array_ref( $node1->[0] ) ) { $node1->[0]->[$i-1] = $node2 } | ||
| 555 : | else { $node1->[0] = [ $node2 ] } | ||
| 556 : | } | ||
| 557 : | |||
| 558 : | |||
| 559 : | #=============================================================================== | ||
| 560 : | # Some tree property tests: | ||
| 561 : | #=============================================================================== | ||
| 562 : | golsen | 1.8 | # Tree is valid? |
| 563 : | # | ||
| 564 : | # $bool = newick_is_valid( $node, $verbose ) | ||
| 565 : | #------------------------------------------------------------------------------- | ||
| 566 : | sub newick_is_valid | ||
| 567 : | { | ||
| 568 : | my $node = shift; | ||
| 569 : | |||
| 570 : | if ( ! array_ref( $node ) ) | ||
| 571 : | { | ||
| 572 : | print STDERR "Node is not array reference\n" if $_[0]; | ||
| 573 : | return 0; | ||
| 574 : | } | ||
| 575 : | |||
| 576 : | my @node = @$node; | ||
| 577 : | if ( ! @node ) | ||
| 578 : | { | ||
| 579 : | print STDERR "Node is empty array reference\n" if $_[0]; | ||
| 580 : | return 0; | ||
| 581 : | } | ||
| 582 : | |||
| 583 : | # Must have descendant or label: | ||
| 584 : | |||
| 585 : | if ( ! ( array_ref( $node[0] ) && @{ $node[0] } ) && ! $node[2] ) | ||
| 586 : | { | ||
| 587 : | print STDERR "Node has neither descendant nor label\n" if $_[0]; | ||
| 588 : | return 0; | ||
| 589 : | } | ||
| 590 : | |||
| 591 : | # If comments are present, they must be array references | ||
| 592 : | |||
| 593 : | foreach ( ( @node > 3 ) ? @node[ 3 .. $#node ] : () ) | ||
| 594 : | { | ||
| 595 : | if ( defined( $_ ) && ! array_ref( $_ ) ) | ||
| 596 : | { | ||
| 597 : | print STDERR "Node has neither descendant or label\n" if $_[0]; | ||
| 598 : | return 0; | ||
| 599 : | } | ||
| 600 : | } | ||
| 601 : | |||
| 602 : | # Inspect the descendants: | ||
| 603 : | |||
| 604 : | foreach ( array_ref( $node[0] ) ? @{ $node[0] } : () ) | ||
| 605 : | { | ||
| 606 : | newick_is_valid( $_, @_ ) || return 0 | ||
| 607 : | } | ||
| 608 : | |||
| 609 : | return 1; | ||
| 610 : | } | ||
| 611 : | |||
| 612 : | |||
| 613 : | #------------------------------------------------------------------------------- | ||
| 614 : | golsen | 1.1 | # Tree is rooted (2 branches at root node)? |
| 615 : | # | ||
| 616 : | # $bool = newick_is_rooted( $node ) | ||
| 617 : | #------------------------------------------------------------------------------- | ||
| 618 : | sub newick_is_rooted { | ||
| 619 : | my $node = $_[0]; | ||
| 620 : | ! array_ref( $node ) ? undef : # Not a node ref | ||
| 621 : | array_ref( $node->[0] ) ? @{ $node->[0] } == 2 : # 2 branches | ||
| 622 : | 0 ; # No descend list | ||
| 623 : | } | ||
| 624 : | |||
| 625 : | |||
| 626 : | #------------------------------------------------------------------------------- | ||
| 627 : | # Tree is unrooted (> 2 branches at root node)? | ||
| 628 : | # | ||
| 629 : | # $bool = newick_is_unrooted( $node ) | ||
| 630 : | #------------------------------------------------------------------------------- | ||
| 631 : | sub newick_is_unrooted { | ||
| 632 : | my $node = $_[0]; | ||
| 633 : | ! array_ref( $node ) ? undef : # Not a node ref | ||
| 634 : | array_ref( $node->[0] ) ? @{ $node->[0] } >= 3 : # Over 2 branches | ||
| 635 : | 0 ; # No descend list | ||
| 636 : | } | ||
| 637 : | |||
| 638 : | |||
| 639 : | #------------------------------------------------------------------------------- | ||
| 640 : | # Tree is rooted on a tip (1 branch at root node)? | ||
| 641 : | # | ||
| 642 : | # $bool = newick_is_tip_rooted( $node ) | ||
| 643 : | #------------------------------------------------------------------------------- | ||
| 644 : | sub newick_is_tip_rooted { | ||
| 645 : | my $node = $_[0]; | ||
| 646 : | ! array_ref( $node ) ? undef : # Not a node ref | ||
| 647 : | array_ref( $node->[0] ) ? @{ $node->[0] } == 1 : # 1 branch | ||
| 648 : | 0 ; # No descend list | ||
| 649 : | } | ||
| 650 : | |||
| 651 : | #=============================================================================== | ||
| 652 : | # Everything below this point refers to parts of the tree structure using | ||
| 653 : | # only the routines above. | ||
| 654 : | #=============================================================================== | ||
| 655 : | # Tree is bifurcating? If so, return number of descendents of root node. | ||
| 656 : | # | ||
| 657 : | # $n_desc = newick_is_bifurcating( $node ) | ||
| 658 : | #------------------------------------------------------------------------------- | ||
| 659 : | sub newick_is_bifurcating { | ||
| 660 : | my ( $node, $not_root ) = @_; | ||
| 661 : | if ( ! array_ref( $node ) ) { return undef } # Bad arg | ||
| 662 : | |||
| 663 : | my $n = newick_n_desc( $node ); | ||
| 664 : | $n == 0 && ! $not_root ? 0 : | ||
| 665 : | $n == 1 && $not_root ? 0 : | ||
| 666 : | $n == 3 && $not_root ? 0 : | ||
| 667 : | $n > 3 ? 0 : | ||
| 668 : | $n > 2 && ! newick_is_bifurcating( newick_desc_i( $node, 3, 1 ) ) ? 0 : | ||
| 669 : | $n > 1 && ! newick_is_bifurcating( newick_desc_i( $node, 2, 1 ) ) ? 0 : | ||
| 670 : | $n > 0 && ! newick_is_bifurcating( newick_desc_i( $node, 1, 1 ) ) ? 0 : | ||
| 671 : | $n | ||
| 672 : | } | ||
| 673 : | |||
| 674 : | |||
| 675 : | #------------------------------------------------------------------------------- | ||
| 676 : | # Number of tips: | ||
| 677 : | # | ||
| 678 : | # $n = newick_tip_count( $node ) | ||
| 679 : | #------------------------------------------------------------------------------- | ||
| 680 : | sub newick_tip_count { | ||
| 681 : | my ( $node, $not_root ) = @_; | ||
| 682 : | |||
| 683 : | my $imax = newick_n_desc( $node ); | ||
| 684 : | if ( $imax < 1 ) { return 1 } | ||
| 685 : | |||
| 686 : | # Special case for tree rooted on tip | ||
| 687 : | |||
| 688 : | my $n = ( $imax == 1 && ( ! $not_root ) ) ? 1 : 0; | ||
| 689 : | |||
| 690 : | foreach ( newick_desc_list( $node ) ) { $n += newick_tip_count( $_, 1 ) } | ||
| 691 : | |||
| 692 : | $n; | ||
| 693 : | } | ||
| 694 : | |||
| 695 : | |||
| 696 : | #------------------------------------------------------------------------------- | ||
| 697 : | # List of tip nodes: | ||
| 698 : | # | ||
| 699 : | golsen | 1.9 | # @tips = newick_tip_ref_list( $noderef ) |
| 700 : | # \@tips = newick_tip_ref_list( $noderef ) | ||
| 701 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 702 : | sub newick_tip_ref_list { | ||
| 703 : | my ( $node, $not_root ) = @_; | ||
| 704 : | |||
| 705 : | my $imax = newick_n_desc( $node ); | ||
| 706 : | if ( $imax < 1 ) { return $node } | ||
| 707 : | |||
| 708 : | my @list = (); | ||
| 709 : | |||
| 710 : | # Tree rooted on tip? | ||
| 711 : | if ( $imax == 1 && ! $not_root && newick_lbl( $node ) ) { push @list, $node } | ||
| 712 : | |||
| 713 : | foreach ( newick_desc_list( $node ) ) { | ||
| 714 : | push @list, newick_tip_ref_list( $_, 1 ); | ||
| 715 : | } | ||
| 716 : | |||
| 717 : | golsen | 1.9 | wantarray ? @list : \@list; |
| 718 : | golsen | 1.1 | } |
| 719 : | |||
| 720 : | |||
| 721 : | #------------------------------------------------------------------------------- | ||
| 722 : | # List of tips: | ||
| 723 : | # | ||
| 724 : | # @tips = newick_tip_list( $node ) | ||
| 725 : | golsen | 1.9 | # \@tips = newick_tip_list( $node ) |
| 726 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 727 : | sub newick_tip_list { | ||
| 728 : | golsen | 1.9 | my @tips = map { newick_lbl( $_ ) } newick_tip_ref_list( $_[0] ); |
| 729 : | wantarray ? @tips : \@tips; | ||
| 730 : | golsen | 1.1 | } |
| 731 : | |||
| 732 : | |||
| 733 : | #------------------------------------------------------------------------------- | ||
| 734 : | # First tip node in tree: | ||
| 735 : | # | ||
| 736 : | # $tipref = newick_first_tip_ref( $node ) | ||
| 737 : | #------------------------------------------------------------------------------- | ||
| 738 : | sub newick_first_tip_ref { | ||
| 739 : | my ( $node, $not_root ) = @_; | ||
| 740 : | valid_node( $node ) || return undef; | ||
| 741 : | |||
| 742 : | # Arrived at tip, or start of a tip-rooted tree? | ||
| 743 : | my $n = newick_n_desc( $node ); | ||
| 744 : | if ( ( $n < 1 ) || ( $n == 1 && ! $not_root ) ) { return $node } | ||
| 745 : | |||
| 746 : | newick_first_tip_ref( newick_desc_i( $node, 1 ), 1 ); | ||
| 747 : | } | ||
| 748 : | |||
| 749 : | |||
| 750 : | #------------------------------------------------------------------------------- | ||
| 751 : | # First tip name in tree: | ||
| 752 : | # | ||
| 753 : | # $tip = newick_first_tip( $node ) | ||
| 754 : | #------------------------------------------------------------------------------- | ||
| 755 : | sub newick_first_tip { | ||
| 756 : | my ( $noderef ) = @_; | ||
| 757 : | |||
| 758 : | my $tipref; | ||
| 759 : | array_ref( $tipref = newick_first_tip_ref( $noderef ) ) ? newick_lbl( $tipref ) | ||
| 760 : | golsen | 1.9 | : undef; |
| 761 : | golsen | 1.1 | } |
| 762 : | |||
| 763 : | |||
| 764 : | #------------------------------------------------------------------------------- | ||
| 765 : | # List of duplicated tip labels. | ||
| 766 : | # | ||
| 767 : | # @tips = newick_duplicated_tips( $node ) | ||
| 768 : | golsen | 1.9 | # \@tips = newick_duplicated_tips( $node ) |
| 769 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 770 : | sub newick_duplicated_tips { | ||
| 771 : | golsen | 1.9 | my @tips = &duplicates( newick_tip_list( $_[0] ) ); |
| 772 : | wantarray ? @tips : \@tips; | ||
| 773 : | golsen | 1.1 | } |
| 774 : | |||
| 775 : | |||
| 776 : | #------------------------------------------------------------------------------- | ||
| 777 : | # Tip in tree? | ||
| 778 : | # | ||
| 779 : | # $bool = newick_tip_in_tree( $node, $tipname ) | ||
| 780 : | #------------------------------------------------------------------------------- | ||
| 781 : | sub newick_tip_in_tree { | ||
| 782 : | my ( $node, $tip, $not_root ) = @_; | ||
| 783 : | |||
| 784 : | my $n = newick_n_desc( $node ); | ||
| 785 : | if ( $n < 1 ) { return ( newick_lbl( $node ) eq $tip) ? 1 : 0 } | ||
| 786 : | |||
| 787 : | # Special case for tree rooted on tip | ||
| 788 : | |||
| 789 : | if ( $n == 1 && ( ! $not_root ) && newick_lbl( $node ) eq $tip ) { return 1 } | ||
| 790 : | |||
| 791 : | foreach ( newick_desc_list( $node ) ) { | ||
| 792 : | if ( newick_tip_in_tree( $_, $tip, 1 ) ) { return 1 } | ||
| 793 : | } | ||
| 794 : | |||
| 795 : | 0; # Fall through means not found | ||
| 796 : | } | ||
| 797 : | |||
| 798 : | |||
| 799 : | #------------------------------------------------------------------------------- | ||
| 800 : | # Tips shared between 2 trees. | ||
| 801 : | # | ||
| 802 : | # @tips = newick_shared_tips( $tree1, $tree2 ) | ||
| 803 : | golsen | 1.9 | # \@tips = newick_shared_tips( $tree1, $tree2 ) |
| 804 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 805 : | sub newick_shared_tips { | ||
| 806 : | golsen | 1.9 | my ( $tree1, $tree2 ) = @_; |
| 807 : | my $tips1 = newick_tip_list( $tree1 ); | ||
| 808 : | my $tips2 = newick_tip_list( $tree2 ); | ||
| 809 : | my @tips = &intersection( $tips1, $tips2 ); | ||
| 810 : | wantarray ? @tips : \@tips; | ||
| 811 : | golsen | 1.1 | } |
| 812 : | |||
| 813 : | |||
| 814 : | #------------------------------------------------------------------------------- | ||
| 815 : | # Tree length. | ||
| 816 : | # | ||
| 817 : | # $length = newick_tree_length( $node ) | ||
| 818 : | #------------------------------------------------------------------------------- | ||
| 819 : | sub newick_tree_length { | ||
| 820 : | my ( $node, $not_root ) = @_; | ||
| 821 : | |||
| 822 : | my $x = $not_root ? newick_x( $node ) : 0; | ||
| 823 : | defined( $x ) || ( $x = 1 ); # Convert undefined to 1 | ||
| 824 : | |||
| 825 : | foreach ( newick_desc_list( $node ) ) { $x += newick_tree_length( $_, 1 ) } | ||
| 826 : | |||
| 827 : | $x; | ||
| 828 : | } | ||
| 829 : | |||
| 830 : | |||
| 831 : | #------------------------------------------------------------------------------- | ||
| 832 : | golsen | 1.9 | # Hash of tip nodes and corresponding distances from root: |
| 833 : | # | ||
| 834 : | # %tip_distances = newick_tip_distances( $node ) | ||
| 835 : | # \%tip_distances = newick_tip_distances( $node ) | ||
| 836 : | #------------------------------------------------------------------------------- | ||
| 837 : | sub newick_tip_distances | ||
| 838 : | { | ||
| 839 : | my ( $node, $x, $hash ) = @_; | ||
| 840 : | my $root = ! $hash; | ||
| 841 : | ref( $hash ) eq 'HASH' or $hash = {}; | ||
| 842 : | |||
| 843 : | $x ||= 0; | ||
| 844 : | $x += newick_x( $node ) || 0; | ||
| 845 : | |||
| 846 : | # Is it a tip? | ||
| 847 : | |||
| 848 : | my $n_desc = newick_n_desc( $node ); | ||
| 849 : | if ( ! $n_desc ) | ||
| 850 : | { | ||
| 851 : | $hash->{ newick_lbl( $node ) } = $x; | ||
| 852 : | return $hash; | ||
| 853 : | } | ||
| 854 : | |||
| 855 : | # Tree rooted on tip? | ||
| 856 : | |||
| 857 : | if ( ( $n_desc == 1 ) && $root && ( newick_lbl( $node ) ) ) | ||
| 858 : | { | ||
| 859 : | $hash->{ newick_lbl( $node ) } = 0; # Distance to root is zero | ||
| 860 : | } | ||
| 861 : | |||
| 862 : | foreach ( newick_desc_list( $node ) ) | ||
| 863 : | { | ||
| 864 : | newick_tip_distances( $_, $x, $hash ); | ||
| 865 : | } | ||
| 866 : | |||
| 867 : | wantarray ? %$hash : $hash; | ||
| 868 : | } | ||
| 869 : | |||
| 870 : | |||
| 871 : | #------------------------------------------------------------------------------- | ||
| 872 : | golsen | 1.1 | # Tree max X. |
| 873 : | # | ||
| 874 : | # $xmax = newick_max_X( $node ) | ||
| 875 : | #------------------------------------------------------------------------------- | ||
| 876 : | sub newick_max_X { | ||
| 877 : | my ( $node, $not_root ) = @_; | ||
| 878 : | |||
| 879 : | my $xmax = 0; | ||
| 880 : | foreach ( newick_desc_list( $node ) ) { | ||
| 881 : | my $x = newick_max_X( $_, 1 ); | ||
| 882 : | if ( $x > $xmax ) { $xmax = $x } | ||
| 883 : | } | ||
| 884 : | |||
| 885 : | my $x = $not_root ? newick_x( $node ) : 0; | ||
| 886 : | $xmax + ( defined( $x ) ? $x : 1 ); # Convert undefined to 1 | ||
| 887 : | } | ||
| 888 : | |||
| 889 : | |||
| 890 : | #------------------------------------------------------------------------------- | ||
| 891 : | # Most distant tip from root: distance and path. | ||
| 892 : | # | ||
| 893 : | # ( $xmax, @path ) = newick_most_distant_tip_path( $tree ) | ||
| 894 : | #------------------------------------------------------------------------------- | ||
| 895 : | sub newick_most_distant_tip_path { | ||
| 896 : | my ( $node, $not_root ) = @_; | ||
| 897 : | |||
| 898 : | my $imax = newick_n_desc( $node ); | ||
| 899 : | my $xmax = ( $imax > 0 ) ? -1 : 0; | ||
| 900 : | my @pmax = (); | ||
| 901 : | for ( my $i = 1; $i <= $imax; $i++ ) { | ||
| 902 : | my ( $x, @path ) = newick_most_distant_tip_path( newick_desc_i( $node, $i ), 1 ); | ||
| 903 : | if ( $x > $xmax ) { $xmax = $x; @pmax = ( $i, @path ) } | ||
| 904 : | } | ||
| 905 : | |||
| 906 : | my $x = $not_root ? newick_x( $node ) : 0; | ||
| 907 : | $xmax += defined( $x ) ? $x : 0; # Convert undefined to 1 | ||
| 908 : | ( $xmax, $node, @pmax ); | ||
| 909 : | } | ||
| 910 : | |||
| 911 : | |||
| 912 : | #------------------------------------------------------------------------------- | ||
| 913 : | # Most distant tip from root, and its distance. | ||
| 914 : | # | ||
| 915 : | # ( $tipref, $xmax ) = newick_most_distant_tip_ref( $tree ) | ||
| 916 : | #------------------------------------------------------------------------------- | ||
| 917 : | sub newick_most_distant_tip_ref { | ||
| 918 : | my ( $node, $not_root ) = @_; | ||
| 919 : | |||
| 920 : | my $imax = newick_n_desc( $node ); | ||
| 921 : | my $xmax = ( $imax > 0 ) ? -1 : 0; | ||
| 922 : | my $tmax = $node; | ||
| 923 : | foreach ( newick_desc_list( $node ) ) { | ||
| 924 : | my ( $t, $x ) = newick_most_distant_tip_ref( $_, 1 ); | ||
| 925 : | if ( $x > $xmax ) { $xmax = $x; $tmax = $t } | ||
| 926 : | } | ||
| 927 : | |||
| 928 : | my $x = $not_root ? newick_x( $node ) : 0; | ||
| 929 : | $xmax += defined( $x ) ? $x : 1; # Convert undefined to 1 | ||
| 930 : | ( $tmax, $xmax ); | ||
| 931 : | } | ||
| 932 : | |||
| 933 : | |||
| 934 : | #------------------------------------------------------------------------------- | ||
| 935 : | # Name of most distant tip from root, and its distance. | ||
| 936 : | # | ||
| 937 : | # ( $tipname, $xmax ) = newick_most_distant_tip_name( $tree ) | ||
| 938 : | #------------------------------------------------------------------------------- | ||
| 939 : | sub newick_most_distant_tip_name { | ||
| 940 : | my ( $tipref, $xmax ) = newick_most_distant_tip_ref( $_[0] ); | ||
| 941 : | ( newick_lbl( $tipref ), $xmax ) | ||
| 942 : | } | ||
| 943 : | |||
| 944 : | |||
| 945 : | #------------------------------------------------------------------------------- | ||
| 946 : | golsen | 1.8 | # Tree tip insertion point (with standard node labels): |
| 947 : | # | ||
| 948 : | # [ $node1, $x1, $node2, $x2, $x ] | ||
| 949 : | # = newick_tip_insertion_point( $tree, $tip ) | ||
| 950 : | # | ||
| 951 : | # Which means: tip is on a branch of length x that is inserted into the branch | ||
| 952 : | # connecting node1 and node2, at distance x1 from node1 and x2 from node2. | ||
