Bio/TreeIO/phyloxml.pm

   1 # $Id: phyloxml.pm 11507 2007-06-23 01:37:45Z jason $
   2 #
   3 # BioPerl module for Bio::TreeIO::phyloxml
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Mira Han <mirhan@indiana.edu>
   8 #
   9 # Copyright Mira Han
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format.
  18
  19 =head1 SYNOPSIS
  20
  21   # do not use this module directly
  22   use Bio::TreeIO;
  23   my $treeio = Bio::TreeIO->new(-format => 'phyloxml',
  24                                 -file => 'tree.dnd');
  25   my $tree = $treeio->next_tree;
  26
  27 =head1 DESCRIPTION
  28
  29 This module handles parsing and writing of phyloXML format.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to the
  37 Bioperl mailing list.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Support
  43
  44 Please direct usage questions or support issues to the mailing list:
  45
  46 I<bioperl-l@bioperl.org>
  47
  48 rather than to the module maintainer directly. Many experienced and
  49 reponsive experts will be able look at the problem and quickly
  50 address it. Please include a thorough description of the problem
  51 with code and data examples if at all possible.
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted viax the
  57 web:
  58
  59   https://github.com/bioperl/bioperl-live/issues
  60
  61 =head1 AUTHOR - Mira Han
  62
  63 Email mirhan@indiana.edu
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72
  73 # Let the code begin...
  74
  75
  76 package Bio::TreeIO::phyloxml;
  77 use strict;
  78
  79 # Object preamble - inherits from Bio::Root::Root
  80
  81 use Bio::Tree::Tree;
  82 use Bio::Tree::AnnotatableNode;
  83 use Bio::Annotation::SimpleValue;
  84 use Bio::Annotation::Relation;
  85 use XML::LibXML;
  86 use XML::LibXML::Reader;
  87 use base qw(Bio::TreeIO);
  88
  89
  90 sub _initialize
  91 {
  92   my($self, %args) = @_;
  93   $args{-treetype} ||= 'Bio::Tree::Tree';
  94   $args{-nodetype} ||= 'Bio::Tree::AnnotatableNode';
  95   $self->SUPER::_initialize(%args);
  96
  97   # phyloxml TreeIO does not use SAX,
  98   # therefore no need to attach EventHandler
  99   # instead we will define a reader that is a pull-parser of libXML
 100   if ($self->mode eq 'r') {
 101     if ($self->_fh) {
 102       $self->{'_reader'} = XML::LibXML::Reader->new(
 103                         IO => $self->_fh,
 104                         no_blanks => 1
 105                         );
 106     }
 107     if (!$self->{'_reader'}) {
 108       $self->throw("XML::LibXML::Reader not initialized");
 109     }
 110   }
 111   elsif ($self->mode eq 'w') {
 112     # print default lines
 113     $self->_print('<?xml version="1.0" encoding="UTF-8"?>',"\n");
 114     $self->_print('<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">');
 115   }
 116
 117   $self->treetype($args{-treetype});
 118   $self->nodetype($args{-nodetype});
 119   $self->{'_lastitem'} = {}; # holds open items and the attribute hash
 120   $self->_init_func();
 121 }
 122
 123 sub _init_func
 124 {
 125   my ($self) = @_;
 126   my %start_elements = (
 127     'phylogeny' => \&element_phylogeny,
 128     'clade' => \&element_clade,
 129     'sequence_relation' => \&element_relation,
 130     'clade_relation' => \&element_relation,
 131   );
 132   $self->{'_start_elements'} = \%start_elements;
 133   my %end_elements = (
 134     'phylogeny' => \&end_element_phylogeny,
 135     'clade' => \&end_element_clade,
 136     'sequence_relation' => \&end_element_relation,
 137     'clade_relation' => \&end_element_relation,
 138   );
 139   $self->{'_end_elements'} = \%end_elements;
 140 }
 141
 142 sub DESTROY {
 143   my $self = shift;
 144   if ($self->mode eq 'w') {
 145     $self->_print('</phyloxml>');
 146     $self->flush if $self->_flush_on_write && defined $self->_fh;
 147   }
 148   $self->SUPER::DESTROY;
 149 }
 150
 151 =head2 next_tree
 152
 153  Title   : next_tree
 154  Usage   : my $tree = $treeio->next_tree
 155  Function: Gets the next tree in the stream
 156  Returns : Bio::Tree::TreeI
 157  Args    : none
 158
 159 =cut
 160
 161 sub next_tree
 162 {
 163   my ($self) = @_;
 164   my $reader = $self->{'_reader'};
 165   my $tree;
 166   while ($reader->read)
 167   {
 168     if ($reader->nodeType == XML_READER_TYPE_END_ELEMENT)
 169     {
 170       if ($reader->name eq 'phylogeny')
 171       {
 172         $tree = $self->end_element_phylogeny();
 173         last;
 174       }
 175     }
 176     $self->processXMLNode;
 177   }
 178   return $tree;
 179 }
 180
 181 =head2 add_attribute
 182
 183  Title   : add_phyloXML_annotation
 184  Usage   : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -attr=>"id_source = \"A\"")
 185  Function: add attributes to an object
 186  Returns : the node that we added annotations to
 187  Args    : -obj   => object that will have the Annotation. (Bio::Tree::AnnotatableNode)
 188            -attr  => string in the form "A = B", where A is the attribute name and B is the attribute value
 189
 190 =cut
 191
 192 sub add_attribute
 193 {
 194   my ($self, @args) = @_;
 195   my ($obj, $attr) = $self->_rearrange([qw(OBJ ATTR)], @args);
 196
 197   if ($attr) {
 198     $attr = '<dummy '.$attr.'/>';
 199   }
 200
 201   my $oldreader = $self->{'_reader'};   # save reader
 202   $self->{'_reader'} = XML::LibXML::Reader->new(
 203                 string => $attr,
 204                 no_blanks => 1
 205                 );
 206   my $reader = $self->{'_reader'};
 207   $self->{'_currentannotation'} = []; # holds annotationcollection
 208   $self->{'_currenttext'} = '';
 209   #$self->{'_id_link'} = {};
 210
 211   # pretend we saw a <clade> element
 212   $self->{'_lastitem'}->{'dummy'}++;
 213   push @{$self->{'_lastitem'}->{'current'}}, { 'dummy'=>{}};  # current holds current element and empty hash for its attributes
 214
 215   # push object to annotate
 216   push @{$self->{'_currentitems'}}, $obj;
 217
 218   # read attributes of element
 219   while ($reader->read)
 220   {
 221     #$self->processXMLNode;
 222     $self->processAttribute($self->current_attr);
 223   }
 224
 225   # if there is id_source add sequence to _id_link
 226   if (exists $self->current_attr->{'id_source'}) {
 227     my $idsrc = $self->current_attr->{'id_source'};
 228     $self->{'_id_link'}->{$idsrc} = $obj;
 229   }
 230
 231   # check idref
 232   my $idref = '';
 233   if (exists $self->current_attr->{'id_ref'}) {
 234     $idref = $self->current_attr->{'id_ref'};
 235   }
 236
 237   my $srcbyidref = '';
 238   $srcbyidref = $self->{'_id_link'}->{$idref};
 239
 240   # exception when id_ref is defined but id_src is not, or vice versa.
 241   if ($idref xor $srcbyidref) {
 242     $self->throw("id_ref and id_src incompatible: $idref, $srcbyidref");
 243   }
 244
 245   # if attribute exists then add Annotation::Collection with tag '_attr'
 246   my $newac = $obj->annotation;
 247   if ( scalar keys %{$self->current_attr} ) {
 248     my $newattr = Bio::Annotation::Collection->new();
 249     foreach my $tag (keys %{$self->current_attr}) {
 250       my $sv = Bio::Annotation::SimpleValue->new(
 251           -value => $self->current_attr->{$tag}
 252           );
 253       $newattr->add_Annotation($tag, $sv);
 254     }
 255     $newac->add_Annotation('_attr', $newattr);
 256   }
 257
 258   # pop from temporary list
 259   pop @{$self->{'_currentitems'}};
 260   $self->{'_lastitem'}->{ $reader->name }-- if $reader->name;
 261   pop @{$self->{'_lastitem'}->{'current'}};
 262
 263   $self->{'_reader'} = $oldreader;  # restore reader
 264   return $obj;
 265
 266 }
 267
 268 =head2 add_phyloXML_annotation
 269
 270  Title   : add_phyloXML_annotation
 271  Usage   : my $node = $treeio->add_phyloXML_annotation(-obj=>$node, -xml=>$xmlstring)
 272            my $tree = $treeio->add_phyloXML_annotation('-obj'=>$tree, '-xml'=>'<sequence_relation id_ref_0="A" id_ref_1="B" type="orthology"/>')
 273
 274  Function: add annotations to a node in the phyloXML format string
 275  Returns : the node that we added annotations to
 276  Args    : -obj   => object that will have the Annotation. (Bio::Tree::AnnotatableNode)
 277            -xml  => string in phyloXML format that describes the annotation for the node
 278
 279 =cut
 280
 281 sub add_phyloXML_annotation
 282 {
 283   my ($self, @args) = @_;
 284   my ($obj, $xml_string) = $self->_rearrange([qw(OBJ XML)], @args);
 285
 286   $xml_string = '<phyloxml>'.$xml_string.'</phyloxml>';
 287   $self->debug( $xml_string );
 288
 289   my $oldreader = $self->{'_reader'};   # save reader
 290   $self->{'_reader'} = XML::LibXML::Reader->new(
 291                 string => $xml_string,
 292                 no_blanks => 1
 293                 );
 294   my $reader = $self->{'_reader'};
 295   #$self->{'_currentannotation'} = []; # holds annotationcollection
 296   #$self->{'_currenttext'} = '';
 297   #$self->{'_id_link'} = {};
 298
 299   # pretend we saw a <clade> element
 300   $self->{'_lastitem'}->{'clade'}++;
 301   push @{$self->{'_lastitem'}->{'current'}}, { 'clade'=>{}};  # current holds current element and empty hash for its attributes
 302   # our object to annotate (nodeI)
 303   # push into temporary list
 304   push @{$self->{'_currentitems'}}, $obj;
 305
 306   $reader->read;    #read away the first element 'phyloxml'
 307   while ($reader->read)
 308   {
 309     $self->processXMLNode;
 310   }
 311
 312   # pop from temporary list
 313   pop @{$self->{'_currentitems'}};
 314   $self->{'_lastitem'}->{ $reader->name }-- if $reader->name;
 315   pop @{$self->{'_lastitem'}->{'current'}};
 316
 317   $self->{'_reader'} = $oldreader;  # restore reader
 318   return $obj;
 319 }
 320
 321
 322 =head2 write_tree
 323
 324  Title   : write_tree
 325  Usage   : $treeio->write_tree($tree);
 326  Function: Write a tree out to data stream in phyloxml format
 327  Returns : none
 328  Args    : Bio::Tree::TreeI object
 329
 330 =cut
 331
 332 sub write_tree
 333 {
 334   my ($self, @trees) = @_;
 335   foreach my $tree (@trees) {
 336     my $root = $tree->get_root_node;
 337     $self->_print("<phylogeny");
 338     my @tags = $tree->get_all_tags();
 339     my $attr_str = '';
 340     foreach my $tag (@tags) {
 341       my @values = $tree->get_tag_values($tag);
 342       foreach (@values) {
 343         $attr_str .= " ".$tag."=\"".$_."\"";
 344       }
 345     }
 346     # check if rooted
 347     my ($b_rooted) = $tree->get_tag_values('rooted');
 348     if ($b_rooted) {
 349       $attr_str .= " rooted=\"true\"";
 350     }
 351     else {
 352       if($tree->is_binary($tree->get_root_node)) {
 353         $attr_str .= " rooted=\"true\"";
 354       }
 355       else {
 356         $attr_str .= " rooted=\"false\"";
 357       }
 358     }
 359     $self->_print($attr_str);
 360     $self->_print(">");
 361     if ($root->isa('Bio::Tree::AnnotatableNode')) {
 362       $self->_print($self->_write_tree_Helper_annotatableNode($root));
 363     }
 364     else {
 365       $self->_print($self->_write_tree_Helper_generic($root));
 366     }
 367
 368     # print clade relations
 369     while (my $str = pop (@{$self->{'_tree_attr'}->{'clade_relation'}})) {
 370       $self->_print($str);
 371     }
 372     # print sequence relations
 373     while (my $str = pop (@{$self->{'_tree_attr'}->{'sequence_relation'}})) {
 374       $self->_print($str);
 375     }
 376     $self->_print("</phylogeny>");
 377   }
 378   $self->flush if $self->_flush_on_write && defined $self->_fh;
 379   return;
 380 }
 381
 382 =head2 _write_tree_Helper_annotatableNode
 383
 384  Title   : _write_tree_Helper_annotatableNode
 385  Usage   : internal method used by write_tree, not to be used directly
 386  Function: recursive helper function of write_tree for the annotatableNodes.
 387            translates annotations into xml elements.