| 953 : | # | ||
| 954 : | # x1 +------ n1a (lowest sorting tip of this subtree) | ||
| 955 : | # +--------n1 | ||
| 956 : | # | +------n1b (lowest sorting tip of this subtree) | ||
| 957 : | # tip-------n | ||
| 958 : | # x | +------------- n2a (lowest sorting tip of this subtree) | ||
| 959 : | # +------n2 | ||
| 960 : | # x2 +-------- n2b (lowest sorting tip of this subtree) | ||
| 961 : | # | ||
| 962 : | # The designations of 1 vs 2, and a vs b are chosen such that: | ||
| 963 : | # n1a < n1b, and n2a < n2b, and n1a < n2a | ||
| 964 : | # | ||
| 965 : | # Then the statandard description becomes: | ||
| 966 : | # | ||
| 967 : | # [ [ $n1a, min(n1b,n2a), max(n1b,n2a) ], x1, | ||
| 968 : | # [ $n2a, min(n2b,n1a), max(n2b,n1a) ], x2, | ||
| 969 : | # x | ||
| 970 : | # ] | ||
| 971 : | # | ||
| 972 : | #------------------------------------------------------------------------------- | ||
| 973 : | sub newick_tip_insertion_point | ||
| 974 : | { | ||
| 975 : | my ( $tree, $tip ) = @_; | ||
| 976 : | $tree && $tip && ref( $tree ) eq 'ARRAY' or return undef; | ||
| 977 : | $tree = copy_newick_tree( $tree ) or return undef; | ||
| 978 : | $tree = reroot_newick_to_tip( $tree, $tip ) or return undef; | ||
| 979 : | my $node = $tree; | ||
| 980 : | |||
| 981 : | my $x = 0; # Distance to node | ||
| 982 : | my $dl = newick_desc_ref( $node ); # Descendent list of tip node; | ||
| 983 : | $node = $dl->[0]; # Node adjacent to tip | ||
| 984 : | $dl = newick_desc_ref( $node ); | ||
| 985 : | while ( $dl && ( @$dl == 1 ) ) # Traverse unbranched nodes | ||
| 986 : | { | ||
| 987 : | $node = $dl->[0]; | ||
| 988 : | $x += newick_x( $node ); | ||
| 989 : | $dl = newick_desc_ref( $node ); | ||
| 990 : | } | ||
| 991 : | $x += newick_x( $node ); | ||
| 992 : | |||
| 993 : | # We are now at the node that is the insertion point. | ||
| 994 : | # Is it a tip? | ||
| 995 : | |||
| 996 : | my @description; | ||
| 997 : | |||
| 998 : | if ( ( ! $dl ) || @$dl == 0 ) | ||
| 999 : | { | ||
| 1000 : | @description = ( [ newick_lbl( $node ) ], 0, undef, 0, $x ); | ||
| 1001 : | } | ||
| 1002 : | |||
| 1003 : | # Is it a trifurcation or greater, in which case it does not go | ||
| 1004 : | # away with tip deletion? | ||
| 1005 : | |||
| 1006 : | elsif ( @$dl > 2 ) | ||
| 1007 : | { | ||
| 1008 : | @description = ( [ std_node_name( $node, $node ) ], 0, undef, 0, $x ); | ||
| 1009 : | } | ||
| 1010 : | |||
| 1011 : | # The node is bifurcating. We need to describe it. | ||
| 1012 : | |||
| 1013 : | else | ||
| 1014 : | { | ||
| 1015 : | golsen | 1.9 | my ( $n1, $x1 ) = describe_descendant( $dl->[0] ); |
| 1016 : | my ( $n2, $x2 ) = describe_descendant( $dl->[1] ); | ||
| 1017 : | golsen | 1.8 | |
| 1018 : | if ( @$n1 == 2 ) { push @$n1, $n2->[0] } | ||
| 1019 : | if ( @$n2 == 2 ) | ||
| 1020 : | { | ||
| 1021 : | @$n2 = sort { lc $a cmp lc $b } ( @$n2, $n1->[0] ); | ||
| 1022 : | } | ||
| 1023 : | if ( @$n1 == 3 ) { @$n2 = sort { lc $a cmp lc $b } @$n2 } | ||
| 1024 : | @description = ( $n1, $x1, $n2, $x2, $x ); | ||
| 1025 : | } | ||
| 1026 : | |||
| 1027 : | return wantarray ? @description : \@description; | ||
| 1028 : | } | ||
| 1029 : | |||
| 1030 : | |||
| 1031 : | golsen | 1.9 | sub describe_descendant |
| 1032 : | golsen | 1.8 | { |
| 1033 : | my $node = shift; | ||
| 1034 : | |||
| 1035 : | my $x = 0; # Distance to node | ||
| 1036 : | my $dl = newick_desc_ref( $node ); # Descendent list of tip node; | ||
| 1037 : | while ( $dl && ( @$dl == 1 ) ) # Traverse unbranched nodes | ||
| 1038 : | { | ||
| 1039 : | $node = $dl->[0]; | ||
| 1040 : | golsen | 1.9 | $x += newick_x( $node ); |
| 1041 : | golsen | 1.8 | $dl = newick_desc_ref( $node ); |
| 1042 : | } | ||
| 1043 : | $x += newick_x( $node ); | ||
| 1044 : | |||
| 1045 : | # Is it a tip? Return list of one tip; | ||
| 1046 : | |||
| 1047 : | if ( ( ! $dl ) || @$dl == 0 ) | ||
| 1048 : | { | ||
| 1049 : | return ( [ newick_lbl( $node ) ], $x ); | ||
| 1050 : | } | ||
| 1051 : | |||
| 1052 : | # Get tips of each descendent, keeping lowest sorting from each. | ||
| 1053 : | # Return the two lowest of those (the third will come from the | ||
| 1054 : | # other side of the original node). | ||
| 1055 : | |||
| 1056 : | golsen | 1.9 | my @rep_tips = sort { lc $a cmp lc $b } |
| 1057 : | map { ( sort { lc $a cmp lc $b } newick_tip_list( $_ ) )[0] } | ||
| 1058 : | @$dl; | ||
| 1059 : | return ( [ @rep_tips[0,1] ], $x ); | ||
| 1060 : | golsen | 1.8 | } |
| 1061 : | |||
| 1062 : | |||
| 1063 : | #------------------------------------------------------------------------------- | ||
| 1064 : | golsen | 1.1 | # Standard node name: |
| 1065 : | # Tip label if at a tip | ||
| 1066 : | # Three sorted tip labels intersecting at node, each being smallest | ||
| 1067 : | # of all the tips of their subtrees | ||
| 1068 : | # | ||
| 1069 : | golsen | 1.9 | # @TipOrTips = std_node_name( $tree, $node ) |
| 1070 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 1071 : | sub std_node_name { | ||
| 1072 : | my $tree = $_[0]; | ||
| 1073 : | |||
| 1074 : | # Node reference is last element of path to node | ||
| 1075 : | |||
| 1076 : | my $noderef = ( path_to_node( @_ ) )[-1]; | ||
| 1077 : | defined( $noderef ) || return (); | ||
| 1078 : | |||
| 1079 : | if ( node_is_tip( $noderef ) || $noderef eq $tree ) { # Is it a tip? | ||
| 1080 : | return newick_lbl( $noderef ); | ||
| 1081 : | } | ||
| 1082 : | |||
| 1083 : | # Work through lists of tips in descendant subtrees, removing them from | ||
| 1084 : | # @rest, and keeping the best tip for each subtree. | ||
| 1085 : | |||
| 1086 : | golsen | 1.8 | my @rest = newick_tip_list( $tree ); |
| 1087 : | golsen | 1.9 | my @best = map |
| 1088 : | { | ||
| 1089 : | golsen | 1.8 | my @tips = sort { lc $a cmp lc $b } newick_tip_list( $_ ); |
| 1090 : | golsen | 1.9 | @rest = &set_difference( \@rest, \@tips ); |
| 1091 : | golsen | 1.1 | $tips[0]; |
| 1092 : | golsen | 1.9 | } newick_desc_list( $noderef ); |
| 1093 : | golsen | 1.1 | |
| 1094 : | # Best of the rest of the tree | ||
| 1095 : | push @best, ( sort { lc $a cmp lc $b } @rest )[0]; | ||
| 1096 : | |||
| 1097 : | # Take the top 3, in order: | ||
| 1098 : | |||
| 1099 : | ( @best >= 3 ) ? ( sort { lc $a cmp lc $b } @best )[0 .. 2] : (); | ||
| 1100 : | } | ||
| 1101 : | |||
| 1102 : | |||
| 1103 : | #=============================================================================== | ||
| 1104 : | # Functions to find paths in trees. | ||
| 1105 : | # | ||
| 1106 : | # Path descriptions are of form: | ||
| 1107 : | # ( $node0, $i0, $node1, $i1, $node2, $i2, ..., $nodeN ) # Always odd | ||
| 1108 : | # () is returned upon failure | ||
| 1109 : | # | ||
| 1110 : | # Numbering of descendants is 1-based. | ||
| 1111 : | #=============================================================================== | ||
| 1112 : | # Path to tip: | ||
| 1113 : | # | ||
| 1114 : | # @path = path_to_tip( $treenode, $tipname ) | ||
| 1115 : | #------------------------------------------------------------------------------- | ||
| 1116 : | sub path_to_tip { | ||
| 1117 : | my ( $node, $tip, @path0 ) = @_; | ||
| 1118 : | |||
| 1119 : | push @path0, $node; | ||
| 1120 : | my $imax = newick_n_desc( $node ); | ||
| 1121 : | if ( $imax < 1 ) { return ( newick_lbl( $node ) eq $tip ) ? @path0 : () } | ||
| 1122 : | |||
| 1123 : | # Special case for tree rooted on tip | ||
| 1124 : | |||
| 1125 : | if ( ( $imax == 1 ) # One descendant | ||
| 1126 : | && ( @path0 == 1 ) # First step in path | ||
| 1127 : | && ( newick_lbl( $node ) eq $tip ) # Label matches | ||
| 1128 : | ) { return @path0 } | ||
| 1129 : | |||
| 1130 : | my @path; | ||
| 1131 : | for (my $i = 1; $i <= $imax; $i++ ) { | ||
| 1132 : | @path = path_to_tip( newick_desc_i( $node, $i ), $tip, ( @path0, $i ) ); | ||
| 1133 : | if ( @path ) { return @path } | ||
| 1134 : | } | ||
| 1135 : | |||
| 1136 : | (); # Not found | ||
| 1137 : | } | ||
| 1138 : | |||
| 1139 : | |||
| 1140 : | #------------------------------------------------------------------------------- | ||
| 1141 : | # Path to named node. | ||
| 1142 : | # Like path to tip, but will find named internal nodes as well. | ||
| 1143 : | # | ||
| 1144 : | # @path = path_to_named_node( $treenode, $name ) | ||
| 1145 : | #------------------------------------------------------------------------------- | ||
| 1146 : | sub path_to_named_node { | ||
| 1147 : | my ( $node, $name, @path0 ) = @_; | ||
| 1148 : | |||
| 1149 : | push @path0, $node; | ||
| 1150 : | if ( newick_lbl( $node ) eq $name ) { return @path0 } | ||
| 1151 : | |||
| 1152 : | my @path; | ||
| 1153 : | my $imax = newick_n_desc( $node ); | ||
| 1154 : | for ( my $i = 1; $i <= $imax; $i++ ) { | ||
| 1155 : | @path = path_to_named_node( newick_desc_i( $node, $i ), $name, ( @path0, $i ) ); | ||
| 1156 : | if ( @path ) { return @path } | ||
| 1157 : | } | ||
| 1158 : | |||
| 1159 : | (); # Not found | ||
| 1160 : | } | ||
| 1161 : | |||
| 1162 : | |||
| 1163 : | #------------------------------------------------------------------------------- | ||
| 1164 : | # Path to node reference. | ||
| 1165 : | # | ||
| 1166 : | # @path = path_to_node_ref( $treenode, $noderef ) | ||
| 1167 : | #------------------------------------------------------------------------------- | ||
| 1168 : | sub path_to_node_ref { | ||
| 1169 : | my ( $node, $noderef, @path0 ) = @_; | ||
| 1170 : | |||
| 1171 : | push @path0, $node; | ||
| 1172 : | if ( $node eq $noderef ) { return @path0 } | ||
| 1173 : | |||
| 1174 : | my @path; | ||
| 1175 : | my $imax = newick_n_desc( $node ); | ||
| 1176 : | for ( my $i = 1; $i <= $imax; $i++ ) { | ||
| 1177 : | golsen | 1.12 | @path = path_to_node_ref( newick_desc_i( $node, $i ), $noderef, ( @path0, $i ) ); |
| 1178 : | return @path if @path; | ||
| 1179 : | golsen | 1.1 | } |
| 1180 : | |||
| 1181 : | (); # Not found | ||
| 1182 : | } | ||
| 1183 : | |||
| 1184 : | |||
| 1185 : | #------------------------------------------------------------------------------- | ||
| 1186 : | # Path to node, as defined by 1 or 3 tips. | ||
| 1187 : | # | ||
| 1188 : | # @path = path_to_node( $node, $tip1, $tip2, $tip3 ) # 3 tip names | ||
| 1189 : | # @path = path_to_node( $node, [ $tip1, $tip2, $tip3 ] ) # Allow array ref | ||
| 1190 : | # @path = path_to_node( $node, $tip1 ) # Use path_to_tip | ||
| 1191 : | # @path = path_to_node( $node, [ $tip1 ] ) # Use path_to_tip | ||
| 1192 : | #------------------------------------------------------------------------------- | ||
| 1193 : | sub path_to_node { | ||
| 1194 : | my ( $node, $tip1, $tip2, $tip3 ) = @_; | ||
| 1195 : | array_ref( $node ) && defined( $tip1 ) || return (); | ||
| 1196 : | |||
| 1197 : | # Allow arg 2 to be an array reference | ||
| 1198 : | if ( array_ref( $tip1 ) ) { ( $tip1, $tip2, $tip3 ) = @$tip1 } | ||
| 1199 : | |||
| 1200 : | my @p1 = path_to_tip( $node, $tip1 ); # Path to first tip | ||
| 1201 : | @p1 || return (); # Was the tip found? | ||
| 1202 : | defined( $tip2 ) && defined( $tip3 ) || return @p1; # Two more defined? | ||
| 1203 : | |||
| 1204 : | my @p2 = path_to_tip( $node, $tip2 ); | ||
| 1205 : | my @p3 = path_to_tip( $node, $tip3 ); | ||
| 1206 : | @p2 && @p3 || return (); # Were they found? | ||
| 1207 : | |||
| 1208 : | # Find the common prefix for each pair of paths | ||
| 1209 : | golsen | 1.9 | my @p12 = &common_prefix( \@p1, \@p2 ); |
| 1210 : | my @p13 = &common_prefix( \@p1, \@p3 ); | ||
| 1211 : | my @p23 = &common_prefix( \@p2, \@p3 ); | ||
| 1212 : | golsen | 1.1 | |
| 1213 : | # Return the longest common prefix of any two paths | ||
| 1214 : | ( @p12 >= @p13 && @p12 >= @p23 ) ? @p12 : | ||
| 1215 : | ( @p13 >= @p23 ) ? @p13 : | ||
| 1216 : | @p23 ; | ||
| 1217 : | } | ||
| 1218 : | |||
| 1219 : | |||
| 1220 : | #------------------------------------------------------------------------------- | ||
| 1221 : | # Distance along path. | ||
| 1222 : | # | ||
| 1223 : | # $distance = newick_path_length( @path ) | ||
| 1224 : | #------------------------------------------------------------------------------- | ||
| 1225 : | sub newick_path_length { | ||
| 1226 : | my $node = shift; # Discard the first node | ||
| 1227 : | array_ref( $node ) || return undef; | ||
| 1228 : | @_ ? distance_along_path_2( @_ ) : 0; | ||
| 1229 : | } | ||
| 1230 : | |||
| 1231 : | |||
| 1232 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1233 : | # This expects to get path minus root node: | ||
| 1234 : | # | ||
| 1235 : | # $distance = distance_along_path_2( @path ) | ||
| 1236 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1237 : | sub distance_along_path_2 { | ||
| 1238 : | shift; # Discard descendant number | ||
| 1239 : | my $node = shift; | ||
| 1240 : | array_ref( $node ) || return undef; | ||
| 1241 : | my $d1 = newick_x( $node ); | ||
| 1242 : | golsen | 1.8 | my $d2 = @_ ? distance_along_path_2( @_ ) : 0; |
| 1243 : | golsen | 1.1 | defined( $d1 ) && defined( $d2 ) ? $d1 + $d2 : undef; |
| 1244 : | } | ||
| 1245 : | |||
| 1246 : | |||
| 1247 : | #------------------------------------------------------------------------------- | ||
| 1248 : | # Tip-to-tip distance. | ||
| 1249 : | # | ||
| 1250 : | # $distance = tip_to_tip_distance( $tree, $tip1, $tip2 ) | ||
| 1251 : | #------------------------------------------------------------------------------- | ||
| 1252 : | sub tip_to_tip_distance { | ||
| 1253 : | my ( $node, $tip1, $tip2 ) = @_; | ||
| 1254 : | |||
| 1255 : | array_ref( $node ) && defined( $tip1 ) | ||
| 1256 : | && defined( $tip2 ) || return undef; | ||
| 1257 : | my @p1 = path_to_tip( $node, $tip1 ); | ||
| 1258 : | my @p2 = path_to_tip( $node, $tip2 ); | ||
| 1259 : | @p1 && @p2 || return undef; # Were they found? | ||
| 1260 : | |||
| 1261 : | # Find the unique suffixes of the two paths | ||
| 1262 : | golsen | 1.9 | my ( $suf1, $suf2 ) = &unique_suffixes( \@p1, \@p2 ); # Common node is lost |
| 1263 : | golsen | 1.1 | my $d1 = @$suf1 ? distance_along_path_2( @$suf1 ) : 0; |
| 1264 : | my $d2 = @$suf2 ? distance_along_path_2( @$suf2 ) : 0; | ||
| 1265 : | |||
| 1266 : | defined( $d1 ) && defined( $d2 ) ? $d1 + $d2 : undef; | ||
| 1267 : | } | ||
| 1268 : | |||
| 1269 : | |||
| 1270 : | #------------------------------------------------------------------------------- | ||
| 1271 : | # Node-to-node distance. | ||
| 1272 : | # Nodes can be: $tipname | ||
| 1273 : | # [ $tipname ] | ||
| 1274 : | # [ $tipname1, $tipname2, $tipname3 ] | ||
| 1275 : | # | ||
| 1276 : | # $distance = node_to_node_distance( $tree, $node1, $node2 ) | ||
| 1277 : | #------------------------------------------------------------------------------- | ||
| 1278 : | sub node_to_node_distance { | ||
| 1279 : | my ( $node, $node1, $node2 ) = @_; | ||
| 1280 : | |||
| 1281 : | array_ref( $node ) && defined( $node1 ) | ||
| 1282 : | && defined( $node2 ) || return undef; | ||
| 1283 : | golsen | 1.8 | my @p1 = path_to_node( $node, $node1 ) or return undef; |
| 1284 : | my @p2 = path_to_node( $node, $node2 ) or return undef; | ||
| 1285 : | golsen | 1.1 | |
| 1286 : | # Find the unique suffixes of the two paths | ||
| 1287 : | golsen | 1.9 | my ( $suf1, $suf2 ) = &unique_suffixes( \@p1, \@p2 ); # Common node is lost |
| 1288 : | golsen | 1.1 | my $d1 = @$suf1 ? distance_along_path_2( @$suf1 ) : 0; |
| 1289 : | my $d2 = @$suf2 ? distance_along_path_2( @$suf2 ) : 0; | ||
| 1290 : | |||
| 1291 : | defined( $d1 ) && defined( $d2 ) ? $d1 + $d2 : undef; | ||
| 1292 : | } | ||
| 1293 : | |||
| 1294 : | |||
| 1295 : | #=============================================================================== | ||
| 1296 : | # Tree manipulations: | ||
| 1297 : | #=============================================================================== | ||
| 1298 : | # Copy tree. | ||
| 1299 : | # Lists are copied, except that references to empty lists go to undef. | ||
| 1300 : | # Only defined fields are added, so tree list may be shorter than 8 fields. | ||
| 1301 : | # | ||
| 1302 : | overbeek | 1.4 | # $treecopy = copy_newick_tree( $tree ) |
| 1303 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 1304 : | overbeek | 1.4 | sub copy_newick_tree { |
| 1305 : | golsen | 1.1 | my ( $node ) = @_; |
| 1306 : | array_ref( $node ) || return undef; | ||
| 1307 : | |||
| 1308 : | my $nn = []; # Reference to a new node structure | ||
| 1309 : | # Build a new descendant list, if not empty | ||
| 1310 : | my @dl = newick_desc_list( $node ); | ||
| 1311 : | overbeek | 1.4 | set_newick_desc_ref( $nn, @dl ? [ map { copy_newick_tree( $_ ) } @dl ] |
| 1312 : | golsen | 1.1 | : undef |
| 1313 : | ); | ||
| 1314 : | |||
| 1315 : | # Copy label and x, if defined | ||
| 1316 : | my ( $l, $x ); | ||
| 1317 : | if ( defined( $l = newick_lbl( $node ) ) ) { set_newick_lbl( $nn, $l ) } | ||
| 1318 : | if ( defined( $x = newick_x( $node ) ) ) { set_newick_x( $nn, $x ) } | ||
| 1319 : | |||
| 1320 : | # Build new comment lists, when not empty ( does not extend array unless | ||
| 1321 : | # necessary) | ||
| 1322 : | my $c; | ||
| 1323 : | if ( $c = newick_c1( $node ) and @$c ) { set_newick_c1( $nn, [ @$c ] ) } | ||
| 1324 : | if ( $c = newick_c2( $node ) and @$c ) { set_newick_c2( $nn, [ @$c ] ) } | ||
| 1325 : | if ( $c = newick_c3( $node ) and @$c ) { set_newick_c3( $nn, [ @$c ] ) } | ||