 388  Returns : string describing the node
 389  Args    : Bio::Node::AnnotatableNode object, string
 390
 391 =cut
 392
 393 sub _write_tree_Helper_annotatableNode
 394 {
 395   my ($self, $node, $str) = @_;     # this self is a Bio::Tree::phyloxml
 396
 397   my $ac = $node->annotation;
 398
 399   # if clade_relation exists
 400   my @relations = $ac->get_Annotations('clade_relation');
 401   foreach (@relations) {
 402     my $clade_rel = $self->_relation_to_string($node, $_, '');
 403     # set as tree attr
 404     push (@{$self->{'_tree_attr'}->{'clade_relation'}}, $clade_rel);
 405   }
 406
 407   # start <clade>
 408   $str .= '<clade';
 409   my ($attr) = $ac->get_Annotations('_attr'); # check id_source
 410     if ($attr) {
 411       my ($id_source) = $attr->get_Annotations('id_source');
 412       if ($id_source) {
 413         $str .= " id_source=\"".$id_source->value."\"";
 414       }
 415     }
 416   $str .= ">";
 417
 418   # print all descendent nodes
 419   foreach my $child ( $node->each_Descendent() ) {
 420     $str = $self->_write_tree_Helper_annotatableNode($child, $str);
 421   }
 422
 423   # print all annotations
 424   $str = print_annotation( $node, $str, $ac );
 425
 426   # print all sequences
 427   if ($node->has_sequence) {
 428     foreach my $seq (@{$node->sequence}) {
 429       # if sequence_relation exists
 430       my @relations = $seq->annotation->get_Annotations('sequence_relation');
 431       foreach (@relations) {
 432         my $sequence_rel = $self->_relation_to_string($seq, $_, '');
 433         # set as tree attr
 434         push (@{$self->{'_tree_attr'}->{'sequence_relation'}}, $sequence_rel);
 435       }
 436       $str = print_seq_annotation( $node, $str, $seq );
 437     }
 438   }
 439
 440   $str .= "</clade>";
 441
 442   return $str;
 443 }
 444
 445 =head2 _write_tree_Helper_generic
 446
 447  Title   : _write_tree_Helper_generic
 448  Usage   : internal method used by write_tree, not to be used directly
 449  Function: recursive helper function of write_tree for generic NodesI.
 450            all tags are translated into property elements.
 451  Returns : string describing the node
 452  Args    : Bio::Node::NodeI object, string
 453
 454 =cut
 455
 456 sub _write_tree_Helper_generic
 457 {
 458   my ($self, $node, $str) = @_;     # this self is a Bio::Tree::phyloxml
 459
 460   # start <clade>
 461   $str .= '<clade>';
 462
 463   # print all descendent nodes
 464   foreach my $child ( $node->each_Descendent() ) {
 465     $str = $self->_write_tree_Helper_generic($child, $str);
 466   }
 467
 468   # print all tags
 469   my @tags = $node->get_all_tags();
 470   foreach my $tag (@tags) {
 471     my @values = $node->get_tag_values($tag);
 472     foreach my $val (@values) {
 473       $str .= "<property datatype=\"xsd:string\" ref=\"tag:$tag\" applies_to=\"clade\">";
 474       $str .=$val;
 475       $str .= "</property>";
 476     }
 477   }
 478
 479   # print NodeI features
 480   if ($node->id) {
 481     $str .= "<name>";
 482     $str .= $node->id;
 483     $str .= "</name>";
 484   }
 485   if ($node->branch_length) {
 486     $str .= "<branch_length>";
 487     $str .= $node->branch_length;
 488     $str .= "</branch_length>";
 489   }
 490   if ($node->bootstrap) {
 491     $str .= "<confidence type = \"bootstrap\">";
 492     $str .= $node->bootstrap;
 493     $str .= "</confidence>";
 494   }
 495
 496   $str .= "</clade>";
 497   return $str;
 498 }
 499
 500 =head2 _relation_to_string
 501
 502  Title   : _relation_to_string
 503  Usage   : internal method used by write_tree, not to be used directly
 504  Function: internal function used by write_tree to translate Annotation::Relation objects into xml elements.
 505  Returns : string describing the node
 506  Args    : Bio::Node::AnnotatableNode (or Bio::SeqI) object that contains the Annotation::Relation,
 507            the Annotation::Relation object,
 508            the string
 509
 510 =cut
 511
 512 # It may be more appropriate to make Annotation::Relation have
 513 # a to_string callback function,
 514 # and have this subroutine set as the callback when we are in
 515 # phyloXML context.
 516 # I've put it here for now, since write_tree is the only place it is used.
 517
 518 sub _relation_to_string {
 519   my ($self, $obj, $rel, $str) = @_;
 520
 521   my @attr = $obj->annotation->get_Annotations('_attr'); # check id_source
 522   if (@attr) {
 523     my @id_source = $attr[0]->get_Annotations('id_source');
 524   }
 525   my ($id_ref_0) = $obj->annotation->get_nested_Annotations(
 526                                       '-keys' => ['id_source'],
 527                                       '-recursive' => 1);
 528   my ($id_ref_1) = $rel->to->annotation->get_nested_Annotations(
 529                                       '-keys' => ['id_source'],
 530                                       '-recursive' => 1);
 531
 532   my $confidence = $rel->confidence();
 533   my $confidence_type = $rel->confidence_type();
 534   $str .= "<";
 535   $str .= $rel->tagname;
 536   $str .= " id_ref_0=\"".$id_ref_0->value."\"";
 537   $str .= " id_ref_1=\"".$id_ref_1->value."\"";
 538   $str .= " type=\"".$rel->type."\"";
 539   if ($confidence) {
 540     $str .= " ><confidence";
 541     if ($confidence_type) {
 542       $str .= " type=\"".$confidence_type."\"";
 543     }
 544     $str .= ">";
 545     $str .= $confidence;
 546     $str .= "</confidence>";
 547     $str .= "</";
 548     $str .= $rel->tagname;
 549     $str .= ">";
 550   }
 551   else {
 552     $str .= "/>";
 553   }
 554   return $str;
 555 }
 556
 557 =head2 read_annotation
 558
 559  Title   : read_annotation
 560  Usage   : $treeio->read_annotation(-obj=>$node, -path=>$path, -attr=>1);
 561  Function: read text value (or attribute value) of the annotations corresponding to the element path
 562  Returns : list of text values of the annotations matching the path
 563  Args    : -obj   => object that contains the Annotation. (Bio::Tree::AnnotatableNode or Bio::SeqI)
 564            -path  => path of the nested elements
 565            -attr  => Boolean value to indicate whether to get the attribute of the element or the text value.
 566                     (default is 0, meaning text value is returned)
 567
 568 =cut
 569
 570 # It may be more appropriate to make a separate Annotation::phyloXML object
 571 # and have this subroutine within that object so it can handle the
 572 # reading and writing of the values and attributes.
 573 # but since tagTree is a temporary stub and I didn't want to make
 574 # a redundant object I've put it here for now.
 575
 576 sub read_annotation
 577 {
 578   my ($self, @args) = @_;
 579   my ($obj, $path, $attr) = $self->_rearrange([qw(OBJ PATH ATTR)], @args);
 580   my $ac = $obj->annotation;
 581   if ($attr) {
 582     my @elements = split ('/', $path);
 583     my $final = pop @elements;
 584     push (@elements, '_attr');
 585     push (@elements, $final);
 586     $path = join ('/', @elements);
 587     return $self->_read_annotation_attr_Helper( [$ac], $path);
 588   }
 589   else {
 590     return $self->_read_annotation_text_Helper( [$ac], $path);
 591   }
 592 }
 593
 594 sub _read_annotation_text_Helper
 595 {
 596   my ($self, $acs, $path) = @_;
 597   my @elements = split ('/', $path);
 598   my $key = shift @elements;
 599   my @nextacs = ();
 600   foreach my $ac (@$acs) {
 601     foreach my $ann ($ac->get_Annotations($key)) {
 602       if ($ann->isa('Bio::AnnotationCollectionI')) {push (@nextacs, $ann)}
 603     }
 604   }
 605   if (@elements == 0) {
 606     my @values = ();
 607     my @texts = map {$_->get_Annotations('_text')} @nextacs;
 608     foreach (@texts) {
 609       $_ && push (@values, $_->value);
 610     }
 611     return @values;
 612   }
 613   else {
 614     $path = join ('/', @elements);
 615     return $self->_read_annotation_text_Helper( \@nextacs, $path);
 616   }
 617 }
 618
 619 sub _read_annotation_attr_Helper
 620 {
 621   my ($self, $acs, $path) = @_;
 622   my @elements = split ('/', $path);
 623   my $key = shift @elements;
 624   my @nextacs = ();
 625   foreach my $ac (@$acs) {
 626     foreach my $ann ($ac->get_Annotations($key)) {
 627       if ($ann->isa('Bio::AnnotationCollectionI')) {push (@nextacs, $ann)}
 628     }
 629   }
 630   if (@elements == 1) {
 631     my $attrname = $elements[0];
 632     my @sv = map {$_->get_Annotations($attrname)} @nextacs;
 633     return map {$_->value} @sv;
 634   }
 635   else {
 636     $path = join ('/', @elements);
 637     return $self->_read_annotation_attr_Helper( \@nextacs, $path);
 638   }
 639 }
 640
 641 =head1 Methods for parsing the XML document
 642
 643 =cut
 644
 645 =head2 processXMLNode
 646
 647  Title   : processXMLNode
 648  Usage   : $treeio->processXMLNode
 649  Function: read the XML node and process according to the node type
 650  Returns : none
 651  Args    : none
 652
 653 =cut
 654
 655 sub processXMLNode
 656 {
 657   my ($self) = @_;
 658   my $reader = $self->{'_reader'};
 659   my $nodetype = $reader->nodeType;
 660   if ( $nodetype == XML_READER_TYPE_ELEMENT)
 661   {
 662     $self->{'_lastitem'}->{$reader->name}++;
 663     push @{$self->{'_lastitem'}->{'current'}}, { $reader->name=>{}};  # current holds current element and empty hash for its attributes
 664
 665     if (exists $self->{'_start_elements'}->{$reader->name}) {
 666       my $method = $self->{'_start_elements'}->{$reader->name};
 667       $self->$method();
 668     }
 669     else {
 670       $self->element_default();
 671     }
 672     if ($reader->isEmptyElement) {
 673       # element is complete
 674       # set nodetype so it can jump and
 675       # do procedures for XML_READER_TYPE_END_ELEMENT
 676       $nodetype = XML_READER_TYPE_END_ELEMENT;
 677     }
 678   }
 679   if ($nodetype == XML_READER_TYPE_TEXT)
 680   {
 681     $self->{'_currenttext'} = $reader->value;
 682   }
 683   if ($nodetype == XML_READER_TYPE_END_ELEMENT)
 684   {
 685     if (exists $self->{'_end_elements'}->{$reader->name}) {
 686       my $method = $self->{'_end_elements'}->{$reader->name};
 687       $self->$method();
 688     }
 689     else {
 690       $self->end_element_default();
 691     }
 692     $self->{'_lastitem'}->{ $reader->name }--;
 693     pop @{$self->{'_lastitem'}->{'current'}};
 694     $self->{'_currenttext'} = '';
 695   }
 696 }
 697
 698
 699 =head2 processAttribute
 700
 701  Title   : processAttribute
 702  Usage   : $treeio->processAttribute(\%hash_for_attribute);
 703  Function: reads the attributes of the current element into a hash
 704  Returns : none
 705  Args    : hash reference where the attributes will be stored.
 706
 707 =cut
 708
 709 sub processAttribute
 710 {
 711   my ($self, $data) = @_;
 712   my $reader = $self->{'_reader'};
 713
 714   # several ways of reading attributes:
 715   # read all attributes:
 716   if ($reader-> moveToFirstAttribute) {
 717     do {
 718        $data->{$reader->name()} = $reader->value;
 719     } while ($reader-> moveToNextAttribute);
 720     $reader-> moveToElement;
 721   }
 722 }
 723
 724
 725 =head2 element_phylogeny
 726
 727  Title   : element_phylogeny
 728  Usage   : $treeio->element_phylogeny
 729  Function: initialize the parsing of a tree
 730  Returns : none
 731  Args    : none
 732
 733 =cut
 734
 735 sub element_phylogeny
 736 {
 737   my ($self) = @_;
 738   $self->{'_currentitems'} = []; # holds nodes while parsing current level
 739   $self->{'_currentnodes'} = []; # holds nodes while constructing tree
 740   $self->{'_currentannotation'} = []; # holds annotationcollection
 741   $self->{'_currenttext'} = '';
 742   $self->{'_levelcnt'} = [];
 743   $self->{'_id_link'} = {};
 744   $self->{'_tree_attr'} = $self->current_attr;
 745   $self->processAttribute($self->current_attr);
 746   return;
 747 }
 748
 749 =head2 end_element_phylogeny
 750
 751  Title   : end_element_phylogeny
 752  Usage   : $treeio->end_element_phylogeny
 753  Function: ends the parsing of a tree building a Tree::TreeI object.
 754  Returns : Tree::TreeI
 755  Args    : none
 756
 757 =cut
 758
 759 sub end_element_phylogeny
 760 {
 761   my ($self) = @_;
 762
 763   my $root;
 764   # if there is more than one node in _currentnodes
 765   # aggregate the nodes into trees basically ad-hoc.