| 1326 : | if ( $c = newick_c4( $node ) and @$c ) { set_newick_c4( $nn, [ @$c ] ) } | ||
| 1327 : | if ( $c = newick_c5( $node ) and @$c ) { set_newick_c5( $nn, [ @$c ] ) } | ||
| 1328 : | |||
| 1329 : | $nn; | ||
| 1330 : | } | ||
| 1331 : | |||
| 1332 : | |||
| 1333 : | #------------------------------------------------------------------------------- | ||
| 1334 : | # Use a hash to relabel the nodes in a newick tree. | ||
| 1335 : | # | ||
| 1336 : | # $newtree = newick_relabel_nodes( $node, \%new_name ) | ||
| 1337 : | #------------------------------------------------------------------------------- | ||
| 1338 : | sub newick_relabel_nodes { | ||
| 1339 : | my ( $node, $new_name ) = @_; | ||
| 1340 : | |||
| 1341 : | my ( $lbl, $new ); | ||
| 1342 : | if ( defined( $lbl = newick_lbl( $node ) ) | ||
| 1343 : | && ( $lbl ne "" ) | ||
| 1344 : | && defined( $new = $new_name->{ $lbl } ) | ||
| 1345 : | ) { | ||
| 1346 : | set_newick_lbl( $node, $new ); | ||
| 1347 : | } | ||
| 1348 : | |||
| 1349 : | foreach ( newick_desc_list( $node ) ) { | ||
| 1350 : | newick_relabel_nodes( $_, $new_name ); | ||
| 1351 : | } | ||
| 1352 : | |||
| 1353 : | $node; | ||
| 1354 : | } | ||
| 1355 : | |||
| 1356 : | |||
| 1357 : | #------------------------------------------------------------------------------- | ||
| 1358 : | # Use a hash to relabel the nodes in a newick tree (case insensitive). | ||
| 1359 : | # | ||
| 1360 : | # $newtree = newick_relabel_nodes_i( $node, \%new_name ) | ||
| 1361 : | #------------------------------------------------------------------------------- | ||
| 1362 : | sub newick_relabel_nodes_i { | ||
| 1363 : | my ( $node, $new_name ) = @_; | ||
| 1364 : | |||
| 1365 : | # Add any necessary lowercase keys to the hash: | ||
| 1366 : | |||
| 1367 : | my $lc_lbl; | ||
| 1368 : | foreach ( keys %$new_name ) { | ||
| 1369 : | $lc_lbl = lc $_; | ||
| 1370 : | ( $lc_lbl eq $_ ) or ( $new_name->{ $lc_lbl } = $new_name->{ $_ } ); | ||
| 1371 : | } | ||
| 1372 : | |||
| 1373 : | newick_relabel_nodes_i2( $node, $new_name ); | ||
| 1374 : | } | ||
| 1375 : | |||
| 1376 : | |||
| 1377 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1378 : | # Do the actual relabeling | ||
| 1379 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1380 : | sub newick_relabel_nodes_i2 { | ||
| 1381 : | my ( $node, $new_name ) = @_; | ||
| 1382 : | |||
| 1383 : | my ( $lbl, $new ); | ||
| 1384 : | if ( defined( $lbl = newick_lbl( $node ) ) | ||
| 1385 : | && ( $lbl ne "" ) | ||
| 1386 : | && defined( $new = $new_name->{ lc $lbl } ) | ||
| 1387 : | ) { | ||
| 1388 : | set_newick_lbl( $node, $new ); | ||
| 1389 : | } | ||
| 1390 : | |||
| 1391 : | foreach ( newick_desc_list( $node ) ) { | ||
| 1392 : | newick_relabel_nodes_i2( $_, $new_name ); | ||
| 1393 : | } | ||
| 1394 : | |||
| 1395 : | $node; | ||
| 1396 : | } | ||
| 1397 : | |||
| 1398 : | |||
| 1399 : | #------------------------------------------------------------------------------- | ||
| 1400 : | # Use a hash to relabel the tips in a newick tree. | ||
| 1401 : | # | ||
| 1402 : | # $newtree = newick_relabel_tips( $node, \%new_name ) | ||
| 1403 : | #------------------------------------------------------------------------------- | ||
| 1404 : | sub newick_relabel_tips { | ||
| 1405 : | my ( $node, $new_name ) = @_; | ||
| 1406 : | |||
| 1407 : | my @desc = newick_desc_list( $node ); | ||
| 1408 : | |||
| 1409 : | if ( @desc ) { | ||
| 1410 : | foreach ( @desc ) { newick_relabel_tips( $_, $new_name ) } | ||
| 1411 : | } | ||
| 1412 : | else { | ||
| 1413 : | my ( $lbl, $new ); | ||
| 1414 : | if ( defined( $lbl = newick_lbl( $node ) ) | ||
| 1415 : | && ( $lbl ne "" ) | ||
| 1416 : | && defined( $new = $new_name->{ $lbl } ) | ||
| 1417 : | ) { | ||
| 1418 : | set_newick_lbl( $node, $new ); | ||
| 1419 : | } | ||
| 1420 : | } | ||
| 1421 : | |||
| 1422 : | $node; | ||
| 1423 : | } | ||
| 1424 : | |||
| 1425 : | |||
| 1426 : | #------------------------------------------------------------------------------- | ||
| 1427 : | # Use a hash to relabel the tips in a newick tree (case insensitive). | ||
| 1428 : | # | ||
| 1429 : | # $newtree = newick_relabel_tips_i( $node, \%new_name ) | ||
| 1430 : | #------------------------------------------------------------------------------- | ||
| 1431 : | sub newick_relabel_tips_i { | ||
| 1432 : | my ( $node, $new_name ) = @_; | ||
| 1433 : | |||
| 1434 : | # Add any necessary lowercase keys to the hash: | ||
| 1435 : | |||
| 1436 : | my $lc_lbl; | ||
| 1437 : | foreach ( keys %$new_name ) { | ||
| 1438 : | $lc_lbl = lc $_; | ||
| 1439 : | ( $lc_lbl eq $_ ) or ( $new_name->{ $lc_lbl } = $new_name->{ $_ } ); | ||
| 1440 : | } | ||
| 1441 : | |||
| 1442 : | newick_relabel_tips_i2( $node, $new_name ); | ||
| 1443 : | } | ||
| 1444 : | |||
| 1445 : | |||
| 1446 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1447 : | # Do the actual relabeling | ||
| 1448 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1449 : | sub newick_relabel_tips_i2 { | ||
| 1450 : | my ( $node, $new_name ) = @_; | ||
| 1451 : | |||
| 1452 : | my @desc = newick_desc_list( $node ); | ||
| 1453 : | |||
| 1454 : | if ( @desc ) { | ||
| 1455 : | foreach ( @desc ) { newick_relabel_tips_i2( $_, $new_name ) } | ||
| 1456 : | } | ||
| 1457 : | else { | ||
| 1458 : | my ( $lbl, $new ); | ||
| 1459 : | if ( defined( $lbl = newick_lbl( $node ) ) | ||
| 1460 : | && ( $lbl ne "" ) | ||
| 1461 : | && defined( $new = $new_name->{ lc $lbl } ) | ||
| 1462 : | ) { | ||
| 1463 : | set_newick_lbl( $node, $new ); | ||
| 1464 : | } | ||
| 1465 : | } | ||
| 1466 : | |||
| 1467 : | $node; | ||
| 1468 : | } | ||
| 1469 : | |||
| 1470 : | |||
| 1471 : | #------------------------------------------------------------------------------- | ||
| 1472 : | # Set undefined branch lenghts (except root) to length x. | ||
| 1473 : | # | ||
| 1474 : | # $n_changed = newick_set_undefined_branches( $node, $x ) | ||
| 1475 : | #------------------------------------------------------------------------------- | ||
| 1476 : | sub newick_set_undefined_branches { | ||
| 1477 : | my ( $node, $x, $not_root ) = @_; | ||
| 1478 : | |||
| 1479 : | my $n = 0; | ||
| 1480 : | if ( $not_root && ! defined( newick_x( $node ) ) ) { | ||
| 1481 : | set_newick_x( $node, $x ); | ||
| 1482 : | $n++; | ||
| 1483 : | } | ||
| 1484 : | |||
| 1485 : | foreach ( newick_desc_list( $node ) ) { | ||
| 1486 : | $n += newick_set_undefined_branches( $_, $x, 1 ); | ||
| 1487 : | } | ||
| 1488 : | |||
| 1489 : | $n; | ||
| 1490 : | } | ||
| 1491 : | |||
| 1492 : | |||
| 1493 : | #------------------------------------------------------------------------------- | ||
| 1494 : | # Set all branch lenghts (except root) to length x. | ||
| 1495 : | # | ||
| 1496 : | # $n_changed = newick_set_all_branches( $node, $x ) | ||
| 1497 : | #------------------------------------------------------------------------------- | ||
| 1498 : | sub newick_set_all_branches { | ||
| 1499 : | my ( $node, $x, $not_root ) = @_; | ||
| 1500 : | |||
| 1501 : | my $n = 0; | ||
| 1502 : | overbeek | 1.7 | if ( $not_root ) |
| 1503 : | { | ||
| 1504 : | golsen | 1.1 | set_newick_x( $node, $x ); |
| 1505 : | $n++; | ||
| 1506 : | } | ||
| 1507 : | |||
| 1508 : | overbeek | 1.7 | foreach ( newick_desc_list( $node ) ) |
| 1509 : | { | ||
| 1510 : | golsen | 1.1 | $n += newick_set_all_branches( $_, $x, 1 ); |
| 1511 : | } | ||
| 1512 : | |||
| 1513 : | $n; | ||
| 1514 : | } | ||
| 1515 : | |||
| 1516 : | |||
| 1517 : | #------------------------------------------------------------------------------- | ||
| 1518 : | overbeek | 1.7 | # Rescale all branch lenghts by factor. |
| 1519 : | # | ||
| 1520 : | # $node = newick_rescale_branches( $node, $factor ) | ||
| 1521 : | #------------------------------------------------------------------------------- | ||
| 1522 : | sub newick_rescale_branches { | ||
| 1523 : | my ( $node, $factor ) = @_; | ||
| 1524 : | |||
| 1525 : | my $x = newick_x( $node ); | ||
| 1526 : | set_newick_x( $node, $factor * $x ) if $x; | ||
| 1527 : | |||
| 1528 : | foreach ( newick_desc_list( $node ) ) | ||
| 1529 : | { | ||
| 1530 : | newick_rescale_branches( $_, $factor ); | ||
| 1531 : | } | ||
| 1532 : | |||
| 1533 : | $node; | ||
| 1534 : | } | ||
| 1535 : | |||
| 1536 : | |||
| 1537 : | #------------------------------------------------------------------------------- | ||
| 1538 : | golsen | 1.5 | # Set negative branches to zero. The original tree is modfied. |
| 1539 : | # | ||
| 1540 : | # $n_changed = newick_fix_negative_branches( $tree ) | ||
| 1541 : | #------------------------------------------------------------------------------- | ||
| 1542 : | sub newick_fix_negative_branches { | ||
| 1543 : | my ( $tree ) = @_; | ||
| 1544 : | array_ref( $tree ) or return undef; | ||
| 1545 : | my $n_changed = 0; | ||
| 1546 : | my $x = newick_x( $tree ); | ||
| 1547 : | if ( defined( $x ) and $x < 0 ) | ||
| 1548 : | { | ||
| 1549 : | set_newick_x( $tree, 0 ); | ||
| 1550 : | $n_changed++; | ||
| 1551 : | } | ||
| 1552 : | |||
| 1553 : | foreach ( newick_desc_list( $tree ) ) | ||
| 1554 : | { | ||
| 1555 : | $n_changed += newick_fix_negative_branches( $_ ); | ||
| 1556 : | } | ||
| 1557 : | |||
| 1558 : | $n_changed; | ||
| 1559 : | } | ||
| 1560 : | |||
| 1561 : | |||
| 1562 : | #------------------------------------------------------------------------------- | ||
| 1563 : | golsen | 1.8 | # Remove comments from a newick tree (e.g., before writing for phylip). |
| 1564 : | # | ||
| 1565 : | # $node = newick_strip_comments( $node ) | ||
| 1566 : | #------------------------------------------------------------------------------- | ||
| 1567 : | sub newick_strip_comments { | ||
| 1568 : | my ( $node ) = @_; | ||
| 1569 : | |||
| 1570 : | @$node = @$node[ 0 .. 2 ]; | ||
| 1571 : | foreach ( newick_desc_list( $node ) ) { newick_strip_comments( $_ ) } | ||
| 1572 : | $node; | ||
| 1573 : | } | ||
| 1574 : | |||
| 1575 : | |||
| 1576 : | #------------------------------------------------------------------------------- | ||
| 1577 : | golsen | 1.1 | # Normalize tree order (in place). |
| 1578 : | # | ||
| 1579 : | # ( $tree, $label1 ) = normalize_newick_tree( $tree ) | ||
| 1580 : | #------------------------------------------------------------------------------- | ||
| 1581 : | sub normalize_newick_tree { | ||
| 1582 : | my ( $node ) = @_; | ||
| 1583 : | |||
| 1584 : | my @descends = newick_desc_list( $node ); | ||
| 1585 : | if ( @descends == 0 ) { return ( $node, lc newick_lbl( $node ) ) } | ||
| 1586 : | |||
| 1587 : | golsen | 1.9 | my %hash = map { ( normalize_newick_tree($_) )[1] => $_ } @descends; |
| 1588 : | golsen | 1.1 | my @keylist = sort { $a cmp $b } keys %hash; |
| 1589 : | set_newick_desc_list( $node, map { $hash{$_} } @keylist ); | ||
| 1590 : | |||
| 1591 : | ( $node, $keylist[0] ); | ||
| 1592 : | } | ||
| 1593 : | |||
| 1594 : | |||
| 1595 : | #------------------------------------------------------------------------------- | ||
| 1596 : | # Reverse tree order (in place). | ||
| 1597 : | # | ||
| 1598 : | # $tree = reverse_newick_tree( $tree ) | ||
| 1599 : | #------------------------------------------------------------------------------- | ||
| 1600 : | sub reverse_newick_tree { | ||
| 1601 : | my ( $node ) = @_; | ||
| 1602 : | |||
| 1603 : | my @descends = newick_desc_list( $node ); | ||
| 1604 : | if ( @descends ) { | ||
| 1605 : | set_newick_desc_list( $node, reverse @descends ); | ||
| 1606 : | foreach ( @descends ) { reverse_newick_tree( $_ ) } | ||
| 1607 : | } | ||
| 1608 : | $node; | ||
| 1609 : | } | ||
| 1610 : | |||
| 1611 : | |||
| 1612 : | #------------------------------------------------------------------------------- | ||
| 1613 : | # Standard unrooted tree (in place). | ||
| 1614 : | # | ||
| 1615 : | # $stdtree = std_unrooted_newick( $tree ) | ||
| 1616 : | #------------------------------------------------------------------------------- | ||
| 1617 : | sub std_unrooted_newick { | ||
| 1618 : | my ( $tree ) = @_; | ||
| 1619 : | |||
| 1620 : | my ( $mintip ) = sort { lc $a cmp lc $b } newick_tip_list( $tree ); | ||
| 1621 : | ( normalize_newick_tree( reroot_newick_next_to_tip( $tree, $mintip ) ) )[0]; | ||
| 1622 : | } | ||
| 1623 : | |||
| 1624 : | |||
| 1625 : | #------------------------------------------------------------------------------- | ||
| 1626 : | # Move largest groups to periphery of tree (in place). | ||
| 1627 : | # | ||
| 1628 : | # dir <= -2 for up-sweeping tree (big groups always first), | ||
| 1629 : | # = -1 for big group first, balanced tree, | ||
| 1630 : | # = 0 for balanced tree, | ||
| 1631 : | # = 1 for small group first, balanced tree, and | ||
| 1632 : | # >= 2 for down-sweeping tree (small groups always top) | ||
| 1633 : | # | ||
| 1634 : | # $tree = aesthetic_newick_tree( $treeref, $dir ) | ||
| 1635 : | #------------------------------------------------------------------------------- | ||
| 1636 : | sub aesthetic_newick_tree { | ||
| 1637 : | my ( $tree, $dir ) = @_; | ||
| 1638 : | my %cnt; | ||
| 1639 : | |||
| 1640 : | $dir = ! $dir ? 0 : # Undefined or zero | ||
| 1641 : | $dir <= -2 ? -1000000 : | ||
| 1642 : | $dir < 0 ? -1 : | ||
| 1643 : | $dir >= 2 ? 1000000 : | ||
| 1644 : | 1 ; | ||
| 1645 : | build_tip_count_hash( $tree, \%cnt ); | ||
| 1646 : | reorder_by_tip_count( $tree, \%cnt, $dir ); | ||
| 1647 : | } | ||
| 1648 : | |||
| 1649 : | |||
| 1650 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1651 : | # Build a hash to look up the number of descendants of each node. | ||
| 1652 : | # Access count with $cntref->{$noderef} | ||
| 1653 : | # | ||
| 1654 : | # $count = build_tip_count_hash( $node, $cnt_hash_ref ) | ||
| 1655 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1656 : | sub build_tip_count_hash { | ||
| 1657 : | my ( $node, $cntref ) = @_; | ||
| 1658 : | my ( $i, $cnt ); | ||
| 1659 : | |||
| 1660 : | if ( newick_n_desc( $node ) < 1 ) { $cnt = 1 } | ||
| 1661 : | else { | ||
| 1662 : | $cnt = 0; | ||
| 1663 : | foreach ( newick_desc_list( $node ) ) { | ||
| 1664 : | $cnt += build_tip_count_hash( $_, $cntref ); | ||
| 1665 : | } | ||
| 1666 : | } | ||
| 1667 : | |||
| 1668 : | $cntref->{$node} = $cnt; | ||
| 1669 : | $cnt; | ||
| 1670 : | } | ||
| 1671 : | |||
| 1672 : | |||
| 1673 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1674 : | # $node = reorder_by_tip_count( $node, $cntref, $dir ) | ||
| 1675 : | # dir < 0 for upward branch (big group first), | ||
| 1676 : | # = 0 for no change, and | ||
| 1677 : | # > 0 for downward branch (small group first). | ||
| 1678 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1679 : | sub reorder_by_tip_count { | ||
| 1680 : | my ( $node, $cntref, $dir ) = @_; | ||
| 1681 : | |||
| 1682 : | my $nd = newick_n_desc( $node ); | ||
| 1683 : | if ( $nd < 1 ) { return $node } # Do nothing to a tip | ||
| 1684 : | |||
| 1685 : | # Reorder this subtree: | ||
| 1686 : | |||
| 1687 : | my $dl_ref = newick_desc_ref( $node ); | ||
| 1688 : | if ( $dir < 0 ) { # Big group first | ||
| 1689 : | @$dl_ref = sort { $cntref->{$b} <=> $cntref->{$a} } @$dl_ref; | ||
| 1690 : | } | ||
| 1691 : | elsif ( $dir > 0 ) { # Small group first | ||
| 1692 : | @$dl_ref = sort { $cntref->{$a} <=> $cntref->{$b} } @$dl_ref; | ||
| 1693 : | } | ||
| 1694 : | |||
| 1695 : | # Reorder within descendant subtrees: | ||
| 1696 : | |||
| 1697 : | my $step = 0; | ||
| 1698 : | if ( abs( $dir ) < 1e5 ) { | ||
| 1699 : | $dir = 1 - $nd; # Midgroup => as is | ||
| 1700 : | # $dir = 1 - $nd + ( $dir < 0 ? -0.5 : 0.5 ); # Midgroup => outward | ||
| 1701 : | $step = 2; | ||
| 1702 : | } | ||
| 1703 : | |||
| 1704 : | for ( my $i = 0; $i < $nd; $i++ ) { | ||
| 1705 : | reorder_by_tip_count( $dl_ref->[$i], $cntref, $dir ); | ||
| 1706 : | $dir += $step; | ||
| 1707 : | } | ||
| 1708 : | |||
| 1709 : | $node; | ||
| 1710 : | } | ||
| 1711 : | |||
| 1712 : | |||
| 1713 : | #------------------------------------------------------------------------------- | ||
| 1714 : | # Move smallest groups to periphery of tree (in place). | ||
| 1715 : | # | ||
| 1716 : | # dir <= -2 for up-sweeping tree (big groups always first), | ||
| 1717 : | # = -1 for big group first, balanced tree, | ||
| 1718 : | # = 0 for balanced tree, | ||
| 1719 : | # = 1 for small group first, balanced tree, and | ||
| 1720 : | # >= 2 for down-sweeping tree (small groups always top) | ||
| 1721 : | # | ||
| 1722 : | # $tree = unaesthetic_newick_tree( $treeref, $dir ) | ||
| 1723 : | #------------------------------------------------------------------------------- | ||
| 1724 : | golsen | 1.9 | sub unaesthetic_newick_tree |
| 1725 : | { | ||
| 1726 : | golsen | 1.1 | my ( $tree, $dir ) = @_; |
| 1727 : | my %cnt; | ||
| 1728 : | |||
| 1729 : | $dir = ! $dir ? 0 : # Undefined or zero | ||
| 1730 : | $dir <= -2 ? -1000000 : | ||
| 1731 : | $dir < 0 ? -1 : | ||
| 1732 : | $dir >= 2 ? 1000000 : | ||
| 1733 : | 1 ; | ||
| 1734 : | build_tip_count_hash( $tree, \%cnt ); | ||
| 1735 : | reorder_against_tip_count( $tree, \%cnt, $dir ); | ||
| 1736 : | } | ||
| 1737 : | |||
| 1738 : | |||
| 1739 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1740 : | # $node = reorder_by_tip_count( $node, $cntref, $dir ) | ||
| 1741 : | # dir < 0 for upward branch (big group first), | ||