 766   if ( @{$self->{'_currentnodes'}} > 1)
 767   {
 768     $root = $self->nodetype->new(
 769                                   -id => '',
 770                                   tostring => \&node_to_string,
 771                                 );
 772     while ( @{$self->{'_currentnodes'}} ) {
 773       my ($node) = ( shift @{$self->{'_currentnodes'}});
 774       $root->add_Descendent($node);
 775     }
 776   }
 777   # if there is only one node in _currentnodes
 778   # that node is root.
 779   elsif ( @{$self->{'_currentnodes'}} == 1)
 780   {
 781     $root = shift @{$self->{'_currentnodes'}};
 782   }
 783
 784   my $tree = $self->treetype->new(
 785     -root => $root,
 786     -id => $self->current_attr->{'name'},
 787     %{$self->current_attr}
 788   );
 789   foreach my $tag ( keys %{$self->current_attr} ) {
 790     $tree->add_tag_value( $tag, $self->current_attr->{$tag} );
 791   }
 792   return $tree;
 793 }
 794
 795 =head2 element_clade
 796
 797  Title   : element_clade
 798  Usage   : $treeio->element_clade
 799  Function: initialize the parsing of a node
 800            creates a new AnnotatableNode with annotations
 801  Returns : none
 802  Args    : none
 803
 804 =cut
 805
 806 sub element_clade
 807 {
 808   my ($self) = @_;
 809   my $reader = $self->{'_reader'};
 810   my %clade_attr = ();    # doesn't use current attribute in order to save memory
 811   $self->processAttribute(\%clade_attr);
 812   # create a node (Annotatable Node)
 813   my $tnode = $self->nodetype->new(
 814                                     -id => '',
 815                                     tostring => \&node_to_string,
 816                                     %clade_attr,
 817                                   );
 818   # add all attributes as annotation collection with tag '_attr'
 819   my $ac = $tnode->annotation;
 820   my $newattr = Bio::Annotation::Collection->new();
 821   foreach my $tag (keys %clade_attr) {
 822     my $sv = Bio::Annotation::SimpleValue->new(
 823               -value => $clade_attr{$tag}
 824              );
 825     $newattr->add_Annotation($tag, $sv);
 826   }
 827   $ac->add_Annotation('_attr', $newattr);
 828
 829   # if there is id_source add clade to _id_link
 830   if (exists $clade_attr{'id_source'}) {
 831     $self->{'_id_link'}->{$clade_attr{'id_source'}} = $tnode;
 832   }
 833   # push into temporary list
 834   push @{$self->{'_currentitems'}}, $tnode;
 835 }
 836
 837 =head2 end_element_clade
 838
 839  Title   : end_element_clade
 840  Usage   : $treeio->end_element_clade
 841  Function: ends the parsing of a node
 842  Returns : none
 843  Args    : none
 844
 845 =cut
 846
 847 sub end_element_clade
 848 {
 849   my ($self) = @_;
 850   my $reader = $self->{'_reader'};
 851
 852   my $curcount = scalar @{$self->{'_currentnodes'}};
 853   my $level   = $reader->depth() - 2;
 854   my $childcnt = $self->{'_levelcnt'}->[$level+1] || 0;
 855
 856   # pop from temporary list
 857   my $tnode = pop @{$self->{'_currentitems'}};
 858   if ( $childcnt > 0) {
 859     if( $childcnt > $curcount)
 860     {
 861       $self->throw("something wrong with event construction treelevel ".
 862         "$level is recorded as having $childcnt nodes  ".
 863         "but current nodes at this level is $curcount\n");
 864     }
 865     my @childnodes = splice( @{$self->{'_currentnodes'}}, - $childcnt);
 866     for ( @childnodes ) {
 867       $tnode->add_Descendent($_);
 868     }
 869     $self->{'_levelcnt'}->[$level+1] = 0;
 870   }
 871   push @{$self->{'_currentnodes'}}, $tnode;
 872   $self->{'_levelcnt'}->[$level]++;
 873
 874 }
 875
 876 =head2 element_relation
 877
 878  Title   : element_relation
 879  Usage   : $treeio->element_relation
 880  Function: starts the parsing of clade relation & sequence relation
 881  Returns : none
 882  Args    : none
 883
 884 =cut
 885
 886 sub element_relation
 887 {
 888   my ($self) = @_;
 889   $self->processAttribute($self->current_attr);
 890   my $relationtype = $self->current_attr->{'type'};
 891   my $id_ref_0 = $self->current_attr->{'id_ref_0'};
 892   my $id_ref_1 = $self->current_attr->{'id_ref_1'};
 893
 894   my @srcbyidref = ();
 895   $srcbyidref[0] = $self->{'_id_link'}->{$id_ref_0};
 896   $srcbyidref[1] = $self->{'_id_link'}->{$id_ref_1};
 897
 898   # exception when id_ref is defined but id_src is not, or vice versa.
 899   if ( ($id_ref_0 xor $srcbyidref[0])||($id_ref_1 xor $srcbyidref[1]) ) {
 900     $self->throw("id_ref and id_src incompatible: $id_ref_0, $id_ref_1, ", $srcbyidref[0], $srcbyidref[1]);
 901   }
 902
 903   # set id_ref_0
 904   my $ac0 = $srcbyidref[0]->annotation;
 905   my $newann = Bio::Annotation::Relation->new(
 906                     '-type' => $relationtype,
 907                     '-to' => $srcbyidref[1],
 908                     '-tagname' => $self->current_element
 909                     );
 910   $ac0->add_Annotation($self->current_element, $newann);
 911   # set id_ref_1
 912   my $ac1 = $srcbyidref[1]->annotation;
 913   $newann = Bio::Annotation::Relation->new(
 914                     '-type' => $relationtype,
 915                     '-to' => $srcbyidref[0],
 916                     '-tagname' => $self->current_element
 917                     );
 918   $ac1->add_Annotation($self->current_element, $newann);
 919   push (@{$self->{'_currentannotation'}}, $newann);
 920 }
 921
 922 =head2 end_element_relation
 923
 924  Title   : end_element_relation
 925  Usage   : $treeio->end_element_relation
 926  Function: ends the parsing of clade relation & sequence relation
 927  Returns : none
 928  Args    : none
 929
 930 =cut
 931
 932 sub end_element_relation
 933 {
 934   my ($self) = @_;
 935   my $ac = pop (@{$self->{'_currentannotation'}});
 936 }
 937
 938
 939 =head2 element_default
 940
 941  Title   : element_default
 942  Usage   : $treeio->element_default
 943  Function: starts the parsing of all other elements
 944  Returns : none
 945  Args    : none
 946
 947 =cut
 948
 949 sub element_default
 950 {
 951   my ($self) = @_;
 952   my $reader = $self->{'_reader'};
 953   my $current = $self->current_element();
 954   my $prev = $self->prev_element();
 955
 956   # read attributes of element
 957   $self->processAttribute($self->current_attr);
 958
 959   # check idref
 960   my $idref = '';
 961   if (exists $self->current_attr->{'id_ref'}) {
 962     $idref = $self->current_attr->{'id_ref'};
 963   }
 964
 965   my $srcbyidref = '';
 966   $srcbyidref = $self->{'_id_link'}->{$idref};
 967
 968   # exception when id_ref is defined but id_src is not, or vice versa.
 969   if ($idref xor $srcbyidref) {
 970     $self->throw("id_ref and id_src incompatible: $idref, $srcbyidref");
 971   }
 972
 973   # we are annotating a Node
 974   # set _currentannotation
 975   if ( ($srcbyidref && $srcbyidref->isa($self->nodetype)) || ((!$srcbyidref) && $prev eq 'clade') ) {
 976       # find node to annotate
 977       my $tnode;
 978       if ($srcbyidref) {
 979         $tnode = $srcbyidref;
 980       }
 981       else {
 982         $tnode = $self->{'_currentitems'}->[-1];
 983       }
 984       my $ac = $tnode->annotation();
 985       # add the new anncollection with the current element as key
 986       my $newann = Bio::Annotation::Collection->new();
 987       $ac->add_Annotation($current, $newann);
 988       # push to current annotation
 989       push (@{$self->{'_currentannotation'}}, $newann);
 990   }
 991   # we are within sequence_relation or clade_relation
 992   elsif ($prev eq 'clade_relation' || $prev eq 'sequence_relation') {
 993     # do nothing?
 994   }
 995   # we are already within an annotation
 996   else {
 997     my $ac = $self->{'_currentannotation'}->[-1];
 998     if ($ac) {
 999       # add the new anncollection with the current element as key
1000       my $newann = Bio::Annotation::Collection->new();
1001       $ac->add_Annotation($current, $newann);
1002       push (@{$self->{'_currentannotation'}}, $newann);
1003     }
1004   }
1005 }
1006
1007
1008 =head2 end_element_default
1009
1010  Title   : end_element_default
1011  Usage   : $treeio->end_element_default
1012  Function: ends the parsing of all other elements
1013  Returns : none
1014  Args    : none
1015
1016 =cut
1017
1018 sub end_element_default
1019 {
1020   my ($self) = @_;
1021   my $reader = $self->{'_reader'};
1022   my $current = $self->current_element();
1023   my $prev = $self->prev_element();
1024
1025   # check idsrc
1026   my $idsrc = $self->current_attr->{'id_source'};
1027
1028   # check idref
1029   my $idref = '';
1030   if (exists $self->current_attr->{'id_ref'}) {
1031     $idref = $self->current_attr->{'id_ref'};
1032     delete $self->current_attr->{'id_ref'};
1033   }
1034
1035   my $srcbyidref = '';
1036   $srcbyidref = $self->{'_id_link'}->{$idref};
1037
1038   # exception when id_ref is defined but id_src is not, or vice versa.
1039   if ($idref xor $srcbyidref) {
1040     $self->throw("id_ref and id_src incompatible: $idref, $srcbyidref");
1041   }
1042
1043   # we are annotating a Tree
1044   if ((!$srcbyidref) && $prev eq 'phylogeny') {
1045     # annotate Tree via tree attribute
1046     $self->prev_attr->{$current} = $self->{'_currenttext'};
1047   }
1048   # we are within sequence_relation or clade_relation
1049   elsif ($prev eq 'clade_relation' || $prev eq 'sequence_relation') {
1050     my $ann_relation = $self->{'_currentannotation'}->[-1];
1051     # we are here only with <confidence>
1052     if ($current eq 'confidence') {
1053       if (exists $self->current_attr->{'type'}) {
1054         $ann_relation->confidence_type($self->current_attr->{'type'});
1055       }
1056       $ann_relation->confidence($self->{'_currenttext'});
1057     }
1058     else {
1059       $self->throw($current, " is not allowed within <*_relation>");
1060     }
1061   }
1062   # we are annotating a Node
1063   elsif (( $srcbyidref && $srcbyidref->isa($self->nodetype)) || ((!$srcbyidref) && $prev eq 'clade'))
1064   {
1065     # pop from current annotation
1066     my $ac = pop (@{$self->{'_currentannotation'}});
1067     $self->annotateNode( $current, $ac);
1068
1069     # additional setups for compatibility with NodeI
1070     my $tnode;
1071     if ($srcbyidref) {
1072       $tnode = $srcbyidref;
1073     }
1074     else {
1075       $tnode = $self->{'_currentitems'}->[-1];
1076     }
1077     if ($current eq 'name') {
1078       $tnode->id($self->{'_currenttext'});
1079     }
1080     elsif ($current eq 'branch_length') {
1081       $tnode->branch_length($self->{'_currenttext'});
1082     }
1083     elsif ($current eq 'confidence') {
1084       if ((exists $self->current_attr->{'type'}) && ($self->current_attr->{'type'} eq 'bootstrap')) {
1085         $tnode->bootstrap($self->{'_currenttext'}); # this needs to change (adds 'B' annotation)
1086       }
1087     }
1088     elsif ($current eq 'sequence') {
1089       # if annotation is <sequence>
1090       # transform the Bio::Annotation object into a Bio::Seq object
1091       my $str = '';
1092       # retrieve the sequence
1093       if (my ($molseq) = $ac->get_Annotations('mol_seq')) {
1094         my ($strac) = $molseq->get_Annotations('_text');
1095         $str = $strac->value();
1096       }
1097       # create Seq object with sequence
1098       my $newseq = Bio::Seq->new( -seq => $str,
1099           -annotation=>$ac,
1100           -nowarnonempty=>1);
1101       $tnode->sequence($newseq);
1102       $ac->remove_Annotations('mol_seq');
1103       $tnode->annotation->remove_Annotations($current);
1104       # if there is id_source add sequence to _id_link
1105       if ($idsrc) {
1106         $self->{'_id_link'}->{$idsrc} = $newseq;
1107       }
1108     }
1109     elsif ($idsrc && $current eq 'taxonomy') {
1110       # if there is id_source add sequence to _id_link
1111       $self->{'_id_link'}->{$idsrc} = $ac;
1112     }
1113   }
1114   # we are within a default Annotation
1115   else {
1116     my $ac = pop (@{$self->{'_currentannotation'}});
1117     if ($ac) {
1118       $self->annotateNode( $current, $ac);
1119     }
1120   }
1121 }
1122
1123
1124 =head2 annotateNode
1125
1126  Title   : annotateNode
1127  Usage   : $treeio->annotateNode($element, $ac)
1128  Function: adds text value and attributes to the AnnotationCollection
1129            that has element name as key. If there are nested elements,
1130            optional AnnotationCollections are added recursively,
1131            with the nested element name as key.