| 1742 : | # = 0 for no change, and | ||
| 1743 : | # > 0 for downward branch (small group first). | ||
| 1744 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 1745 : | golsen | 1.9 | sub reorder_against_tip_count |
| 1746 : | { | ||
| 1747 : | golsen | 1.1 | my ( $node, $cntref, $dir ) = @_; |
| 1748 : | |||
| 1749 : | my $nd = newick_n_desc( $node ); | ||
| 1750 : | if ( $nd < 1 ) { return $node } # Do nothing to a tip | ||
| 1751 : | |||
| 1752 : | # Reorder this subtree: | ||
| 1753 : | |||
| 1754 : | my $dl_ref = newick_desc_ref( $node ); | ||
| 1755 : | if ( $dir > 0 ) { # Big group first | ||
| 1756 : | @$dl_ref = sort { $cntref->{$b} <=> $cntref->{$a} } @$dl_ref; | ||
| 1757 : | } | ||
| 1758 : | elsif ( $dir < 0 ) { # Small group first | ||
| 1759 : | @$dl_ref = sort { $cntref->{$a} <=> $cntref->{$b} } @$dl_ref; | ||
| 1760 : | } | ||
| 1761 : | |||
| 1762 : | # Reorder within descendant subtrees: | ||
| 1763 : | |||
| 1764 : | my $step = 0; | ||
| 1765 : | if (abs( $dir ) < 1e5) { | ||
| 1766 : | $dir = 1 - $nd; # Midgroup => as is | ||
| 1767 : | # $dir = 1 - $nd + ( $dir < 0 ? -0.5 : 0.5 ); # Midgroup => outward | ||
| 1768 : | $step = 2; | ||
| 1769 : | } | ||
| 1770 : | |||
| 1771 : | for ( my $i = 0; $i < $nd; $i++ ) { | ||
| 1772 : | reorder_by_tip_count( $dl_ref->[$i], $cntref, $dir ); | ||
| 1773 : | $dir += $step; | ||
| 1774 : | } | ||
| 1775 : | |||
| 1776 : | $node; | ||
| 1777 : | } | ||
| 1778 : | |||
| 1779 : | |||
| 1780 : | #------------------------------------------------------------------------------- | ||
| 1781 : | # Randomize descendant order at each node (in place). | ||
| 1782 : | # | ||
| 1783 : | # $tree = random_order_newick_tree( $tree ) | ||
| 1784 : | #------------------------------------------------------------------------------- | ||
| 1785 : | golsen | 1.9 | sub random_order_newick_tree |
| 1786 : | { | ||
| 1787 : | golsen | 1.1 | my ( $node ) = @_; |
| 1788 : | |||
| 1789 : | my $nd = newick_n_desc( $node ); | ||
| 1790 : | if ( $nd < 1 ) { return $node } # Do nothing to a tip | ||
| 1791 : | |||
| 1792 : | # Reorder this subtree: | ||
| 1793 : | |||
| 1794 : | my $dl_ref = newick_desc_ref( $node ); | ||
| 1795 : | golsen | 1.9 | @$dl_ref = &random_order( @$dl_ref ); |
| 1796 : | golsen | 1.1 | |
| 1797 : | # Reorder descendants: | ||
| 1798 : | |||
| 1799 : | foreach ( @$dl_ref ) { random_order_newick_tree( $_ ) } | ||
| 1800 : | |||
| 1801 : | $node; | ||
| 1802 : | } | ||
| 1803 : | |||
| 1804 : | |||
| 1805 : | #------------------------------------------------------------------------------- | ||
| 1806 : | # Reroot a tree to the node that lies at the end of a path. | ||
| 1807 : | # | ||
| 1808 : | # $newtree = reroot_newick_by_path( @path ) | ||
| 1809 : | #------------------------------------------------------------------------------- | ||
| 1810 : | golsen | 1.9 | sub reroot_newick_by_path |
| 1811 : | { | ||
| 1812 : | golsen | 1.1 | my ( $node1, $path1, @rest ) = @_; |
| 1813 : | array_ref( $node1 ) || return undef; # Always expect a node | ||
| 1814 : | |||
| 1815 : | defined( $path1 ) && @rest || return $node1; # If no path, we're done | ||
| 1816 : | |||
| 1817 : | my $node2 = $rest[0]; # Next element in path is node 2 | ||
| 1818 : | newick_desc_i( $node1, $path1 ) eq $node2 || return undef; # Check link | ||
| 1819 : | |||
| 1820 : | # Remove node 2 from node 1 descendant list. Could use a simple splice: | ||
| 1821 : | # | ||
| 1822 : | # splice( @$dl1, $path1-1, 1 ); | ||
| 1823 : | # | ||
| 1824 : | golsen | 1.8 | # But the following maintains the cyclic order of the nodes: |
| 1825 : | golsen | 1.1 | |
| 1826 : | my $dl1 = newick_desc_ref( $node1 ); | ||
| 1827 : | my $nd1 = @$dl1; | ||
| 1828 : | if ( $path1 == 1 ) { shift @$dl1 } | ||
| 1829 : | elsif ( $path1 == $nd1 ) { pop @$dl1 } | ||
| 1830 : | else { @$dl1 = ( @$dl1[ $path1 .. $nd1-1 ] | ||
| 1831 : | , @$dl1[ 0 .. $path1-2 ] | ||
| 1832 : | ) | ||
| 1833 : | golsen | 1.8 | } |
| 1834 : | golsen | 1.1 | |
| 1835 : | # Append node 1 to node 2 descendant list (does not alter numbering): | ||
| 1836 : | |||
| 1837 : | my $dl2 = newick_desc_ref( $node2 ); | ||
| 1838 : | if ( array_ref( $dl2 ) ) { push @$dl2, $node1 } | ||
| 1839 : | golsen | 1.8 | else { set_newick_desc_list( $node2, $node1 ) } |
| 1840 : | golsen | 1.1 | |
| 1841 : | # Move c1 comments from node 1 to node 2: | ||
| 1842 : | |||
| 1843 : | my $C11 = newick_c1( $node1 ); | ||
| 1844 : | my $C12 = newick_c1( $node2 ); | ||
| 1845 : | ! defined( $C11 ) || set_newick_c1( $node1, undef ); # Remove them from node 1 | ||
| 1846 : | golsen | 1.8 | if ( $C12 && @$C12 ) { # If node 2 comments and |
| 1847 : | if ( $C11 && @$C11 ) { unshift @$C12, @$C11 } # Node 1, prefix 1 to 2 | ||
| 1848 : | golsen | 1.1 | } |
| 1849 : | golsen | 1.8 | elsif ( $C11 && @$C11 ) { set_newick_c1( $node2, $C11 ) } # Otherwise move node 1 link |
| 1850 : | golsen | 1.1 | |
| 1851 : | # Swap branch lengths and comments for reversal of link direction: | ||
| 1852 : | |||
| 1853 : | my $x1 = newick_x( $node1 ); | ||
| 1854 : | my $x2 = newick_x( $node2 ); | ||
| 1855 : | ! defined( $x1 ) && ! defined ( $x2 ) || set_newick_x( $node1, $x2 ); | ||
| 1856 : | ! defined( $x1 ) && ! defined ( $x2 ) || set_newick_x( $node2, $x1 ); | ||
| 1857 : | |||
| 1858 : | my $c41 = newick_c4( $node1 ); | ||
| 1859 : | my $c42 = newick_c4( $node2 ); | ||
| 1860 : | ! defined( $c42 ) || ! @$c42 || set_newick_c4( $node1, $c42 ); | ||
| 1861 : | ! defined( $c41 ) || ! @$c41 || set_newick_c4( $node2, $c41 ); | ||
| 1862 : | |||
| 1863 : | my $c51 = newick_c5( $node1 ); | ||
| 1864 : | my $c52 = newick_c5( $node2 ); | ||
| 1865 : | ! defined( $c52 ) || ! @$c52 || set_newick_c5( $node1, $c52 ); | ||
| 1866 : | ! defined( $c51 ) || ! @$c51 || set_newick_c5( $node2, $c51 ); | ||
| 1867 : | |||
| 1868 : | reroot_newick_by_path( @rest ); # Node 2 is first element of rest | ||
| 1869 : | } | ||
| 1870 : | |||
| 1871 : | |||
| 1872 : | #------------------------------------------------------------------------------- | ||
| 1873 : | # Move root of tree to named tip. | ||
| 1874 : | # | ||
| 1875 : | # $newtree = reroot_newick_to_tip( $tree, $tip ) | ||
| 1876 : | #------------------------------------------------------------------------------- | ||
| 1877 : | sub reroot_newick_to_tip { | ||
| 1878 : | my ( $tree, $tipname ) = @_; | ||
| 1879 : | reroot_newick_by_path( path_to_tip( $tree, $tipname ) ); | ||
| 1880 : | } | ||
| 1881 : | |||
| 1882 : | |||
| 1883 : | #------------------------------------------------------------------------------- | ||
| 1884 : | # Move root of tree to be node adjacent to a named tip. | ||
| 1885 : | # | ||
| 1886 : | # $newtree = reroot_newick_next_to_tip( $tree, $tip ) | ||
| 1887 : | #------------------------------------------------------------------------------- | ||
| 1888 : | sub reroot_newick_next_to_tip { | ||
| 1889 : | my ( $tree, $tipname ) = @_; | ||
| 1890 : | my @path = path_to_tip( $tree, $tipname ); | ||
| 1891 : | @path || return undef; | ||
| 1892 : | @path == 1 ? reroot_newick_by_path( $tree, 1, newick_desc_i( $tree, 1 ) ) | ||
| 1893 : | : reroot_newick_by_path( @path[0 .. @path-3] ); | ||
| 1894 : | } | ||
| 1895 : | |||
| 1896 : | |||
| 1897 : | #------------------------------------------------------------------------------- | ||
| 1898 : | # Move root of tree to a node, defined by 1 or 3 tip names. | ||
| 1899 : | # | ||
| 1900 : | # $newtree = reroot_newick_to_node( $tree, @node ) | ||
| 1901 : | #------------------------------------------------------------------------------- | ||
| 1902 : | sub reroot_newick_to_node { | ||
| 1903 : | reroot_newick_by_path( path_to_node( @_ ) ); | ||
| 1904 : | } | ||
| 1905 : | |||
| 1906 : | |||
| 1907 : | #------------------------------------------------------------------------------- | ||
| 1908 : | # Move root of tree to a node, defined by reference. | ||
| 1909 : | # | ||
| 1910 : | # $newtree = reroot_newick_to_node_ref( $tree, $noderef ) | ||
| 1911 : | #------------------------------------------------------------------------------- | ||
| 1912 : | sub reroot_newick_to_node_ref { | ||
| 1913 : | my ( $tree, $node ) = @_; | ||
| 1914 : | reroot_newick_by_path( path_to_node_ref( $tree, $node ) ); | ||
| 1915 : | } | ||
| 1916 : | |||
| 1917 : | |||
| 1918 : | #------------------------------------------------------------------------------- | ||
| 1919 : | golsen | 1.9 | # Reroot a newick tree along the path between 2 nodes: |
| 1920 : | # | ||
| 1921 : | # $tree = reroot_newick_between_nodes( $tree, $node1, $node2, $fraction ) | ||
| 1922 : | #------------------------------------------------------------------------------- | ||
| 1923 : | sub reroot_newick_between_nodes | ||
| 1924 : | { | ||
| 1925 : | my ( $tree, $node1, $node2, $fraction ) = @_; | ||
| 1926 : | array_ref( $tree ) or return undef; | ||
| 1927 : | $fraction >= 0 && $fraction <= 1 or return undef; | ||
| 1928 : | |||
| 1929 : | # Find the paths to the nodes: | ||
| 1930 : | |||
| 1931 : | my @path1 = path_to_node( $tree, $node1 ) or return undef; | ||
| 1932 : | my @path2 = path_to_node( $tree, $node2 ) or return undef; | ||
| 1933 : | |||
| 1934 : | golsen | 1.12 | reroot_newick_between_nodes_by_path( $tree, \@path1, \@path2, $fraction ) |
| 1935 : | } | ||
| 1936 : | |||
| 1937 : | |||
| 1938 : | #------------------------------------------------------------------------------- | ||
| 1939 : | # Reroot a newick tree along the path between 2 nodes: | ||
| 1940 : | # | ||
| 1941 : | # $tree = reroot_newick_between_node_refs( $tree, $node1, $node2, $fraction ) | ||
| 1942 : | #------------------------------------------------------------------------------- | ||
| 1943 : | sub reroot_newick_between_node_refs | ||
| 1944 : | { | ||
| 1945 : | my ( $tree, $node1, $node2, $fraction ) = @_; | ||
| 1946 : | array_ref( $tree ) or return undef; | ||
| 1947 : | |||
| 1948 : | # Find the paths to the nodes: | ||
| 1949 : | |||
| 1950 : | my @path1 = path_to_node_ref( $tree, $node1 ) or return undef; | ||
| 1951 : | my @path2 = path_to_node_ref( $tree, $node2 ) or return undef;; | ||
| 1952 : | |||
| 1953 : | reroot_newick_between_nodes_by_path( $tree, \@path1, \@path2, $fraction ) | ||
| 1954 : | } | ||
| 1955 : | |||
| 1956 : | |||
| 1957 : | #------------------------------------------------------------------------------- | ||
| 1958 : | # Reroot a newick tree along the path between 2 nodes defined by paths: | ||
| 1959 : | # | ||
| 1960 : | # $tree = reroot_newick_between_nodes_by_path( $tree, $path1, $path2, $fraction ) | ||
| 1961 : | #------------------------------------------------------------------------------- | ||
| 1962 : | sub reroot_newick_between_nodes_by_path | ||
| 1963 : | { | ||
| 1964 : | my ( $tree, $path1, $path2, $fraction ) = @_; | ||
| 1965 : | array_ref( $tree ) and array_ref( $path1 ) and array_ref( $path2 ) | ||
| 1966 : | or return undef; | ||
| 1967 : | $fraction >= 0 && $fraction <= 1 or return undef; | ||
| 1968 : | |||
| 1969 : | my @path1 = @$path1; | ||
| 1970 : | my @path2 = @$path2; | ||
| 1971 : | |||
| 1972 : | golsen | 1.9 | # Trim the common prefix, saving it: |
| 1973 : | |||
| 1974 : | my @prefix = (); | ||
| 1975 : | while ( $path1[1] == $path2[1] ) | ||
| 1976 : | { | ||
| 1977 : | push @prefix, splice( @path1, 0, 2 ); | ||
| 1978 : | splice( @path2, 0, 2 ); | ||
| 1979 : | } | ||
| 1980 : | |||
| 1981 : | my ( @path, $dist ); | ||
| 1982 : | if ( @path1 < 3 ) | ||
| 1983 : | { | ||
| 1984 : | @path2 >= 3 or return undef; # node1 = node2 | ||
| 1985 : | $dist = $fraction * newick_path_length( @path2 ); | ||
| 1986 : | @path = @path2; | ||
| 1987 : | } | ||
| 1988 : | elsif ( @path2 < 3 ) | ||
| 1989 : | { | ||
| 1990 : | $dist = ( 1 - $fraction ) * newick_path_length( @path1 ); | ||
| 1991 : | @path = @path1; | ||
| 1992 : | } | ||
| 1993 : | else | ||
| 1994 : | { | ||
| 1995 : | my $dist1 = newick_path_length( @path1 ); | ||
| 1996 : | my $dist2 = newick_path_length( @path2 ); | ||
| 1997 : | $dist = $fraction * ( $dist1 + $dist2 ) - $dist1; | ||
| 1998 : | @path = ( $dist <= 0 ) ? @path1 : @path2; | ||
| 1999 : | $dist = abs( $dist ); | ||
| 2000 : | } | ||
| 2001 : | |||
| 2002 : | # Descend tree until we reach the insertion branch: | ||
| 2003 : | |||
| 2004 : | my $x; | ||
| 2005 : | while ( ( $dist > ( $x = newick_x( $path[2] ) ) ) && ( @path > 3 ) ) | ||
| 2006 : | { | ||
| 2007 : | $dist -= $x; | ||
| 2008 : | push @prefix, splice( @path, 0, 2 ); | ||
| 2009 : | } | ||
| 2010 : | |||
| 2011 : | # Insert the new node: | ||
| 2012 : | |||
| 2013 : | my $newnode = [ [ $path[2] ], undef, $dist ]; | ||
| 2014 : | set_newick_desc_i( $path[0], $path[1], $newnode ); | ||
| 2015 : | set_newick_x( $path[2], ( ( $x > $dist ) ? ( $x - $dist ) : 0 ) ); | ||
| 2016 : | |||
| 2017 : | # We can now build the path from root to the new node | ||
| 2018 : | |||
| 2019 : | reroot_newick_by_path( @prefix, @path[0,1], $newnode ); | ||
| 2020 : | } | ||
| 2021 : | |||
| 2022 : | |||
| 2023 : | #------------------------------------------------------------------------------- | ||
| 2024 : | golsen | 1.1 | # Move root of tree to an approximate midpoint. |
| 2025 : | # | ||
| 2026 : | # $newtree = reroot_newick_to_approx_midpoint( $tree ) | ||
| 2027 : | #------------------------------------------------------------------------------- | ||
| 2028 : | sub reroot_newick_to_approx_midpoint { | ||
| 2029 : | my ( $tree ) = @_; | ||
| 2030 : | golsen | 1.5 | |
| 2031 : | golsen | 1.1 | # Compile average tip to node distances assending |
| 2032 : | |||
| 2033 : | my $dists1 = average_to_tips_1( $tree ); | ||
| 2034 : | |||
| 2035 : | golsen | 1.12 | # Compile average tip to node distances descending, returning midpoint |
| 2036 : | # cadidates as a list of [ $node1, $node2, $fraction ] | ||
| 2037 : | |||
| 2038 : | my @mids = average_to_tips_2( $dists1, undef, undef ); | ||
| 2039 : | |||
| 2040 : | # Reroot to first midpoint candidate | ||
| 2041 : | |||
| 2042 : | return $tree if ! @mids; | ||
| 2043 : | my ( $node1, $node2, $fraction ) = @{ $mids[0] }; | ||
| 2044 : | reroot_newick_to_node_ref( $tree, $fraction >= 0.5 ? $node2 : $node1 ); | ||
| 2045 : | } | ||
| 2046 : | |||
| 2047 : | |||
| 2048 : | #------------------------------------------------------------------------------- | ||
| 2049 : | # Move root of tree to a midpoint. | ||
| 2050 : | # | ||
| 2051 : | # $newtree = reroot_newick_to_midpoint( $tree ) | ||
| 2052 : | #------------------------------------------------------------------------------- | ||
| 2053 : | sub reroot_newick_to_midpoint { | ||
| 2054 : | my ( $tree ) = @_; | ||
| 2055 : | |||
| 2056 : | # Compile average tip to node distances assending | ||
| 2057 : | |||
| 2058 : | my $dists1 = average_to_tips_1( $tree ); | ||
| 2059 : | golsen | 1.1 | |
| 2060 : | golsen | 1.12 | # Compile average tip to node distances descending, returning midpoint |
| 2061 : | # [ $node1, $node2, $fraction ] | ||
| 2062 : | golsen | 1.1 | |
| 2063 : | golsen | 1.12 | my @mids = average_to_tips_2( $dists1, undef, undef ); |
| 2064 : | golsen | 1.1 | |
| 2065 : | golsen | 1.12 | @mids ? reroot_newick_between_node_refs( $tree, @{ $mids[0] } ) : $tree; |
| 2066 : | golsen | 1.1 | } |
| 2067 : | |||
| 2068 : | |||
| 2069 : | golsen | 1.12 | #------------------------------------------------------------------------------- |
| 2070 : | # Compile average tip to node distances assending | ||
| 2071 : | #------------------------------------------------------------------------------- | ||
| 2072 : | golsen | 1.1 | sub average_to_tips_1 { |
| 2073 : | my ( $node ) = @_; | ||
| 2074 : | |||
| 2075 : | my @desc_dists = map { average_to_tips_1( $_ ) } newick_desc_list( $node ); | ||
| 2076 : | my $x_below = 0; | ||
| 2077 : | if ( @desc_dists ) | ||
| 2078 : | { | ||
| 2079 : | foreach ( @desc_dists ) { $x_below += $_->[0] } | ||
| 2080 : | $x_below /= @desc_dists; | ||
| 2081 : | } | ||
| 2082 : | golsen | 1.12 | |
| 2083 : | golsen | 1.1 | my $x = newick_x( $node ) || 0; |
| 2084 : | my $x_net = $x_below + $x; | ||
| 2085 : | |||
| 2086 : | [ $x_net, $x, $x_below, [ @desc_dists ], $node ] | ||
| 2087 : | } | ||
| 2088 : | |||
| 2089 : | golsen | 1.9 | |
| 2090 : | golsen | 1.12 | #------------------------------------------------------------------------------- |
| 2091 : | # Compile average tip to node distances descending, returning midpoint as | ||
| 2092 : | # [ $node1, $node2, $fraction_of_dist_between ] | ||
| 2093 : | #------------------------------------------------------------------------------- | ||
| 2094 : | golsen | 1.1 | sub average_to_tips_2 { |
| 2095 : | my ( $dists1, $x_above, $anc_node ) = @_; | ||
| 2096 : | my ( undef, $x, $x_below, $desc_list, $node ) = @$dists1; | ||
| 2097 : | |||
| 2098 : | # Are we done? Root is in this node's branch, or "above"? | ||
| 2099 : | |||
| 2100 : | golsen | 1.12 | my @mids = (); |
| 2101 : | golsen | 1.1 | if ( defined( $x_above ) && ( ( $x_above + $x ) >= $x_below ) ) |
| 2102 : | { | ||
| 2103 : | # At this point the root can only be in this node's branch, | ||
| 2104 : | # or "above" it in the current rooting of the tree (which | ||
| 2105 : | # would mean that the midpoint is actually down a different | ||
| 2106 : | # path from the root of the current tree). | ||