1132            The structure of each AnnotationCollection is
1133            'element' => AnnotationCollection {
1134                '_text' => SimpleValue (text value)
1135                '_attr' => AnnotationCollection {
1136                    attribute1 => SimpleValue (attribute value 1)
1137                    attribute2 => SimpleValue (attribute value 2)
1138                    ...
1139                }
1140                ['nested element' => AnnotationCollection ]
1141            }
1142  Returns : none
1143  Args    : none
1144
1145 =cut
1146
1147 sub annotateNode
1148 {
1149   my ($self, $element,  $newac) = @_;
1150   # if attribute exists then add Annotation::Collection with tag '_attr'
1151   if ( scalar keys %{$self->current_attr} ) {
1152     my $newattr = Bio::Annotation::Collection->new();
1153     foreach my $tag (keys %{$self->current_attr}) {
1154       my $sv = Bio::Annotation::SimpleValue->new(
1155                 -value => $self->current_attr->{$tag}
1156                );
1157       $newattr->add_Annotation($tag, $sv);
1158     }
1159     $newac->add_Annotation('_attr', $newattr);
1160   }
1161   # if text exists add text as SimpleValue with tag '_text'
1162   if ( $self->{'_currenttext'} ) {
1163     my $newvalue = Bio::Annotation::SimpleValue->new( -value => $self->{'_currenttext'} );
1164     $newac->add_Annotation('_text', $newvalue);
1165   }
1166 }
1167
1168
1169 =head1 Methods for exploring the document
1170
1171 =cut
1172
1173 =head2 current_attr
1174
1175  Title   : current_attr
1176  Usage   : $attr_hash = $treeio->current_attr;
1177  Function: returns the attribute hash for current item
1178  Returns : reference of the attribute hash
1179  Args    : none
1180
1181 =cut
1182
1183 sub current_attr {
1184   my ($self) = @_;
1185
1186   return 0 if ! defined $self->{'_lastitem'} ||
1187     ! defined $self->{'_lastitem'}->{'current'}->[-1];
1188   my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-1]};
1189   (@keys == 1) || die "there should be only one key for each hash";
1190   return $self->{'_lastitem'}->{'current'}->[-1]->{$keys[0]};
1191 }
1192
1193 =head2 prev_attr
1194
1195  Title   : prev_attr
1196  Usage   : $hash_ref = $treeio->prev_attr
1197  Function: returns the attribute hash for previous item
1198  Returns : reference of the attribute hash
1199  Args    : none
1200
1201 =cut
1202
1203 sub prev_attr {
1204   my ($self) = @_;
1205
1206   return 0 if ! defined $self->{'_lastitem'} ||
1207     ! defined $self->{'_lastitem'}->{'current'}->[-2];
1208   my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-2]};
1209   (@keys == 1) || die "there should be only one key for each hash";
1210   return $self->{'_lastitem'}->{'current'}->[-2]->{$keys[0]};
1211 }
1212
1213 =head2 current_element
1214
1215  Title   : current_element
1216  Usage   : $element = $treeio->current_element
1217  Function: returns the name of the current element
1218  Returns : string (element name)
1219  Args    : none
1220
1221 =cut
1222
1223 sub current_element {
1224   my ($self) = @_;
1225
1226   return 0 if ! defined $self->{'_lastitem'} ||
1227     ! defined $self->{'_lastitem'}->{'current'}->[-1];
1228   my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-1]};
1229   (@keys == 1) || die "there should be only one key for each hash";
1230   return $keys[0];
1231 }
1232
1233 =head2 prev_element
1234
1235  Title   : prev_element
1236  Usage   : $element = $treeio->current_element
1237  Function: returns the name of the previous element
1238  Returns : string (element name)
1239  Args    : none
1240
1241 =cut
1242
1243 sub prev_element {
1244   my ($self) = @_;
1245
1246   return 0 if ! defined $self->{'_lastitem'} ||
1247     ! defined $self->{'_lastitem'}->{'current'}->[-2];
1248   my @keys = keys %{$self->{'_lastitem'}->{'current'}->[-2]};
1249   (@keys == 1) || die "there should be only one key for each hash";
1250   return $keys[0];
1251 }
1252
1253
1254 =head2 treetype
1255
1256  Title   : treetype
1257  Usage   : $obj->treetype($newval)
1258  Function: returns the tree type (default is Bio::Tree::Tree)
1259  Returns : value of treetype
1260  Args    : newvalue (optional)
1261
1262
1263 =cut
1264
1265 sub treetype{
1266    my ($self,$value) = @_;
1267    if( defined $value) {
1268       $self->{'treetype'} = $value;
1269     }
1270     return $self->{'treetype'};
1271 }
1272
1273 =head2 nodetype
1274
1275  Title   : nodetype
1276  Usage   : $obj->nodetype($newval)
1277  Function: returns the node type (default is Bio::Node::AnnotatableNode)
1278  Returns : value of nodetype
1279  Args    : newvalue (optional)
1280
1281 =cut
1282
1283 sub nodetype{
1284    my ($self,$value) = @_;
1285    if( defined $value) {
1286       $self->{'nodetype'} = $value;
1287     }
1288     return $self->{'nodetype'};
1289 }
1290
1291
1292 =head1 Methods for implementing to_string callback for AnnotatableNode
1293
1294 =cut
1295
1296 =head2 node_to_string
1297
1298  Title   : node_to_string
1299  Usage   : $annotatablenode->to_string_callback(\&node_to_string)
1300  Function: set as callback in AnnotatableNode, prints the node information in string
1301  Returns : string of node information
1302  Args    : none
1303
1304 =cut
1305
1306 # this function is similar to _write_tree_Helper_annotatableNode,
1307 # but it is not recursive
1308 sub node_to_string
1309 {
1310   my ($self) = @_;     # this self is a Bio::Tree::AnnotatableNode
1311                        # not a Bio::TreeIO::phyloxml
1312   my $str = '';
1313   my $ac = $self->annotation;
1314
1315   # start <clade>
1316   $str .= '<clade';
1317   my @attr = $ac->get_Annotations('_attr'); # check id_source
1318   if (@attr) {
1319     my @id_source = $attr[0]->get_Annotations('id_source');
1320     if (@id_source) {
1321       $str .= " id_source=\"".$id_source[0]->value."\"";
1322     }
1323   }
1324   $str .= '>';
1325
1326   # print all annotations
1327   $str = print_annotation( $self, $str, $ac );
1328   # print all sequences
1329   if ($self->has_sequence) {
1330     foreach my $seq (@{$self->sequence}) {
1331       $str = print_seq_annotation( $self, $str, $seq );
1332     }
1333   }
1334
1335   $str .= '</clade>';
1336   return $str;