| 2107 : | # | ||
| 2108 : | # Is the root in the current branch? | ||
| 2109 : | |||
| 2110 : | if ( ( $x_below + $x ) >= $x_above ) | ||
| 2111 : | { | ||
| 2112 : | golsen | 1.12 | # We will need to make a new node for the root, $fract of |
| 2113 : | # the way from $node to $anc_node: | ||
| 2114 : | my $fract = ( $x > 0 ) ? 0.5 * ( ( $x_above - $x_below ) / $x + 1 ) | ||
| 2115 : | : 0.5; | ||
| 2116 : | push @mids, [ $node, $anc_node, $fract ]; | ||
| 2117 : | golsen | 1.1 | } |
| 2118 : | } | ||
| 2119 : | |||
| 2120 : | golsen | 1.12 | # The root might be somewhere below this node: |
| 2121 : | golsen | 1.1 | |
| 2122 : | golsen | 1.5 | my $n_1 = @$desc_list - ( $anc_node ? 0 : 1 ); |
| 2123 : | golsen | 1.1 | my $ttl_dist = ( @$desc_list * $x_below ) + ( defined( $x_above ) ? ( $x_above + $x ) : 0 ); |
| 2124 : | |||
| 2125 : | foreach ( @$desc_list ) | ||
| 2126 : | { | ||
| 2127 : | # If input tree is tip_rooted, $n-1 can be 0, so: | ||
| 2128 : | |||
| 2129 : | my $above2 = $n_1 ? ( ( $ttl_dist - $_->[0] ) / $n_1 ) : 0; | ||
| 2130 : | golsen | 1.12 | push @mids, average_to_tips_2( $_, $above2, $node ); |
| 2131 : | golsen | 1.1 | } |
| 2132 : | |||
| 2133 : | golsen | 1.12 | return @mids; |
| 2134 : | golsen | 1.1 | } |
| 2135 : | |||
| 2136 : | golsen | 1.9 | |
| 2137 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 2138 : | golsen | 1.5 | # Move root of tree to an approximate midpoint. Weight by tips. |
| 2139 : | # | ||
| 2140 : | # $newtree = reroot_newick_to_approx_midpoint_w( $tree ) | ||
| 2141 : | #------------------------------------------------------------------------------- | ||
| 2142 : | sub reroot_newick_to_approx_midpoint_w { | ||
| 2143 : | my ( $tree ) = @_; | ||
| 2144 : | |||
| 2145 : | golsen | 1.12 | # Compile average tip to node distances assending from tips |
| 2146 : | |||
| 2147 : | my $dists1 = average_to_tips_1_w( $tree ); | ||
| 2148 : | |||
| 2149 : | # Compile average tip to node distances descending, returning midpoints | ||
| 2150 : | |||
| 2151 : | my @mids = average_to_tips_2_w( $dists1, undef, undef, undef ); | ||
| 2152 : | |||
| 2153 : | # Reroot to first midpoint candidate | ||
| 2154 : | |||
| 2155 : | return $tree if ! @mids; | ||
| 2156 : | my ( $node1, $node2, $fraction ) = @{ $mids[0] }; | ||
| 2157 : | reroot_newick_to_node_ref( $tree, $fraction >= 0.5 ? $node2 : $node1 ); | ||
| 2158 : | } | ||
| 2159 : | |||
| 2160 : | |||
| 2161 : | #------------------------------------------------------------------------------- | ||
| 2162 : | # Move root of tree to an approximate midpoint. Weight by tips. | ||
| 2163 : | # | ||
| 2164 : | # $newtree = reroot_newick_to_midpoint_w( $tree ) | ||
| 2165 : | #------------------------------------------------------------------------------- | ||
| 2166 : | sub reroot_newick_to_midpoint_w { | ||
| 2167 : | my ( $tree ) = @_; | ||
| 2168 : | |||
| 2169 : | golsen | 1.5 | # Compile average tip to node distances assending |
| 2170 : | |||
| 2171 : | my $dists1 = average_to_tips_1_w( $tree ); | ||
| 2172 : | |||
| 2173 : | # Compile average tip to node distances descending, returning midpoint node | ||
| 2174 : | |||
| 2175 : | golsen | 1.12 | my @mids = average_to_tips_2_w( $dists1, undef, undef, undef ); |
| 2176 : | golsen | 1.5 | |
| 2177 : | golsen | 1.12 | # Reroot at first candidate midpoint |
| 2178 : | golsen | 1.5 | |
| 2179 : | golsen | 1.12 | @mids ? reroot_newick_between_node_refs( $tree, @{ $mids[0] } ) : $tree; |
| 2180 : | golsen | 1.5 | } |
| 2181 : | |||
| 2182 : | |||
| 2183 : | sub average_to_tips_1_w { | ||
| 2184 : | my ( $node ) = @_; | ||
| 2185 : | |||
| 2186 : | my @desc_dists = map { average_to_tips_1_w( $_ ) } newick_desc_list( $node ); | ||
| 2187 : | my $x_below = 0; | ||
| 2188 : | my $n_below = 1; | ||
| 2189 : | if ( @desc_dists ) | ||
| 2190 : | { | ||
| 2191 : | $n_below = 0; | ||
| 2192 : | my $n; | ||
| 2193 : | foreach ( @desc_dists ) | ||
| 2194 : | { | ||
| 2195 : | $n_below += $n = $_->[1]; | ||
| 2196 : | $x_below += $n * $_->[0]; | ||
| 2197 : | } | ||
| 2198 : | $x_below /= $n_below; | ||
| 2199 : | } | ||
| 2200 : | golsen | 1.12 | |
| 2201 : | golsen | 1.5 | my $x = newick_x( $node ) || 0; |
| 2202 : | my $x_net = $x_below + $x; | ||
| 2203 : | |||
| 2204 : | [ $x_net, $n_below, $x, $x_below, [ @desc_dists ], $node ] | ||
| 2205 : | } | ||
| 2206 : | |||
| 2207 : | |||
| 2208 : | sub average_to_tips_2_w { | ||
| 2209 : | my ( $dists1, $x_above, $n_above, $anc_node ) = @_; | ||
| 2210 : | my ( undef, $n_below, $x, $x_below, $desc_list, $node ) = @$dists1; | ||
| 2211 : | |||
| 2212 : | # Are we done? Root is in this node's branch, or "above"? | ||
| 2213 : | |||
| 2214 : | golsen | 1.12 | my @mids = (); |
| 2215 : | golsen | 1.5 | if ( defined( $x_above ) && ( ( $x_above + $x ) >= $x_below ) ) |
| 2216 : | { | ||
| 2217 : | # At this point the root can only be in this node's branch, | ||
| 2218 : | # or "above" it in the current rooting of the tree (which | ||
| 2219 : | # would mean that the midpoint is actually down a different | ||
| 2220 : | # path from the root of the current tree). | ||
| 2221 : | # | ||
| 2222 : | golsen | 1.12 | # Is their a root in the current branch? |
| 2223 : | golsen | 1.5 | |
| 2224 : | if ( ( $x_below + $x ) >= $x_above ) | ||
| 2225 : | { | ||
| 2226 : | golsen | 1.12 | # We will need to make a new node for the root, $fract of |
| 2227 : | # the way from $node to $anc_node: | ||
| 2228 : | my $fract = ( $x > 0 ) ? 0.5 * ( ( $x_above - $x_below ) / $x + 1 ) | ||
| 2229 : | : 0.5; | ||
| 2230 : | push @mids, [ $node, $anc_node, $fract ]; | ||
| 2231 : | golsen | 1.5 | } |
| 2232 : | } | ||
| 2233 : | |||
| 2234 : | # The root must be some where below this node: | ||
| 2235 : | |||
| 2236 : | $n_above ||= 0; | ||
| 2237 : | my $n = $n_above + $n_below; | ||
| 2238 : | my $ttl_w_dist = ( $n_below * $x_below ) | ||
| 2239 : | + ( defined( $x_above ) ? $n_above * ( $x_above + $x ) : 0 ); | ||
| 2240 : | |||
| 2241 : | foreach ( @$desc_list ) | ||
| 2242 : | { | ||
| 2243 : | my $n_2 = $_->[1]; # n in subtree | ||
| 2244 : | my $n_above2 = $n - $n_2; # tip rooted has 1 above | ||
| 2245 : | |||
| 2246 : | # If input tree is tip_rooted, $n_above2 can be 0, so: | ||
| 2247 : | |||
| 2248 : | my $x_above2 = $n_above2 ? ( ( $ttl_w_dist - $n_2 * $_->[0] ) / $n_above2 ) | ||
| 2249 : | : 0; | ||
| 2250 : | golsen | 1.12 | push @mids, average_to_tips_2_w( $_, $x_above2, $n_above2 || 1, $node ); |
| 2251 : | golsen | 1.5 | } |
| 2252 : | |||
| 2253 : | golsen | 1.12 | return @mids; |
| 2254 : | golsen | 1.5 | } |
| 2255 : | |||
| 2256 : | golsen | 1.9 | |
| 2257 : | golsen | 1.5 | #------------------------------------------------------------------------------- |
| 2258 : | golsen | 1.1 | # Move root of tree from tip to adjacent node. |
| 2259 : | # | ||
| 2260 : | # $newtree = uproot_tip_rooted_newick( $tree ) | ||
| 2261 : | #------------------------------------------------------------------------------- | ||
| 2262 : | sub uproot_tip_rooted_newick { | ||
| 2263 : | my ( $node ) = @_; | ||
| 2264 : | newick_is_tip_rooted( $node ) || return $node; | ||
| 2265 : | |||
| 2266 : | # Path to the sole descendant: | ||
| 2267 : | |||
| 2268 : | reroot_newick_by_path( $node, 1, newick_desc_i( $node, 1 ) ); | ||
| 2269 : | } | ||
| 2270 : | |||
| 2271 : | |||
| 2272 : | #------------------------------------------------------------------------------- | ||
| 2273 : | # Remove root bifurcation. | ||
| 2274 : | # | ||
| 2275 : | # Root node label, label comment and descendant list comment are discarded. | ||
| 2276 : | # | ||
| 2277 : | # $newtree = uproot_newick( $tree ) | ||
| 2278 : | #------------------------------------------------------------------------------- | ||
| 2279 : | sub uproot_newick { | ||
| 2280 : | my ( $node0 ) = @_; | ||
| 2281 : | newick_is_rooted( $node0 ) || return $node0; | ||
| 2282 : | |||
| 2283 : | my ( $node1, $node2 ) = newick_desc_list( $node0 ); | ||
| 2284 : | |||
| 2285 : | # Ensure that node1 has at least 1 descendant | ||
| 2286 : | |||
| 2287 : | if ( newick_n_desc( $node1 ) ) { | ||
| 2288 : | push @{ newick_desc_ref( $node1 ) }, $node2; # Add node2 to descend list | ||
| 2289 : | } | ||
| 2290 : | |||
| 2291 : | # Or node2 has at least 1 descendant | ||
| 2292 : | |||
| 2293 : | elsif ( newick_n_desc( $node2 ) ) { | ||
| 2294 : | unshift @{ newick_desc_ref( $node2 ) }, $node1; # Add node1 to descend list | ||
| 2295 : | ( $node1, $node2 ) = ( $node2, $node1 ); # And reverse labels | ||
| 2296 : | } | ||
| 2297 : | |||
| 2298 : | # We could make this into a tip rooted tree, but for now: | ||
| 2299 : | |||
| 2300 : | else { return $node0 } | ||
| 2301 : | |||
| 2302 : | # Prefix node1 branch to that of node2: | ||
| 2303 : | |||
| 2304 : | add_to_newick_branch( $node2, $node1 ); | ||
| 2305 : | set_newick_x( $node1, undef ); | ||
| 2306 : | |||
| 2307 : | # Tree prefix comment lists (as references): | ||
| 2308 : | |||
| 2309 : | my $C10 = newick_c1( $node0 ); | ||
| 2310 : | my $C11 = newick_c1( $node1 ); | ||
| 2311 : | golsen | 1.9 | if ( $C11 && @$C11 ) { |
| 2312 : | golsen | 1.1 | if ( $C10 && @$C10 ) { unshift @$C11, @$C10 } # Prefix to node1 comments |
| 2313 : | } | ||
| 2314 : | elsif ( $C10 && @$C10 ) { | ||
| 2315 : | set_newick_c1( $node1, $C10 ) # Or move node0 comments to node1 | ||
| 2316 : | } | ||
| 2317 : | |||
| 2318 : | $node1; | ||
| 2319 : | } | ||
| 2320 : | |||
| 2321 : | |||
| 2322 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2323 : | # Prefix branch of node2 to that of node1: | ||
| 2324 : | # | ||
| 2325 : | # $node1 = add_to_newick_branch( $node1, $node2 ) | ||
| 2326 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2327 : | sub add_to_newick_branch { | ||
| 2328 : | my ( $node1, $node2 ) = @_; | ||
| 2329 : | array_ref( $node1 ) || die "add_to_newick_branch: arg 1 not array ref\n"; | ||
| 2330 : | array_ref( $node2 ) || die "add_to_newick_branch: arg 2 not array ref\n"; | ||
| 2331 : | |||
| 2332 : | # Node structure template: | ||
| 2333 : | # my ( $DL, $L, $X, $C1, $C2, $C3, $C4, $C5 ) = @$node; | ||
| 2334 : | |||
| 2335 : | # Fix branch lengths for joining of two branches: | ||
| 2336 : | |||
| 2337 : | set_newick_x( $node1, newick_x( $node1 ) + newick_x( $node2 ) ); | ||
| 2338 : | |||
| 2339 : | # Merge branch length comments: | ||
| 2340 : | |||
| 2341 : | my $C41 = newick_c4( $node1 ); # Ref to node1 C4 | ||
| 2342 : | my $C42 = newick_c4( $node2 ); # Ref to node2 C4 | ||
| 2343 : | if ( $C41 && @$C41 ) { | ||
| 2344 : | if ( $C42 && @$C42 ) { unshift @$C41, @$C42 } # Add node2 comment | ||
| 2345 : | } | ||
| 2346 : | elsif ( $C42 && @$C42 ) { set_newick_c4( $node1, $C42 ) } # Or move node1 comment | ||
| 2347 : | |||
| 2348 : | my $C51 = newick_c5( $node1 ); # Ref to node1 C5 | ||
| 2349 : | my $C52 = newick_c5( $node2 ); # Ref to node2 C5 | ||
| 2350 : | if ( $C51 && @$C51 ) { | ||
| 2351 : | if ( $C52 && @$C52 ) { unshift @$C51, @$C52 } # Add node2 comment | ||
| 2352 : | } | ||
| 2353 : | elsif ( $C52 && @$C52 ) { set_newick_c5( $node1, $C52 ) } # Or move node1 comment | ||
| 2354 : | |||
| 2355 : | $node1; | ||
| 2356 : | } | ||
| 2357 : | |||
| 2358 : | |||
| 2359 : | #------------------------------------------------------------------------------- | ||
| 2360 : | golsen | 1.5 | # Collapse zero-length branches to make multifurcation. The original tree |
| 2361 : | # is modified. | ||
| 2362 : | # | ||
| 2363 : | # $tree = collapse_zero_length_branches( $tree ) | ||
| 2364 : | # $tree = collapse_zero_length_branches( $tree, $not_root ) | ||
| 2365 : | #------------------------------------------------------------------------------- | ||
| 2366 : | sub collapse_zero_length_branches { | ||
| 2367 : | my ( $tree, $not_root ) = @_; | ||
| 2368 : | array_ref( $tree ) || return undef; | ||
| 2369 : | |||
| 2370 : | my @desc = newick_desc_list( $tree ); | ||
| 2371 : | @desc or return ( $tree ); # Cannot collapse terminal branch | ||
| 2372 : | |||
| 2373 : | # Analyze descendants: | ||
| 2374 : | |||
| 2375 : | $not_root ||= 0; | ||
| 2376 : | my @new_desc = (); | ||
| 2377 : | my $changed = 0; | ||
| 2378 : | foreach ( @desc ) | ||
| 2379 : | { | ||
| 2380 : | my ( undef, @to_add ) = collapse_zero_length_branches( $_, $not_root+1 ); | ||
| 2381 : | if ( @to_add ) | ||
| 2382 : | { | ||
| 2383 : | push @new_desc, @to_add; | ||
| 2384 : | $changed = 1; | ||
| 2385 : | } | ||
| 2386 : | else | ||
| 2387 : | { | ||
| 2388 : | push @new_desc, $_; | ||
| 2389 : | } | ||
| 2390 : | } | ||
| 2391 : | set_newick_desc_ref( $tree, [ @new_desc ] ) if $changed; | ||
| 2392 : | |||
| 2393 : | # Collapse if not root, not tip and zero (or negative) branch: | ||
| 2394 : | |||
| 2395 : | my $collapse = $not_root && @new_desc && ( newick_x( $tree ) <= 0 ) ? 1 : 0; | ||
| 2396 : | ( $tree, ( $collapse ? @new_desc : () ) ); | ||
| 2397 : | } | ||
| 2398 : | |||
| 2399 : | golsen | 1.8 | #------------------------------------------------------------------------------- |
| 2400 : | # Add a subtree to a newick tree node: | ||
| 2401 : | # | ||
| 2402 : | # $node = newick_insert_at_node( $node, $subtree ) | ||
| 2403 : | #------------------------------------------------------------------------------- | ||
| 2404 : | sub newick_insert_at_node | ||
| 2405 : | { | ||
| 2406 : | my ( $node, $subtree ) = @_; | ||
| 2407 : | array_ref( $node ) && array_ref( $subtree ) or return undef; | ||
| 2408 : | |||
| 2409 : | # We could check validity of trees, but .... | ||
| 2410 : | |||
| 2411 : | my $dl = newick_desc_ref( $node ); | ||
| 2412 : | if ( array_ref( $dl ) ) | ||
| 2413 : | { | ||
| 2414 : | push @$dl, $subtree; | ||
| 2415 : | } | ||
| 2416 : | else | ||
| 2417 : | { | ||
| 2418 : | set_newick_desc_ref( $node, [ $subtree ] ); | ||
| 2419 : | } | ||
| 2420 : | return $node; | ||
| 2421 : | } | ||
| 2422 : | |||
| 2423 : | |||
| 2424 : | #------------------------------------------------------------------------------- | ||
| 2425 : | # Insert a subtree into a newick tree along the path between 2 nodes: | ||
| 2426 : | # | ||
| 2427 : | # $tree = newick_insert_between_nodes( $tree, $subtree, $node1, $node2, $fraction ) | ||
| 2428 : | #------------------------------------------------------------------------------- | ||
| 2429 : | sub newick_insert_between_nodes | ||
| 2430 : | { | ||
| 2431 : | my ( $tree, $subtree, $node1, $node2, $fraction ) = @_; | ||
| 2432 : | array_ref( $tree ) && array_ref( $subtree ) or return undef; | ||
| 2433 : | $fraction >= 0 && $fraction <= 1 or return undef; | ||
| 2434 : | |||
| 2435 : | # Find the paths to the nodes: | ||
| 2436 : | |||
| 2437 : | my @path1 = path_to_node( $tree, $node1 ) or return undef; | ||
| 2438 : | my @path2 = path_to_node( $tree, $node2 ) or return undef; | ||
| 2439 : | |||
| 2440 : | # Trim the common prefix: | ||
| 2441 : | |||
| 2442 : | while ( $path1[1] == $path2[1] ) | ||
| 2443 : | { | ||
| 2444 : | splice( @path1, 0, 2 ); | ||
| 2445 : | splice( @path2, 0, 2 ); | ||
| 2446 : | } | ||
| 2447 : | |||
| 2448 : | my ( @path, $dist ); | ||
| 2449 : | if ( @path1 < 3 ) | ||
| 2450 : | { | ||
| 2451 : | @path2 >= 3 or return undef; # node1 = node2 | ||
| 2452 : | golsen | 1.9 | $dist = $fraction * newick_path_length( @path2 ); |
| 2453 : | golsen | 1.8 | @path = @path2; |
| 2454 : | } | ||
| 2455 : | elsif ( @path2 < 3 ) | ||
| 2456 : | { | ||
| 2457 : | $dist = ( 1 - $fraction ) * newick_path_length( @path1 ); | ||
| 2458 : | @path = @path1; | ||
| 2459 : | } | ||
| 2460 : | else | ||
| 2461 : | { | ||
| 2462 : | my $dist1 = newick_path_length( @path1 ); | ||
| 2463 : | my $dist2 = newick_path_length( @path2 ); | ||
| 2464 : | $dist = $fraction * ( $dist1 + $dist2 ) - $dist1; | ||
| 2465 : | @path = ( $dist <= 0 ) ? @path1 : @path2; | ||
| 2466 : | $dist = abs( $dist ); | ||
| 2467 : | } | ||
| 2468 : | |||
| 2469 : | # Descend tree until we reach the insertion branch: | ||
| 2470 : | |||
| 2471 : | my $x; | ||
| 2472 : | while ( ( $dist > ( $x = newick_x( $path[2] ) ) ) && ( @path > 3 ) ) | ||
| 2473 : | { | ||
| 2474 : | $dist -= $x; | ||
| 2475 : | splice( @path, 0, 2 ); | ||
| 2476 : | } | ||
| 2477 : | |||
| 2478 : | # Insert the new node: | ||
| 2479 : | |||
| 2480 : | set_newick_desc_i( $path[0], $path[1], [ [ $path[2], $subtree ], undef, $dist ] ); | ||
| 2481 : | set_newick_x( $path[2], ( ( $x > $dist ) ? ( $x - $dist ) : 0 ) ); | ||
| 2482 : | |||
| 2483 : | return $tree; | ||
| 2484 : | } | ||
| 2485 : | |||
| 2486 : | golsen | 1.5 | |
| 2487 : | #------------------------------------------------------------------------------- | ||
| 2488 : | golsen | 1.1 | # Prune one or more tips from a tree: |
| 2489 : | # Caveat: if one tip is listed, the original tree is modified. | ||
| 2490 : | golsen | 1.5 | # if more than one tip is listed, a copy of the tree is returned |
| 2491 : | golsen | 1.1 | # (even if it is just listing the same tip twice!). |
| 2492 : | # | ||
| 2493 : | # $newtree = prune_from_newick( $tree, $tip ) | ||
| 2494 : | # $newtree = prune_from_newick( $tree, @tips ) | ||
| 2495 : | # $newtree = prune_from_newick( $tree, \@tips ) | ||
| 2496 : | #------------------------------------------------------------------------------- | ||
| 2497 : | sub prune_from_newick { | ||
| 2498 : | my ( $tr, @tips ) = @_; | ||
| 2499 : | if ( @tips == 1 && ref( $tips[0] ) eq "ARRAY" ) { @tips = @{ $tips[0] } } | ||
| 2500 : | golsen | 1.9 | |
| 2501 : | golsen | 1.1 | if ( @tips == 0 ) { return $tr } |
| 2502 : | if ( @tips == 1 ) { return prune_1_from_newick( $tr, @tips ) } | ||
| 2503 : | |||
| 2504 : | my %del = map { ( $_, 1 ) } @tips; | ||
| 2505 : | my @keep = grep { ! $del{ $_ } } newick_tip_list( $tr ); | ||
| 2506 : | newick_subtree( $tr, @keep ); | ||
| 2507 : | } | ||
| 2508 : | |||
| 2509 : | |||
| 2510 : | #------------------------------------------------------------------------------- | ||
| 2511 : | # Prune a tip from a tree: | ||
| 2512 : | # | ||
| 2513 : | # $newtree = prune_1_from_newick( $tree, $tip ) | ||
| 2514 : | #------------------------------------------------------------------------------- | ||
| 2515 : | sub prune_1_from_newick { | ||
| 2516 : | my ( $tr, $tip ) = @_; | ||
| 2517 : | my @path = path_to_tip( $tr, $tip ); | ||
| 2518 : | if ( @path < 3 ) { return $tr } | ||
| 2519 : | |||
| 2520 : | my $node = $path[-1]; # Node with the tip | ||
| 2521 : | my $i1 = $path[-2]; # Descendant number of node in ancestor desc list | ||
| 2522 : | my $anc1 = $path[-3]; # Ancestor of node | ||
| 2523 : | my $nd1 = newick_n_desc( $anc1 ); # Number of descendants of ancestor | ||
| 2524 : | my $anc2 = ( @path >= 5 ) ? $path[-5] : undef; # Ancestor of anc1 | ||
| 2525 : | |||
| 2526 : | # dump_tree( $node ); | ||
| 2527 : | # print STDERR "i1 = $i1\n"; | ||
| 2528 : | # dump_tree( $anc1 ); | ||
| 2529 : | # print STDERR "nd1 = $nd1\n"; | ||
| 2530 : | # defined( $anc2 ) && dump_tree( $anc2 ); | ||
| 2531 : | |||
| 2532 : | if ( $nd1 > 3 || ( $anc2 && $nd1 > 2 ) ) { # Tip joins at multifurcation | ||
| 2533 : | splice( @{ $anc1->[0] }, $i1-1, 1 ); # delete the descendant | ||
| 2534 : | } | ||
| 2535 : | |||
| 2536 : | elsif ( $anc2 ) { # Tip joins at internal bifurcation | ||
| 2537 : | my $sis = newick_desc_i( $anc1, 3-$i1 ); # find sister node | ||
| 2538 : | add_to_newick_branch( $sis, $anc1 ); # combine internal branches | ||
| 2539 : | set_newick_desc_i( $anc2, $path[-4], $sis ); # remove $anc1 | ||
| 2540 : | } | ||
| 2541 : | |||
| 2542 : | elsif ( $nd1 == 2) { # Tip joins bifurcating root node | ||
| 2543 : | my $sis = newick_desc_i( $anc1, 3-$i1 ); # find sister node | ||
| 2544 : | $sis->[1] = $anc1->[1] if ! $sis->[1] && $anc1->[1]; # root label | ||
| 2545 : | $sis->[2] = undef; # root branch len | ||
| 2546 : | $sis->[3] = $anc1->[3] if ! $sis->[3] && $anc1->[3]; # tree comment | ||
| 2547 : | $sis->[4] = $anc1->[4] if ! $sis->[4] && $anc1->[4]; # desc list comment | ||
| 2548 : | golsen | 1.9 | $sis->[5] = $anc1->[5] if ! $sis->[5] && $anc1->[5]; # label comment |
| 2549 : | golsen | 1.1 | $sis->[6] = undef if $sis->[6]; # root branch comment |
| 2550 : | $sis->[7] = undef if $sis->[7]; # root branch comment | ||
| 2551 : | $tr = $sis; # sister is new root | ||
| 2552 : | } | ||
| 2553 : | |||
| 2554 : | elsif ( $nd1 == 3 ) { # Tip joins trifurcating root: | ||
| 2555 : | splice( @{ $anc1->[0] }, $i1-1, 1 ); # delete the descendant, and | ||
| 2556 : | $tr = uproot_newick( $tr ); # fix the rooting | ||
| 2557 : | } | ||
| 2558 : | |||
| 2559 : | else { | ||
| 2560 : | return undef; | ||
| 2561 : | } | ||
| 2562 : | |||
| 2563 : | return $tr; | ||
| 2564 : | } | ||
| 2565 : | |||
| 2566 : | |||
| 2567 : | #------------------------------------------------------------------------------- | ||
| 2568 : | golsen | 1.12 | # Produce a potentially rooted subtree with the desired tips: |
| 2569 : | # | ||
| 2570 : | # Except for (some) tip nodes, the tree produced is a copy. | ||
| 2571 : | # There is no check that requested tips exist. | ||
| 2572 : | # | ||
| 2573 : | # $newtree = rooted_newick_subtree( $tree, @tips ) | ||
| 2574 : | # $newtree = rooted_newick_subtree( $tree, \@tips ) | ||
| 2575 : | #------------------------------------------------------------------------------- | ||
| 2576 : | sub rooted_newick_subtree { | ||
| 2577 : | my ( $tr, @tips ) = @_; | ||
| 2578 : | if ( @tips == 1 && ref( $tips[0] ) eq "ARRAY" ) { @tips = @{ $tips[0] } } | ||
| 2579 : | |||
| 2580 : | if ( @tips < 2 ) { return undef } | ||
| 2581 : | my $keephash = { map { ( $_, 1 ) } @tips }; | ||
| 2582 : | my $tr2 = subtree1( $tr, $keephash ); | ||
| 2583 : | $tr2->[2] = undef if $tr2; # undef root branch length | ||
| 2584 : | $tr2; | ||
| 2585 : | } | ||
| 2586 : | |||
| 2587 : | |||
| 2588 : | #------------------------------------------------------------------------------- | ||
| 2589 : | golsen | 1.1 | # Produce a subtree with the desired tips: |
| 2590 : | # | ||
| 2591 : | # Except for (some) tip nodes, the tree produced is a copy. | ||
| 2592 : | # There is no check that requested tips exist. | ||
| 2593 : | # | ||
| 2594 : | # $newtree = newick_subtree( $tree, @tips ) | ||
| 2595 : | # $newtree = newick_subtree( $tree, \@tips ) | ||
| 2596 : | #------------------------------------------------------------------------------- | ||
| 2597 : | sub newick_subtree { | ||
| 2598 : | my ( $tr, @tips ) = @_; | ||
| 2599 : | if ( @tips == 1 && ref( $tips[0] ) eq "ARRAY" ) { @tips = @{ $tips[0] } } | ||
| 2600 : | |||
| 2601 : | if ( @tips < 2 ) { return undef } | ||
| 2602 : | my $was_rooted = newick_is_rooted( $tr ); | ||
| 2603 : | my $keephash = { map { ( $_, 1 ) } @tips }; | ||
| 2604 : | my $tr2 = subtree1( $tr, $keephash ); | ||
| 2605 : | $tr2 = uproot_newick( $tr2 ) if ! $was_rooted && newick_is_rooted( $tr2 ); | ||
| 2606 : | $tr2->[2] = undef if $tr2; # undef root branch length | ||
| 2607 : | $tr2; | ||
| 2608 : | } | ||
| 2609 : | |||
| 2610 : | |||
| 2611 : | sub subtree1 { | ||
| 2612 : | my ( $tr, $keep ) = @_; | ||
| 2613 : | my @desc1 = newick_desc_list( $tr ); | ||
| 2614 : | |||
| 2615 : | # Is this a tip, and is it in the keep list? | ||
| 2616 : | |||
| 2617 : | if ( @desc1 < 1 ) { | ||
| 2618 : | return ( $keep->{ newick_lbl( $tr ) } ) ? $tr : undef; | ||
| 2619 : | } | ||
| 2620 : | |||
| 2621 : | # Internal node: analyze the descendants: | ||
| 2622 : | |||
| 2623 : | my @desc2 = (); | ||
| 2624 : | foreach ( @desc1 ) { | ||
| 2625 : | my $desc = subtree1( $_, $keep ); | ||
| 2626 : | if ( $desc && @$desc ) { push @desc2, $desc } | ||
| 2627 : | } | ||
| 2628 : | |||
| 2629 : | if ( @desc2 == 0 ) { return undef } | ||
| 2630 : | if ( @desc2 > 1 ) { return [ \@desc2, @$tr[ 1 .. @$tr - 1 ] ] } | ||
| 2631 : | |||
| 2632 : | # Exactly 1 descendant | ||
| 2633 : | |||
| 2634 : | my $desc = $desc2[ 0 ]; | ||
| 2635 : | my @nn = ( $desc->[0], | ||
| 2636 : | $desc->[1] ? $desc->[1] : $tr->[1], | ||
| 2637 : | defined( $tr->[2] ) ? $desc->[2] + $tr->[2] : undef | ||
| 2638 : | ); | ||
| 2639 : | |||
| 2640 : | # Merge comments (only recreating the ones that existed): | ||
| 2641 : | |||
| 2642 : | if ( $tr->[3] && @{$tr->[3]} || $desc->[3] && @{$desc->[3]} ) { | ||
| 2643 : | $nn[3] = [ $tr->[3] ? @{$tr->[3]} : (), $desc->[3] ? @{$desc->[3]} : () ]; | ||
| 2644 : | } | ||
| 2645 : | if ( $tr->[4] && @{$tr->[4]} || $desc->[4] && @{$desc->[4]} ) { | ||
| 2646 : | $nn[4] = [ $tr->[4] ? @{$tr->[4]} : (), $desc->[4] ? @{$desc->[4]} : () ]; | ||
| 2647 : | } | ||
| 2648 : | if ( $tr->[5] && @{$tr->[5]} || $desc->[5] && @{$desc->[5]} ) { | ||
| 2649 : | $nn[5] = [ $tr->[5] ? @{$tr->[5]} : (), $desc->[5] ? @{$desc->[5]} : () ]; | ||
| 2650 : | } | ||
| 2651 : | if ( $tr->[6] && @{$tr->[6]} || $desc->[6] && @{$desc->[6]} ) { | ||
| 2652 : | $nn[6] = [ $tr->[6] ? @{$tr->[6]} : (), $desc->[6] ? @{$desc->[6]} : () ]; | ||
| 2653 : | } | ||
| 2654 : | if ( $tr->[7] && @{$tr->[7]} || $desc->[7] && @{$desc->[7]} ) { | ||
| 2655 : | $nn[7] = [ $tr->[7] ? @{$tr->[7]} : (), $desc->[7] ? @{$desc->[7]} : () ]; | ||
| 2656 : | } | ||
| 2657 : | |||
| 2658 : | return \@nn; | ||
| 2659 : | } | ||
| 2660 : | |||
| 2661 : | |||
| 2662 : | golsen | 1.12 | #------------------------------------------------------------------------------- |
| 2663 : | # The smallest subtree of rooted tree that includes @tips: | ||
| 2664 : | # | ||
| 2665 : | # $node = newick_covering_subtree( $tree, @tips ) | ||
| 2666 : | # $node = newick_covering_subtree( $tree, \@tips ) | ||
| 2667 : | #------------------------------------------------------------------------------- | ||
| 2668 : | |||
| 2669 : | sub newick_covering_subtree { | ||
| 2670 : | my $tree = shift; | ||
| 2671 : | my %tips = map { $_ => 1 } ( ( ref( $_[0] ) eq 'ARRAY' ) ? @{ $_[0] } : @_ ); | ||
| 2672 : | |||
| 2673 : | # Return smallest covering node, if any: | ||
| 2674 : | |||
| 2675 : | ( newick_covering_subtree( $tree, \%tips ) )[ 0 ]; | ||
| 2676 : | } | ||
| 2677 : | |||
| 2678 : | |||
| 2679 : | sub newick_covering_subtree_1 { | ||
| 2680 : | my ( $node, $tips ) = @_; | ||
| 2681 : | my $n_cover = 0; | ||
| 2682 : | my @desc = newick_desc_list( $node ); | ||
| 2683 : | if ( @desc ) | ||
| 2684 : | { | ||
| 2685 : | foreach ( @desc ) | ||
| 2686 : | { | ||
| 2687 : | my ( $subtree, $n ) = newick_covering_subtree_1( $_, $tips ); | ||
| 2688 : | return ( $subtree, $n ) if $subtree; | ||
| 2689 : | $n_cover += $n; | ||
| 2690 : | } | ||
| 2691 : | } | ||
| 2692 : | elsif ( $tips->{ newick_lbl( $node ) } ) | ||
| 2693 : | { | ||
| 2694 : | $n_cover++; | ||
| 2695 : | } | ||
| 2696 : | |||
| 2697 : | # If all tips are covered, return node | ||
| 2698 : | |||
| 2699 : | ( $n_cover == keys %$tips ) ? ( $node, $n_cover ) : ( undef, $n_cover ); | ||
| 2700 : | } | ||
| 2701 : | |||
| 2702 : | |||
| 2703 : | golsen | 1.1 | #=============================================================================== |
| 2704 : | # | ||
| 2705 : | golsen | 1.9 | # Representative subtrees |
| 2706 : | # | ||
| 2707 : | #=============================================================================== | ||
| 2708 : | # Find subtree of size n representating vicinity of the root: | ||
| 2709 : | # | ||
| 2710 : | # $subtree = root_neighborhood_representative_tree( $tree, $n, \%tip_priority ) | ||
| 2711 : | # $subtree = root_neighborhood_representative_tree( $tree, $n ) | ||
| 2712 : | # | ||
| 2713 : | # Note that if $tree is rooted, then the subtree will also be. This can have | ||
| 2714 : | # consequences on downstream programs. | ||
| 2715 : | #------------------------------------------------------------------------------- | ||
| 2716 : | sub root_neighborhood_representative_tree | ||
| 2717 : | { | ||
| 2718 : | my ( $tree, $n, $tip_priority ) = @_; | ||
| 2719 : | array_ref( $tree ) && ( $n >= 2 ) or return undef; | ||
| 2720 : | if ( newick_tip_count( $tree ) <= $n ) { return $tree } | ||
| 2721 : | |||
| 2722 : | $tip_priority ||= default_tip_priority( $tree ); | ||
| 2723 : | my @tips = map { representative_tip_of_newick_node( $_, $tip_priority ) } | ||
| 2724 : | root_proximal_newick_subtrees( $tree, $n ); | ||
| 2725 : | |||
| 2726 : | newick_subtree( copy_newick_tree( $tree ), \@tips ); | ||
| 2727 : | } | ||
| 2728 : | |||
| 2729 : | |||
| 2730 : | #------------------------------------------------------------------------------- | ||
| 2731 : | # Find n tips to represent tree lineages in vicinity of another tip. | ||
| 2732 : | # Default tip priority is short total branch length. | ||
| 2733 : | # | ||
| 2734 : | # \@tips = root_neighborhood_representative_tips( $tree, $n, \%tip_priority ) | ||
| 2735 : | # @tips = root_neighborhood_representative_tips( $tree, $n, \%tip_priority ) | ||
| 2736 : | # \@tips = root_neighborhood_representative_tips( $tree, $n ) | ||
| 2737 : | # @tips = root_neighborhood_representative_tips( $tree, $n ) | ||
| 2738 : | #------------------------------------------------------------------------------- | ||
| 2739 : | sub root_neighborhood_representative_tips | ||
| 2740 : | { | ||
| 2741 : | my ( $tree, $n, $tip_priority ) = @_; | ||
| 2742 : | array_ref( $tree ) && ( $n >= 2 ) or return undef; | ||
| 2743 : | |||
| 2744 : | my @tips; | ||
| 2745 : | if ( newick_tip_count( $tree ) <= $n ) | ||
| 2746 : | { | ||
| 2747 : | @tips = newick_tip_list( $tree ); | ||
| 2748 : | } | ||
| 2749 : | else | ||
| 2750 : | { | ||
| 2751 : | $tip_priority ||= default_tip_priority( $tree ); | ||
| 2752 : | @tips = map { representative_tip_of_newick_node( $_, $tip_priority ) } | ||
| 2753 : | root_proximal_newick_subtrees( $tree, $n ); | ||
| 2754 : | } | ||
| 2755 : | |||
| 2756 : | wantarray ? @tips : \@tips; | ||
| 2757 : | } | ||
| 2758 : | |||
| 2759 : | |||
| 2760 : | #------------------------------------------------------------------------------- | ||
| 2761 : | # Find subtree of size n representating vicinity of a tip: | ||
| 2762 : | # | ||
| 2763 : | # $subtree = tip_neighborhood_representative_tree( $tree, $tip, $n, \%tip_priority ) | ||
| 2764 : | # $subtree = tip_neighborhood_representative_tree( $tree, $tip, $n ) | ||
| 2765 : | #------------------------------------------------------------------------------- | ||
| 2766 : | sub tip_neighborhood_representative_tree | ||
| 2767 : | { | ||
| 2768 : | my ( $tree, $tip, $n, $tip_priority ) = @_; | ||
| 2769 : | array_ref( $tree ) && $tip && ( $n >= 2 ) or return undef; | ||
| 2770 : | newick_tip_in_tree( $tree, $tip ) or return undef; | ||
| 2771 : | |||
| 2772 : | my $tree1 = copy_newick_tree( $tree ); | ||
| 2773 : | if ( newick_tip_count( $tree1 ) - 1 <= $n ) | ||
| 2774 : | { | ||
| 2775 : | return prune_from_newick( $tree1, $tip ) | ||
| 2776 : | } | ||
| 2777 : | |||
| 2778 : | $tree1 = reroot_newick_to_tip( $tree1, $tip ); | ||
| 2779 : | $tree1 = newick_desc_i( $tree1, 1 ); # Node immediately below tip | ||
| 2780 : | my @tips = root_neighborhood_representative_tips( $tree1, $n, $tip_priority ); | ||
| 2781 : | newick_subtree( copy_newick_tree( $tree ), \@tips ); | ||
| 2782 : | } | ||
| 2783 : | |||
| 2784 : | |||
| 2785 : | #------------------------------------------------------------------------------- | ||
| 2786 : | # Find n tips to represent tree lineages in vicinity of another tip. | ||
| 2787 : | # Default tip priority is short total branch length. | ||
| 2788 : | # | ||
| 2789 : | # \@tips = tip_neighborhood_representative_tips( $tree, $tip, $n, \%tip_priority ) | ||
| 2790 : | # @tips = tip_neighborhood_representative_tips( $tree, $tip, $n, \%tip_priority ) | ||
| 2791 : | # \@tips = tip_neighborhood_representative_tips( $tree, $tip, $n ) | ||
| 2792 : | # @tips = tip_neighborhood_representative_tips( $tree, $tip, $n ) | ||
| 2793 : | #------------------------------------------------------------------------------- | ||
| 2794 : | sub tip_neighborhood_representative_tips | ||
| 2795 : | { | ||
| 2796 : | my ( $tree, $tip, $n, $tip_priority ) = @_; | ||
| 2797 : | array_ref( $tree ) && $tip && ( $n >= 2 ) or return undef; | ||
| 2798 : | newick_tip_in_tree( $tree, $tip ) or return undef; | ||
| 2799 : | |||
| 2800 : | my @tips = newick_tip_list( $tree ); | ||
| 2801 : | if ( newick_tip_count( $tree ) - 1 <= $n ) | ||
| 2802 : | { | ||
| 2803 : | @tips = grep { $_ ne $tip } @tips; | ||
| 2804 : | } | ||
| 2805 : | else | ||
| 2806 : | { | ||
| 2807 : | my $tree1 = copy_newick_tree( $tree ); | ||
| 2808 : | $tree1 = reroot_newick_to_tip( $tree1, $tip ); | ||
| 2809 : | $tree1 = newick_desc_i( $tree1, 1 ); # Node immediately below tip | ||
| 2810 : | @tips = root_neighborhood_representative_tips( $tree1, $n, $tip_priority ); | ||
| 2811 : | } | ||
| 2812 : | |||
| 2813 : | wantarray ? @tips : \@tips; | ||
| 2814 : | } | ||
| 2815 : | |||
| 2816 : | |||
| 2817 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2818 : | # Anonymous hash of the negative distance from root to each tip: | ||
| 2819 : | # | ||
| 2820 : | # \%tip_priority = default_tip_priority( $tree ) | ||
| 2821 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2822 : | sub default_tip_priority | ||
| 2823 : | { | ||
| 2824 : | my ( $tree ) = @_; | ||
| 2825 : | my $tip_distances = newick_tip_distances( $tree ) || {}; | ||
| 2826 : | return { map { $_ => -$tip_distances->{$_} } keys %$tip_distances }; | ||
| 2827 : | } | ||
| 2828 : | |||
| 2829 : | |||
| 2830 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2831 : | # Select a tip from a subtree base on a priority value: | ||
| 2832 : | # | ||
| 2833 : | # $tip = representative_tip_of_newick_node( $node, \%tip_priority ) | ||
| 2834 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2835 : | sub representative_tip_of_newick_node | ||
| 2836 : | { | ||
| 2837 : | my ( $node, $tip_priority ) = @_; | ||
| 2838 : | my ( $tip ) = sort { $b->[1] <=> $a->[1] } # The best | ||
| 2839 : | map { [ $_, $tip_priority->{ $_ } ] } | ||
| 2840 : | newick_tip_list( $node ); | ||
| 2841 : | $tip->[0]; # Label from label-priority pair | ||
| 2842 : | } | ||
| 2843 : | |||
| 2844 : | |||
| 2845 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2846 : | # Find n subtrees focused around the root of a tree. Typically each will | ||
| 2847 : | # then be reduced to a single tip to make a representative tree: | ||
| 2848 : | # | ||
| 2849 : | # @subtrees = root_proximal_newick_subtrees( $tree, $n ) | ||
| 2850 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2851 : | sub root_proximal_newick_subtrees | ||
| 2852 : | { | ||
| 2853 : | my ( $tree, $n ) = @_; | ||
| 2854 : | my $node_start_end = newick_branch_intervals( $tree ); | ||