1337 }
1338
1339 =head2 print_annotation
1340
1341  Title   : print_annotation
1342  Usage   : $str = $annotatablenode->print_annotation($str, $annotationcollection)
1343  Function: prints the annotationCollection in a phyloXML format.
1344  Returns : string of annotation information
1345  Args    : string to which the Annotation should be concatenated to,
1346            annotationCollection that holds the Annotations
1347
1348 =cut
1349
1350 # Again, it may be more appropriate to make a separate Annotation::phyloXML object
1351 # and have this subroutine within that object so it can handle the
1352 # reading and writing of the values and attributes.
1353 # especially since this function is used both by
1354 # Bio::TreeIO::phyloxml (through write_tree) and
1355 # Bio::Node::AnnotatableNode (through node_to_string).
1356 # but since tagTree is a temporary stub and I didn't want to make
1357 # a redundant object I've put it here for now.
1358
1359 sub print_annotation
1360 {
1361   my ($self, $str, $ac) = @_;
1362
1363   my @all_anns = $ac->get_Annotations();
1364   foreach my $ann (@all_anns) {
1365     my $key = $ann->tagname;
1366     if ($key eq '_attr') { next; } # attributes are already printed in the previous level
1367     if  ($ann->isa('Bio::Annotation::SimpleValue'))
1368     {
1369       if ($key eq '_text') {
1370         $str .= $ann->value;
1371       }
1372       else {
1373         $str .= "<$key>";
1374         $str .= $ann->value;
1375         $str .= "</$key>";
1376       }
1377     }
1378     elsif ($ann->isa('Bio::Annotation::Collection'))
1379     {
1380       my @attrs = $ann->get_Annotations('_attr');
1381       if (@attrs) {   # if there is a attribute collection
1382         $str .= "<$key";
1383         $str = print_attr($self, $str, $attrs[0]);
1384         $str .= ">";
1385       }
1386       else {
1387         $str .= "<$key>";
1388       }
1389       $str = print_annotation($self, $str, $ann);
1390       $str .= "</$key>";
1391     }
1392   }
1393   return $str;
1394 }
1395
1396 =head2 print_attr
1397
1398  Title   : print_attr
1399  Usage   : $str = $annotatablenode->print_attr($str, $annotationcollection)
1400  Function: prints the annotationCollection in a phyloXML format.
1401  Returns : string of attributes
1402  Args    : string to which the Annotation should be concatenated to,
1403            AnnotationCollection that holds the attributes
1404
1405 =cut
1406
1407 # Again, it may be more appropriate to make a separate Annotation::phyloXML object
1408 # and have this subroutine within that object so it can handle the
1409 # reading and writing of the values and attributes.
1410 # especially since this function is used both by
1411 # Bio::TreeIO::phyloxml and Bio::Node::AnnotatableNode
1412 # (through print_annotation).
1413 # but since tagTree is a temporary stub and I didn't want to make
1414 # a redundant object I've put it here for now.
1415
1416 sub print_attr
1417 {
1418   my ($self, $str, $ac) = @_;
1419   my @all_attrs = $ac->get_Annotations();
1420   foreach my $attr (@all_attrs) {
1421     if  (!$attr->isa('Bio::Annotation::SimpleValue')) {
1422       $self->throw("attribute should be a SimpleValue");
1423     }
1424     $str .= ' ';
1425     $str .= $attr->tagname;
1426     $str .= '=';
1427     $str .= '"'.$attr->value.'"';
1428   }
1429   return $str;
1430 }
1431
1432 =head2 print_sequence_annotation
1433
1434  Title   : print_sequence_annotation
1435  Usage   : $str = $node->print_seq_annotation( $str, $seq );
1436  Function: prints the Bio::Seq object associated with the node
1437            in a phyloXML format.
1438  Returns : string that describes the sequence
1439  Args    : string to which the Annotation should be concatenated to,
1440            Seq object to print in phyloXML
1441
1442 =cut
1443
1444 # Again, it may be more appropriate to make a separate Annotation::phyloXML object
1445 # and have this subroutine within that object so it can handle the
1446 # reading and writing of the values and attributes.
1447 # especially since this function is used both by
1448 # Bio::TreeIO::phyloxml (through write_tree) and
1449 # Bio::Node::AnnotatableNode (through node_to_string).
1450 # but since tagTree is a temporary stub and I didn't want to make
1451 # a redundant object I've put it here for now.
1452
1453
1454 sub print_seq_annotation
1455 {
1456   my ($self, $str, $seq) = @_;
1457
1458   $str .= "<sequence";
1459   my ($attr) = $seq->annotation->get_Annotations('_attr'); # check id_source
1460   if ($attr) {
1461     my ($id_source) = $attr->get_Annotations('id_source');
1462     if ($id_source) {
1463       $str .= " id_source=\"".$id_source->value."\"";
1464     }
1465   }
1466   $str .= ">";
1467
1468   my @all_anns = $seq->annotation->get_Annotations();
1469   foreach my $ann (@all_anns) {
1470     my $key = $ann->tagname;
1471     if ($key eq '_attr') { next; } # attributes are already printed in the previous level
1472     if  ($ann->isa('Bio::Annotation::SimpleValue'))
1473     {
1474       if ($key eq '_text') {
1475         $str .= $ann->value;
1476       }
1477       else {
1478         $str .= "<$key>";
1479         $str .= $ann->value;
1480         $str .= "</$key>";
1481       }
1482     }
1483     elsif ($ann->isa('Bio::Annotation::Collection'))
1484     {
1485       my @attrs = $ann->get_Annotations('_attr');
1486       if (@attrs) {   # if there is a attribute collection
1487         $str .= "<$key";
1488         $str = print_attr($self, $str, $attrs[0]);
1489         $str .= ">";
1490       }
1491       else {
1492         $str .= "<$key>";
1493       }
1494       $str = print_annotation($self, $str, $ann);
1495       $str .= "</$key>";
1496     }
1497   }
1498   # print mol_seq
1499   if ($seq->seq()) {
1500     $str .= "<mol_seq>";
1501     $str .= $seq->seq();
1502     $str .= "</mol_seq>";
1503   }
1504
1505   $str .= "</sequence>";
1506   return $str;
1507 }
1508
1509 1;