| 2855 : | n_representative_branches( $n, $node_start_end ); | ||
| 2856 : | } | ||
| 2857 : | |||
| 2858 : | |||
| 2859 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2860 : | # @node_start_end = newick_branch_intervals( $tree ) | ||
| 2861 : | # \@node_start_end = newick_branch_intervals( $tree ) | ||
| 2862 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2863 : | sub newick_branch_intervals | ||
| 2864 : | { | ||
| 2865 : | my ( $node, $parent_x ) = @_; | ||
| 2866 : | $parent_x ||= 0; | ||
| 2867 : | my ( $desc, undef, $dx ) = @$node; | ||
| 2868 : | my $x = $parent_x + $dx; | ||
| 2869 : | my $interval = [ $node, $parent_x, $desc && @$desc ? $x : 1e100 ]; | ||
| 2870 : | my @intervals = ( $interval, | ||
| 2871 : | map { &newick_branch_intervals( $_, $x ) } @$desc | ||
| 2872 : | ); | ||
| 2873 : | return wantarray ? @intervals : \@intervals; | ||
| 2874 : | } | ||
| 2875 : | |||
| 2876 : | |||
| 2877 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2878 : | # @ids = n_representative_branches( $n, @id_start_end ) | ||
| 2879 : | # @ids = n_representative_branches( $n, \@id_start_end ) | ||
| 2880 : | # \@ids = n_representative_branches( $n, @id_start_end ) | ||
| 2881 : | # \@ids = n_representative_branches( $n, \@id_start_end ) | ||
| 2882 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2883 : | sub n_representative_branches | ||
| 2884 : | { | ||
| 2885 : | my $n = shift; | ||
| 2886 : | # Sort intervals by start point: | ||
| 2887 : | my @unprocessed = sort { $a->[1] <=> $b->[1] } | ||
| 2888 : | ( @_ == 1 ) ? @{ $_[0] } : @_; | ||
| 2889 : | my @active = (); | ||
| 2890 : | my ( $interval, $current_point ); | ||
| 2891 : | foreach $interval ( @unprocessed ) | ||
| 2892 : | { | ||
| 2893 : | $current_point = $interval->[1]; | ||
| 2894 : | # Filter out intervals that have ended. This is N**2 in the number | ||
| 2895 : | # of representatives. Fixing this would require maintaining a sorted | ||
| 2896 : | # active list. | ||
| 2897 : | @active = grep { $_->[2] > $current_point } @active; | ||
| 2898 : | push @active, $interval; | ||
| 2899 : | last if ( @active >= $n ); | ||
| 2900 : | } | ||
| 2901 : | |||
| 2902 : | my @ids = map { $_->[0] } @active; | ||
| 2903 : | return wantarray() ? @ids : \@ids; | ||
| 2904 : | } | ||
| 2905 : | |||
| 2906 : | |||
| 2907 : | #=============================================================================== | ||
| 2908 : | # | ||
| 2909 : | golsen | 1.1 | # Tree writing and reading |
| 2910 : | # | ||
| 2911 : | #=============================================================================== | ||
| 2912 : | overbeek | 1.7 | # writeNewickTree( $tree ) |
| 2913 : | # writeNewickTree( $tree, $file ) | ||
| 2914 : | # writeNewickTree( $tree, \*FH ) | ||
| 2915 : | golsen | 1.1 | #------------------------------------------------------------------------------- |
| 2916 : | sub writeNewickTree { | ||
| 2917 : | my ( $tree, $file ) = @_; | ||
| 2918 : | overbeek | 1.7 | my ( $fh, $close ) = open_output( $file ); |
| 2919 : | $fh or return; | ||
| 2920 : | print $fh ( strNewickTree( $tree ), "\n" ); | ||
| 2921 : | close $fh if $close; | ||
| 2922 : | golsen | 1.1 | } |
| 2923 : | |||
| 2924 : | |||
| 2925 : | #------------------------------------------------------------------------------- | ||
| 2926 : | # fwriteNewickTree( $file, $tree ) # Args reversed to writeNewickTree | ||
| 2927 : | #------------------------------------------------------------------------------- | ||
| 2928 : | sub fwriteNewickTree { writeNewickTree( $_[1], $_[0] ) } | ||
| 2929 : | |||
| 2930 : | |||
| 2931 : | #------------------------------------------------------------------------------- | ||
| 2932 : | # $treestring = strNewickTree( $tree ) | ||
| 2933 : | #------------------------------------------------------------------------------- | ||
| 2934 : | sub strNewickTree { | ||
| 2935 : | my $node = shift @_; | ||
| 2936 : | strNewickSubtree( $node, "" ) . ";"; | ||
| 2937 : | } | ||
| 2938 : | |||
| 2939 : | |||
| 2940 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2941 : | # $string = strNewickSubtree( $node, $prefix ) | ||
| 2942 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2943 : | sub strNewickSubtree { | ||
| 2944 : | my ( $node, $prefix ) = @_; | ||
| 2945 : | my $s; | ||
| 2946 : | |||
| 2947 : | $s = strNewickComments( newick_c1( $node ), $prefix ); | ||
| 2948 : | if ( $s ) { $prefix = " " } | ||
| 2949 : | |||
| 2950 : | my $ndesc; | ||
| 2951 : | if ( $ndesc = newick_n_desc( $node ) ) { | ||
| 2952 : | for (my $d = 1; $d <= $ndesc; $d++) { | ||
| 2953 : | $s .= ( ( $d == 1 ) ? $prefix . "(" : "," ) | ||
| 2954 : | . strNewickSubtree( newick_desc_i( $node, $d ), " " ); | ||
| 2955 : | } | ||
| 2956 : | |||
| 2957 : | $s .= ")" . strNewickComments( newick_c2( $node ), " " ); | ||
| 2958 : | $prefix = " "; | ||
| 2959 : | } | ||
| 2960 : | |||
| 2961 : | if ( defined( newick_lbl( $node ) ) && newick_lbl( $node ) ) { | ||
| 2962 : | $s .= $prefix | ||
| 2963 : | . q_newick_lbl( $node ) | ||
| 2964 : | . strNewickComments( newick_c3( $node ), " " ); | ||
| 2965 : | } | ||
| 2966 : | |||
| 2967 : | if ( defined( newick_x( $node ) ) ) { | ||
| 2968 : | $s .= ":" | ||
| 2969 : | . strNewickComments( newick_c4( $node ), " " ) | ||
| 2970 : | . sprintf( " %.6f", newick_x( $node ) ) | ||
| 2971 : | . strNewickComments( newick_c5( $node ), " " ); | ||
| 2972 : | } | ||
| 2973 : | |||
| 2974 : | $s; | ||
| 2975 : | } | ||
| 2976 : | |||
| 2977 : | |||
| 2978 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2979 : | # $string = strNewickComments( $clist, $prefix ) | ||
| 2980 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2981 : | sub strNewickComments { | ||
| 2982 : | my ( $clist, $prefix ) = @_; | ||
| 2983 : | array_ref( $clist ) && ( @$clist > 0 ) || return ""; | ||
| 2984 : | $prefix . "[" . join( "] [", @$clist ) . "]"; | ||
| 2985 : | } | ||
| 2986 : | |||
| 2987 : | |||
| 2988 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2989 : | # $quoted_label = q_newick_lbl( $label ) | ||
| 2990 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 2991 : | sub q_newick_lbl { | ||
| 2992 : | my $lbl = newick_lbl( $_[0] ); | ||
| 2993 : | defined( $lbl ) && ( $lbl ne "" ) || return undef; | ||
| 2994 : | |||
| 2995 : | if ( $lbl =~ m/^[^][()_:;,]+$/ # Anything but []()_:;, | ||
| 2996 : | && $lbl !~ m/^'/ ) { # and does not start with ' | ||
| 2997 : | $lbl =~ s/ /_/g; # Recode blanks as _ | ||
| 2998 : | return $lbl; | ||
| 2999 : | } | ||
| 3000 : | |||
| 3001 : | else { | ||
| 3002 : | $lbl =~ s/'/''/g; # Double existing single quote marks | ||
| 3003 : | return q(') . $lbl . q('); # Wrap in single quote marks | ||
| 3004 : | } | ||
| 3005 : | } | ||
| 3006 : | |||
| 3007 : | |||
| 3008 : | #=============================================================================== | ||
| 3009 : | # $treestring = formatNewickTree( $tree ) | ||
| 3010 : | #=============================================================================== | ||
| 3011 : | sub formatNewickTree { | ||
| 3012 : | formatNewickSubtree( $_[0], "", "" ) . ";"; | ||
| 3013 : | } | ||
| 3014 : | |||
| 3015 : | |||
| 3016 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3017 : | # $string = formatNewickSubtree( $node, $prefix, $indent ) | ||
| 3018 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3019 : | sub formatNewickSubtree { | ||
| 3020 : | my ( $node, $prefix, $indent ) = @_; | ||
| 3021 : | my $s; | ||
| 3022 : | |||
| 3023 : | $s = formatNewickComments( newick_c1( $node ), $prefix, $indent ); | ||
| 3024 : | if ( $s ) { $prefix = "\n$indent" } | ||
| 3025 : | |||
| 3026 : | if ( my $ndesc = newick_n_desc( $node ) ) { | ||
| 3027 : | for (my $d = 1; $d <= $ndesc; $d++) { | ||
| 3028 : | $s .= ( ( $d == 1 ) ? $prefix . "(" : ",\n$indent " ) | ||
| 3029 : | . formatNewickSubtree( newick_desc_i( $node, $d ), " ", $indent . " " ); | ||
| 3030 : | } | ||
| 3031 : | |||
| 3032 : | $s .= "\n$indent)" . formatNewickComments( newick_c2( $node ), " ", $indent ); | ||
| 3033 : | $prefix = " "; | ||
| 3034 : | } | ||
| 3035 : | |||
| 3036 : | if ( defined( newick_lbl( $node ) ) && newick_lbl( $node ) ) { | ||
| 3037 : | $s .= $prefix | ||
| 3038 : | . q_newick_lbl( $node ) | ||
| 3039 : | . formatNewickComments( newick_c3( $node ), " ", $indent ); | ||
| 3040 : | } | ||
| 3041 : | |||
| 3042 : | if ( defined( newick_x( $node ) ) ) { | ||
| 3043 : | $s .= ":" | ||
| 3044 : | . formatNewickComments( newick_c4( $node ), " ", $indent ) | ||
| 3045 : | . sprintf(" %.6f", newick_x( $node ) ) | ||
| 3046 : | . formatNewickComments( newick_c5( $node ), " ", $indent ); | ||
| 3047 : | } | ||
| 3048 : | |||
| 3049 : | $s; | ||
| 3050 : | } | ||
| 3051 : | |||
| 3052 : | |||
| 3053 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3054 : | # $string = formatNewickComments( $clist, $prefix, $indent ) | ||
| 3055 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3056 : | sub formatNewickComments { | ||
| 3057 : | my ( $clist, $prefix, $indent ) = @_; | ||
| 3058 : | array_ref( $clist ) && @$clist || return ""; | ||
| 3059 : | $prefix . "[" . join( "] [", @$clist ) . "]"; | ||
| 3060 : | } | ||
| 3061 : | |||
| 3062 : | |||
| 3063 : | #=============================================================================== | ||
| 3064 : | overbeek | 1.7 | # $tree = read_newick_tree( $file ) # reads to a semicolon |
| 3065 : | # @trees = read_newick_trees( $file ) # reads to end of file | ||
| 3066 : | #=============================================================================== | ||
| 3067 : | |||
| 3068 : | sub read_newick_tree | ||
| 3069 : | { | ||
| 3070 : | my $file = shift; | ||
| 3071 : | my ( $fh, $close ) = open_input( $file ); | ||
| 3072 : | my $tree; | ||
| 3073 : | my @lines = (); | ||
| 3074 : | golsen | 1.9 | foreach ( <$fh> ) |
| 3075 : | overbeek | 1.7 | { |
| 3076 : | chomp; | ||
| 3077 : | push @lines, $_; | ||
| 3078 : | if ( /;/ ) | ||
| 3079 : | { | ||
| 3080 : | $tree = parse_newick_tree_str( join( ' ', @lines ) ); | ||
| 3081 : | last; | ||
| 3082 : | } | ||
| 3083 : | } | ||
| 3084 : | close $fh if $close; | ||
| 3085 : | |||
| 3086 : | $tree; | ||
| 3087 : | } | ||
| 3088 : | |||
| 3089 : | |||
| 3090 : | sub read_newick_trees | ||
| 3091 : | { | ||
| 3092 : | my $file = shift; | ||
| 3093 : | my ( $fh, $close ) = open_input( $file ); | ||
| 3094 : | my @trees = (); | ||
| 3095 : | my @lines = (); | ||
| 3096 : | golsen | 1.9 | foreach ( <$fh> ) |
| 3097 : | overbeek | 1.7 | { |
| 3098 : | chomp; | ||
| 3099 : | push @lines, $_; | ||
| 3100 : | if ( /;/ ) | ||
| 3101 : | { | ||
| 3102 : | push @trees, parse_newick_tree_str( join( ' ', @lines ) ); | ||
| 3103 : | @lines = () | ||
| 3104 : | } | ||
| 3105 : | } | ||
| 3106 : | close $fh if $close; | ||
| 3107 : | |||
| 3108 : | @trees; | ||
| 3109 : | } | ||
| 3110 : | |||
| 3111 : | |||
| 3112 : | #=============================================================================== | ||
| 3113 : | golsen | 1.1 | # Tree reader adapted from the C language reader in fastDNAml |
| 3114 : | # | ||
| 3115 : | # $tree = parse_newick_tree_str( $string ) | ||
| 3116 : | #=============================================================================== | ||
| 3117 : | sub parse_newick_tree_str { | ||
| 3118 : | my $s = shift @_; | ||
| 3119 : | |||
| 3120 : | my ( $ind, $rootnode ) = parse_newick_subtree( $s, 0 ); | ||
| 3121 : | if ( substr( $s, $ind, 1 ) ne ";") { warn "warning: tree missing ';'\n" } | ||
| 3122 : | $rootnode; | ||
| 3123 : | } | ||
| 3124 : | |||
| 3125 : | |||
| 3126 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3127 : | # Read a subtrees recursively (everything of tree but a semicolon) | ||
| 3128 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3129 : | sub parse_newick_subtree { | ||
| 3130 : | my ( $s, $ind ) = @_; | ||
| 3131 : | |||
| 3132 : | my $newnode = []; | ||
| 3133 : | my @dlist = (); | ||
| 3134 : | my ( $lbl, $x, $c1, $c2, $c3, $c4, $c5 ); | ||
| 3135 : | golsen | 1.9 | |
| 3136 : | golsen | 1.1 | ( $ind, $c1 ) = getNextTreeChar( $s, $ind ); # Comment 1 |
| 3137 : | if ( ! defined( $ind ) ) { treeParseError( "missing subtree" ) } | ||
| 3138 : | if ( $c1 && @$c1 ) { set_newick_c1( $newnode, $c1 ) } | ||
| 3139 : | |||
| 3140 : | if ( substr( $s, $ind, 1 ) eq "(" ) { # New internal node | ||
| 3141 : | while ( ! @dlist || ( substr( $s, $ind, 1 ) eq "," ) ) { | ||
| 3142 : | my $desc; | ||
| 3143 : | ( $ind, $desc ) = parse_newick_subtree( $s, $ind+1 ); | ||
| 3144 : | if (! $ind) { return () } | ||
| 3145 : | push @dlist, $desc; | ||
| 3146 : | } | ||
| 3147 : | if ( substr( $s, $ind, 1 ) ne ")" ) { treeParseError( "missing ')'" ) } | ||
| 3148 : | |||
| 3149 : | ( $ind, $c2 ) = getNextTreeChar( $s, $ind+1 ); # Comment 2 | ||
| 3150 : | if ( $c2 && @$c2 ) { set_newick_c2( $newnode, $c2 ) } | ||
| 3151 : | ( $ind, $lbl ) = parseTreeNodeLabel( $s, $ind ); # Node label | ||
| 3152 : | } | ||
| 3153 : | |||
| 3154 : | elsif ( substr( $s, $ind, 1 ) =~ /[^][(,):;]/ ) { # New tip | ||
| 3155 : | ( $ind, $lbl ) = parseTreeNodeLabel( $s, $ind ); # Tip label | ||
| 3156 : | if (! $ind) { return () } | ||
| 3157 : | } | ||
| 3158 : | |||
| 3159 : | @dlist || $lbl || treeParseError( "no descendant list or label" ); | ||
| 3160 : | |||
| 3161 : | if ( @dlist ) { set_newick_desc_ref( $newnode, \@dlist ) } | ||
| 3162 : | if ( $lbl ) { set_newick_lbl( $newnode, $lbl ) } | ||
| 3163 : | |||
| 3164 : | ( $ind, $c3 ) = getNextTreeChar( $s, $ind ); # Comment 3 | ||
| 3165 : | if ( $c3 && @$c3 ) { set_newick_c3( $newnode, $c3 ) } | ||
| 3166 : | |||
| 3167 : | if (substr( $s, $ind, 1 ) eq ":") { # Branch length | ||
| 3168 : | ( $ind, $c4 ) = getNextTreeChar( $s, $ind+1 ); # Comment 4 | ||
| 3169 : | if ( $c4 && @$c4 ) { set_newick_c4( $newnode, $c4 ) } | ||
| 3170 : | ( $ind, $x ) = parseBranchLength( $s, $ind ); | ||
| 3171 : | if ( defined( $x ) ) { set_newick_x( $newnode, $x ) } | ||
| 3172 : | ( $ind, $c5 ) = getNextTreeChar( $s, $ind ); # Comment 5 | ||
| 3173 : | if ( $c5 && @$c5 ) { set_newick_c5( $newnode, $c5 ) } | ||
| 3174 : | } | ||
| 3175 : | |||
| 3176 : | ( $ind, $newnode ); | ||
| 3177 : | } | ||
| 3178 : | |||
| 3179 : | |||
| 3180 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3181 : | # Read a Newick tree label | ||
| 3182 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3183 : | sub parseTreeNodeLabel { # Empty string is permitted | ||
| 3184 : | my ( $s, $ind ) = @_; | ||
| 3185 : | my ( $lbl, $c ); | ||
| 3186 : | |||
| 3187 : | if ( substr( $s, $ind, 1 ) eq "'") { | ||
| 3188 : | my $ind1 = ++$ind; | ||
| 3189 : | |||
| 3190 : | while ( ) { | ||
| 3191 : | if ( ! defined( $c = substr( $s, $ind, 1 ) ) || $c eq "" ) { | ||
| 3192 : | treeParseError( "missing close quote on label '" . substr( $s, $ind1 ) . "'" ) | ||
| 3193 : | } | ||
| 3194 : | elsif ( $c ne "'" ) { $ind++ } | ||
| 3195 : | elsif ( substr( $s, $ind, 2 ) eq "''" ) { $ind += 2 } | ||
| 3196 : | else { last } | ||
| 3197 : | } | ||
| 3198 : | |||
| 3199 : | $lbl = substr( $s, $ind1, $ind-$ind1 ); | ||
| 3200 : | $lbl =~ s/''/'/g; | ||
| 3201 : | $ind++; | ||
| 3202 : | } | ||
| 3203 : | |||
| 3204 : | else { | ||
| 3205 : | my $ind1 = $ind; | ||
| 3206 : | while ( defined( $c = substr($s, $ind, 1) ) && $c ne "" && $c !~ /[][\s(,):;]/ ) { $ind++ } | ||
| 3207 : | $lbl = substr( $s, $ind1, $ind-$ind1 ); | ||
| 3208 : | $lbl =~ s/_/ /g; | ||
| 3209 : | } | ||
| 3210 : | |||
| 3211 : | ( $ind, $lbl ); | ||
| 3212 : | } | ||
| 3213 : | |||
| 3214 : | |||
| 3215 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3216 : | # Read a Newick tree branch length | ||
| 3217 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3218 : | sub parseBranchLength { | ||
| 3219 : | my ( $s, $ind ) = @_; | ||
| 3220 : | |||
| 3221 : | my $c = substr( $s, $ind, 1 ); | ||
| 3222 : | |||
| 3223 : | my $sign = ( $c ne "-" ) ? 1 : -1; # Sign | ||
| 3224 : | if ( $c =~ /[-+]/ ) { $c = substr( $s, ++$ind, 1 ) } | ||
| 3225 : | |||
| 3226 : | if ( $c !~ /^[.0-9]$/ ) { # Allows starting with decimal | ||
| 3227 : | treeParseError( "invalid branch length character '$c'" ) | ||
| 3228 : | } | ||
| 3229 : | |||
| 3230 : | my $v = 0; | ||
| 3231 : | while ( $c =~ /[0-9]/ ) { # Whole number | ||
| 3232 : | $v = 10 * $v + $c; | ||
| 3233 : | $c = substr( $s, ++$ind, 1 ); | ||
| 3234 : | } | ||
| 3235 : | |||
| 3236 : | if ( $c eq "." ) { # Fraction | ||
| 3237 : | my $f = 0.1; | ||
| 3238 : | $c = substr( $s, ++$ind, 1 ); | ||
| 3239 : | while ( $c =~ /[0-9]/ ) { | ||
| 3240 : | $v += $f * $c; | ||
| 3241 : | $f *= 0.1; | ||
| 3242 : | $c = substr( $s, ++$ind, 1 ); | ||
| 3243 : | } | ||
| 3244 : | } | ||
| 3245 : | |||
| 3246 : | $v *= $sign; | ||
| 3247 : | |||
| 3248 : | if ( $c =~ /[dDeEgG]/ ) { # Exponent | ||
| 3249 : | $c = substr( $s, ++$ind, 1 ); | ||
| 3250 : | my $esign = ( $c ne "-" ) ? 1 : -1; | ||
| 3251 : | if ( $c =~ /^[-+]$/ ) { $c = substr( $s, ++$ind, 1 ) } | ||
| 3252 : | if ( $c !~ /^[0-9]$/ ) { | ||
| 3253 : | treeParseError( "missing branch length exponent '$c'" ) | ||
| 3254 : | } | ||
| 3255 : | |||
| 3256 : | my $e = 0; | ||
| 3257 : | while ( $c =~ /[0-9]/ ) { | ||
| 3258 : | $e = 10 * $e + $c; | ||
| 3259 : | $c = substr( $s, ++$ind, 1 ); | ||
| 3260 : | } | ||
| 3261 : | $e *= $esign; | ||
| 3262 : | $v *= 10**$e; | ||
| 3263 : | } | ||
| 3264 : | |||
| 3265 : | ( $ind, $v ); | ||
| 3266 : | } | ||
| 3267 : | |||
| 3268 : | |||
| 3269 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3270 : | # ( $index, /@commentlist ) = getNextTreeChar( $string, $index ) | ||
| 3271 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3272 : | sub getNextTreeChar { # Move to next nonblank, noncomment character | ||
| 3273 : | my ( $s, $ind ) = @_; | ||
| 3274 : | |||
| 3275 : | my @clist = (); | ||
| 3276 : | |||
| 3277 : | # Skip white space | ||
| 3278 : | if ( substr( $s, $ind ) =~ /^(\s+)/ ) { $ind += length( $1 ) } | ||
| 3279 : | |||
| 3280 : | # Loop while it is a comment: | ||
| 3281 : | while ( substr( $s, $ind, 1 ) eq "[" ) { | ||
| 3282 : | $ind++; | ||
| 3283 : | golsen | 1.11 | my $depth = 1; |
| 3284 : | my $ind2 = $ind; | ||
| 3285 : | golsen | 1.1 | |
| 3286 : | # Find end | ||
| 3287 : | golsen | 1.11 | while ( $depth > 0 ) |
| 3288 : | { | ||
| 3289 : | if ( substr( $s, $ind2 ) =~ /^([^][]*\[)/ ) # nested [ ... ] | ||
| 3290 : | { | ||
| 3291 : | $ind2 += length( $1 ); # Points at char just past [ | ||
| 3292 : | $depth++; # If nested comments are allowed | ||
| 3293 : | } | ||
| 3294 : | elsif ( substr( $s, $ind2 ) =~ /^([^][]*\])/ ) # close bracket | ||
| 3295 : | { | ||
| 3296 : | $ind2 += length( $1 ); # Points at char just past ] | ||
| 3297 : | $depth--; | ||
| 3298 : | } | ||
| 3299 : | else | ||
| 3300 : | { | ||
| 3301 : | treeParseError( "comment missing closing bracket '[" | ||
| 3302 : | . substr( $s, $ind ) . "'" ) | ||
| 3303 : | } | ||
| 3304 : | golsen | 1.1 | } |
| 3305 : | |||
| 3306 : | golsen | 1.11 | my $comment = substr( $s, $ind, $ind2-$ind-1 ); |
| 3307 : | golsen | 1.1 | if ( $comment =~ m/\S/ ) { push @clist, $comment } |
| 3308 : | |||
| 3309 : | golsen | 1.11 | $ind = $ind2; |
| 3310 : | golsen | 1.1 | |
| 3311 : | # Skip white space | ||
| 3312 : | if ( substr( $s, $ind ) =~ /^(\s+)/ ) { $ind += length( $1 ) } | ||
| 3313 : | } | ||
| 3314 : | |||
| 3315 : | ( $ind, @clist ? \@clist : undef ) | ||
| 3316 : | } | ||
| 3317 : | |||
| 3318 : | |||
| 3319 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3320 : | # treeParseError( $message ) | ||
| 3321 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3322 : | sub treeParseError { die "Error: parse_newick_subtree: " . $_[0] . "\n" } | ||
| 3323 : | |||
| 3324 : | |||
| 3325 : | #=============================================================================== | ||
| 3326 : | # Make a printer plot of a tree: | ||
| 3327 : | # | ||
| 3328 : | # $node newick tree root node | ||
| 3329 : | overbeek | 1.4 | # $file undef (= \*STDOUT), \*STDOUT, \*STDERR, or a file name. |
| 3330 : | golsen | 1.1 | # $width the approximate characters for the tree without labels |
| 3331 : | # $min_dx the minimum horizontal branch length | ||
| 3332 : | # $dy the vertical space per taxon | ||
| 3333 : | # | ||
| 3334 : | overbeek | 1.4 | # printer_plot_newick( $node, $file (D=\*STDOUT), $width (D=68), $min_dx (D=2), $dy (D=1) ) |
| 3335 : | golsen | 1.1 | #=============================================================================== |
| 3336 : | sub printer_plot_newick { | ||
| 3337 : | my ( $node, $file, $width, $min_dx, $dy ) = @_; | ||
| 3338 : | |||
| 3339 : | overbeek | 1.7 | my ( $fh, $close ) = open_output( $file ); |
| 3340 : | $fh or return; | ||
| 3341 : | golsen | 1.1 | |
| 3342 : | print $fh join( "\n", text_plot_newick( $node, $width, $min_dx, $dy ) ), "\n"; | ||
| 3343 : | if ( $close ) { close $fh } | ||
| 3344 : | } | ||
| 3345 : | |||
| 3346 : | |||
| 3347 : | #=============================================================================== | ||
| 3348 : | # Make a text plot of a tree: | ||
| 3349 : | # | ||
| 3350 : | # $node newick tree root node | ||
| 3351 : | # $width the approximate characters for the tree without labels | ||
| 3352 : | # $min_dx the minimum horizontal branch length | ||
| 3353 : | # $dy the vertical space per taxon | ||
| 3354 : | # | ||
| 3355 : | # @textlines = text_plot_newick( $node, $width (D=68), $min_dx (D=2), $dy (D=1) ) | ||
| 3356 : | #=============================================================================== | ||
| 3357 : | sub text_plot_newick { | ||
| 3358 : | my ( $node, $width, $min_dx, $dy ) = @_; | ||
| 3359 : | array_ref( $node ) || die "Bad node passed to text_plot_newick\n"; | ||
| 3360 : | defined( $min_dx ) and ( $min_dx >= 0 ) or $min_dx = 2; | ||
| 3361 : | defined( $dy ) and ( $dy >= 1 ) or $dy = 1; | ||
| 3362 : | defined( $width ) or $width = 68; | ||
| 3363 : | |||
| 3364 : | $min_dx = int( $min_dx ); | ||
| 3365 : | $dy = int( $dy ); | ||
| 3366 : | golsen | 1.5 | my $x_scale = $width / ( newick_max_X( $node ) || 1 ); # Div by zero caught by RAE |
| 3367 : | golsen | 1.1 | |
| 3368 : | my $hash = {}; | ||
| 3369 : | layout_printer_plot( $node, $hash, 0, -0.5 * $dy, $x_scale, $min_dx, $dy ); | ||
| 3370 : | |||
| 3371 : | # dump_tree_hash( $node, $hash ); exit; | ||
| 3372 : | |||
| 3373 : | # Generate the lines of the tree one by one: | ||
| 3374 : | |||
| 3375 : | my ( $y1, $y2 ) = @{ $hash->{ $node } }; | ||
| 3376 : | map { text_tree_row( $node, $hash, $_, "", "+" ) } ( $y1 .. $y2 ); | ||
| 3377 : | } | ||
| 3378 : | |||
| 3379 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3380 : | # ( $xmax, $ymax, $root_y ) = layout_printer_plot( $node, $hash, $x0, $y0, $x_scale, $min_dx, $dy ) | ||
| 3381 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3382 : | sub layout_printer_plot { | ||
| 3383 : | my ( $node, $hash, $x0, $y0, $x_scale, $min_dx, $dy ) = @_; | ||
| 3384 : | array_ref( $node ) || die "Bad node ref passed to layout_printer_plot\n"; | ||
| 3385 : | hash_ref( $hash ) || die "Bad hash ref passed to layout_printer_plot\n"; | ||
| 3386 : | |||
| 3387 : | my $dx = newick_x( $node ); | ||
| 3388 : | if ( defined( $dx ) ) { | ||
| 3389 : | $dx *= $x_scale; | ||
| 3390 : | $dx >= $min_dx or $dx = $min_dx; | ||
| 3391 : | } | ||
| 3392 : | else { | ||
| 3393 : | $dx = ( $x0 > 0 ) ? $min_dx : 0; | ||
| 3394 : | } | ||
| 3395 : | $dx = int( $dx + 0.4999 ); | ||
| 3396 : | |||
| 3397 : | my ( $x, $xmax, $y, $ymax, $y1, $y2, $yn1, $yn2 ); | ||
| 3398 : | |||
| 3399 : | $x = $x0 + $dx; | ||
| 3400 : | $y1 = int( $y0 + 0.5 * $dy + 0.4999 ); | ||
| 3401 : | my @dl = newick_desc_list( $node ); | ||
| 3402 : | |||
| 3403 : | if ( ! @dl ) { # A tip | ||
| 3404 : | $xmax = $x; | ||
| 3405 : | $y = $yn1 = $yn2 = $y2 = $y1; | ||
| 3406 : | $ymax = $y + 0.5 * $dy; | ||
| 3407 : | } | ||
| 3408 : | |||
| 3409 : | else { # A subtree | ||
| 3410 : | $xmax = -1; | ||
| 3411 : | my $xmaxi; | ||
| 3412 : | my $yi; | ||
| 3413 : | my @ylist = (); | ||
| 3414 : | $ymax = $y0; | ||
| 3415 : | |||
| 3416 : | foreach ( @dl ) { | ||
| 3417 : | ( $xmaxi, $ymax, $yi ) = layout_printer_plot( $_, $hash, $x, $ymax, $x_scale, $min_dx, $dy ); | ||
| 3418 : | push @ylist, $yi; | ||
| 3419 : | if ( $xmaxi > $xmax ) { $xmax = $xmaxi } | ||
| 3420 : | } | ||
| 3421 : | |||
| 3422 : | # Use of y-list is overkill for saving first and last values, | ||
| 3423 : | # but eases implimentation of alternative y-value calculations. | ||
| 3424 : | |||
| 3425 : | $yn1 = $ylist[ 0]; | ||
| 3426 : | $yn2 = $ylist[-1]; | ||
| 3427 : | $y = int( 0.5 * ( $yn1 + $yn2 ) + 0.4999 ); | ||
| 3428 : | } | ||
| 3429 : | |||
| 3430 : | $y2 = int( $ymax - 0.5 * $dy + 0.4999 ); | ||
| 3431 : | |||
| 3432 : | $hash->{ $node } = [ $y1, $y2, $x0, $x, $y, $yn1, $yn2 ]; | ||
| 3433 : | ( $xmax, $ymax, $y ); | ||
| 3434 : | } | ||
| 3435 : | |||
| 3436 : | |||
| 3437 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3438 : | # Debug routine | ||
| 3439 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3440 : | sub dump_tree { | ||
| 3441 : | my ( $node, $prefix ) = @_; | ||
| 3442 : | defined( $prefix ) or $prefix = ""; | ||
| 3443 : | print STDERR $prefix, join(", ", @$node), "\n"; | ||
| 3444 : | my @dl = $node->[0] ? @{$node->[0]} : (); | ||
| 3445 : | foreach ( @dl ) { dump_tree( $_, $prefix . " " ) } | ||
| 3446 : | $prefix or print STDERR "\n"; | ||
| 3447 : | } | ||
| 3448 : | |||
| 3449 : | |||
| 3450 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3451 : | # Debug routine | ||
| 3452 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3453 : | sub dump_tree_hash { | ||
| 3454 : | my ( $node, $hash, $prefix ) = @_; | ||
| 3455 : | defined( $prefix ) or print STDERR "node; [ y1, y2, x0, x, y, yn1, yn2 ]\n" and $prefix = ""; | ||
| 3456 : | print STDERR $prefix, join(", ", @$node), "; ", join(", ", @{ $hash->{ $node } } ), "\n"; | ||
| 3457 : | my @dl = $node->[0] ? @{$node->[0]} : (); | ||
| 3458 : | foreach (@dl) { dump_tree_hash( $_, $hash, $prefix . " " ) } | ||
| 3459 : | } | ||
| 3460 : | |||
| 3461 : | |||
| 3462 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3463 : | # $line = text_tree_row( $node, $hash, $row, $line, $symb ) | ||
| 3464 : | #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | ||
| 3465 : | sub text_tree_row { | ||
| 3466 : | my ( $node, $hash, $row, $line, $symb ) = @_; | ||
| 3467 : | |||
| 3468 : | my ( $y1, $y2, $x0, $x, $y, $yn1, $yn2 ) = @{ $hash->{ $node } }; | ||
| 3469 : | if ( $row < $y1 || $row > $y2 ) { return $line } | ||
| 3470 : | |||
| 3471 : | if ( length( $line ) < $x0 ) { $line .= " " x ( $x0 - length( $line ) ) } | ||
| 3472 : | |||
| 3473 : | if ( $row == $y ) { | ||
| 3474 : | $line = substr( $line, 0, $x0 ) . $symb . (( $x > $x0 ) ? "-" x ($x - $x0) : ""); | ||
| 3475 : | } | ||
| 3476 : | |||
| 3477 : | elsif ( $row > $yn1 && $row < $yn2 ) { | ||
| 3478 : | if ( length( $line ) < $x ) { $line .= " " x ( $x - length( $line ) ) . "|" } | ||
| 3479 : | else { substr( $line, $x ) = "|" } | ||
| 3480 : | } | ||
| 3481 : | |||
| 3482 : | my @dl = newick_desc_list( $node ); | ||
| 3483 : | |||
| 3484 : | if ( @dl < 1 ) { | ||
| 3485 : | $line .= " " . $node->[1]; | ||
| 3486 : | } | ||
| 3487 : | |||
| 3488 : | else { | ||
| 3489 : | my @list = map { [ $_, "+" ] } @dl; # Print symbol for line | ||
| 3490 : | $list[ 0]->[1] = "/"; | ||
| 3491 : | $list[-1]->[1] = "\\"; | ||
| 3492 : | |||
| 3493 : | foreach ( @list ) { | ||
| 3494 : | my ( $n, $s ) = @$_; | ||
| 3495 : | if ( $row >= $hash->{ $n }->[0] && $row <= $hash->{ $n }->[1] ) { | ||
| 3496 : | $line = text_tree_row( $n, $hash, $row, $line, $s ); | ||
| 3497 : | } | ||
| 3498 : | } | ||
| 3499 : | |||
| 3500 : | if ( $row == $y ) { substr( $line, $x, 1 ) = "+" } | ||
| 3501 : | } | ||
| 3502 : | |||
| 3503 : | return $line; | ||
| 3504 : | } | ||
| 3505 : | |||
| 3506 : | |||
| 3507 : | overbeek | 1.7 | #=============================================================================== |
| 3508 : | # Open an input file stream: | ||
| 3509 : | # | ||
| 3510 : | # ( $handle, undef ) = open_input( ); # \*STDIN | ||
| 3511 : | # ( $handle, undef ) = open_input( \*FH ); | ||
| 3512 : | # ( $handle, 1 ) = open_input( $file ); # need to close $handle | ||
| 3513 : | # | ||
| 3514 : | #=============================================================================== | ||
| 3515 : | sub open_input | ||
| 3516 : | { | ||
| 3517 : | my $file = shift; | ||
| 3518 : | my $fh; | ||
| 3519 : | if ( ! defined( $file ) ) { return ( \*STDIN ) } | ||
| 3520 : | elsif ( ref( $file ) eq 'GLOB' ) { return ( $file ) } | ||
| 3521 : | elsif ( open( $fh, "<$file" ) ) { return ( $fh, 1 ) } # Need to close | ||
| 3522 : | |||
| 3523 : | print STDERR "gjonewick::open_input could not open '$file' for reading\n"; | ||
| 3524 : | return undef; | ||
| 3525 : | } | ||
| 3526 : | |||
| 3527 : | |||
| 3528 : | #=============================================================================== | ||
| 3529 : | # Open an output file stream: | ||
| 3530 : | # | ||
| 3531 : | # ( $handle, undef ) = open_output( ); # \*STDOUT | ||
| 3532 : | # ( $handle, undef ) = open_output( \*FH ); | ||
| 3533 : | # ( $handle, 1 ) = open_output( $file ); # need to close $handle | ||
| 3534 : | # | ||
| 3535 : | #=============================================================================== | ||
| 3536 : | sub open_output | ||
| 3537 : | { | ||
| 3538 : | my $file = shift; | ||
| 3539 : | my $fh; | ||
| 3540 : | if ( ! defined( $file ) ) { return ( \*STDOUT ) } | ||
| 3541 : | elsif ( ref( $file ) eq 'GLOB' ) { return ( $file ) } | ||
| 3542 : | elsif ( ( open $fh, ">$file" ) ) { return ( $fh, 1 ) } # Need to close | ||
| 3543 : | |||
| 3544 : | print STDERR "gjonewick::open_output could not open '$file' for writing\n"; | ||
| 3545 : | return undef; | ||
| 3546 : | } | ||
| 3547 : | |||
| 3548 : | golsen | 1.9 | |
| 3549 : | #=============================================================================== | ||
| 3550 : | # Some subroutines copied from gjolists | ||
| 3551 : | #=============================================================================== | ||
| 3552 : | # Return the common prefix of two lists: | ||
| 3553 : | # | ||
| 3554 : | # @common = common_prefix( \@list1, \@list2 ) | ||
| 3555 : | #----------------------------------------------------------------------------- | ||
| 3556 : | sub common_prefix | ||
| 3557 : | { | ||
| 3558 : | my ($l1, $l2) = @_; | ||
| 3559 : | ref($l1) eq "ARRAY" || die "common_prefix: arg 1 is not an array ref\n"; | ||
| 3560 : | ref($l2) eq "ARRAY" || die "common_prefix: arg 2 is not an array ref\n"; | ||
| 3561 : | |||
| 3562 : | my $i = 0; | ||
| 3563 : | my $l1_i; | ||
| 3564 : | while ( defined( $l1_i = $l1->[$i] ) && $l1_i eq $l2->[$i] ) { $i++ } | ||
| 3565 : | |||
| 3566 : | return @$l1[ 0 .. ($i-1) ]; # perl handles negative range | ||
| 3567 : | } | ||
| 3568 : | |||
| 3569 : | |||
| 3570 : | #----------------------------------------------------------------------------- | ||
| 3571 : | # Return the unique suffixes of each of two lists: | ||
| 3572 : | # | ||
| 3573 : | # ( \@suffix1, \@suffix2 ) = unique_suffixes( \@list1, \@list2 ) | ||
| 3574 : | #----------------------------------------------------------------------------- | ||
| 3575 : | sub unique_suffixes | ||
| 3576 : | { | ||
| 3577 : | my ($l1, $l2) = @_; | ||
| 3578 : | ref($l1) eq "ARRAY" || die "common_prefix: arg 1 is not an array ref\n"; | ||
| 3579 : | ref($l2) eq "ARRAY" || die "common_prefix: arg 2 is not an array ref\n"; | ||
| 3580 : | |||
| 3581 : | my $i = 0; | ||
| 3582 : | my @l1 = @$l1; | ||
| 3583 : | my @l2 = @$l2; | ||
| 3584 : | my $l1_i; | ||
| 3585 : | while ( defined( $l1_i = $l1[$i] ) && $l1_i eq $l2[$i] ) { $i++ } | ||
| 3586 : | |||
| 3587 : | splice @l1, 0, $i; | ||
| 3588 : | splice @l2, 0, $i; | ||
| 3589 : | return ( \@l1, \@l2 ); | ||
| 3590 : | } | ||
| 3591 : | |||
| 3592 : | |||
| 3593 : | #------------------------------------------------------------------------------- | ||
| 3594 : | # List of values duplicated in a list (stable in order by second occurance): | ||
| 3595 : | # | ||
| 3596 : | # @dups = duplicates( @list ) | ||
| 3597 : | #------------------------------------------------------------------------------- | ||
| 3598 : | sub duplicates | ||
| 3599 : | { | ||
| 3600 : | my %cnt = (); | ||
| 3601 : | grep { ++$cnt{$_} == 2 } @_; | ||
| 3602 : | } | ||
| 3603 : | |||
| 3604 : | |||
| 3605 : | #------------------------------------------------------------------------------- | ||
| 3606 : | # Randomize the order of a list: | ||
| 3607 : | # | ||
| 3608 : | # @random = random_order( @list ) | ||
| 3609 : | #------------------------------------------------------------------------------- | ||
| 3610 : | sub random_order | ||
| 3611 : | { | ||
| 3612 : | my ( $i, $j ); | ||
| 3613 : | for ( $i = @_ - 1; $i > 0; $i-- ) | ||
| 3614 : | { | ||
| 3615 : | $j = int( ($i+1) * rand() ); | ||
| 3616 : | ( $_[$i], $_[$j] ) = ( $_[$j], $_[$i] ); # Interchange i and j | ||
| 3617 : | } | ||
| 3618 : | |||
| 3619 : | @_; | ||
| 3620 : | } | ||
| 3621 : | |||
| 3622 : | |||
| 3623 : | #----------------------------------------------------------------------------- | ||
| 3624 : | # Intersection of two or more sets: | ||
| 3625 : | # | ||
| 3626 : | # @intersection = intersection( \@set1, \@set2, ... ) | ||
| 3627 : | #----------------------------------------------------------------------------- | ||
| 3628 : | sub intersection | ||
| 3629 : | { | ||
| 3630 : | my $set = shift; | ||
| 3631 : | my @intersection = @$set; | ||
| 3632 : | |||
| 3633 : | foreach $set ( @_ ) | ||
| 3634 : | { | ||
| 3635 : | my %set = map { $_ => 1 } @$set; | ||
| 3636 : | @intersection = grep { exists $set{ $_ } } @intersection; | ||
| 3637 : | } | ||
| 3638 : | |||
| 3639 : | @intersection; | ||
| 3640 : | } | ||
| 3641 : | |||
| 3642 : | |||
| 3643 : | #----------------------------------------------------------------------------- | ||
| 3644 : | # Elements in set 1, but not set 2: | ||
| 3645 : | # | ||
| 3646 : | # @difference = set_difference( \@set1, \@set2 ) | ||
| 3647 : | #----------------------------------------------------------------------------- | ||
| 3648 : | sub set_difference | ||
| 3649 : | { | ||
| 3650 : | my ($set1, $set2) = @_; | ||
| 3651 : | my %set2 = map { $_ => 1 } @$set2; | ||
| 3652 : | grep { ! ( exists $set2{$_} ) } @$set1; | ||
| 3653 : | } | ||
| 3654 : | |||
| 3655 : | |||
| 3656 : | golsen | 1.1 | 1; |
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