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Summary

Bio::Tools::EUtilities::Summary::Item - simple layered object for DocSum item data

Package variables

Inherit

Bio::Root::Root Bio::Tools::EUtilities::EUtilDataI

Synopsis

  # Items can be nested up to three levels at this time. These levels can be
  # accessed via Item, ListItem, or StructureItem methods:

  while (my $item = $docsum->next_Item) {
     print "Name: ",$item->get_name,"\n";
     print "Data: ",$item->get_content,"\n";
     print "Type: ",$item->get_type,"\n";
     while (my $ls = $item->next_ListItem) {
        # do same here
        while (my $struct = $ls->next_StructureItem) {
           # do more stuff here
        }
     }
  }

Description

DocSum data, as returned from esummary, normally is a simple list of
item-content-content_type groups. However, items can also contain nested data to
represent more complex data (such as structural data). Up to three nested layers
may appear in any document summary.
This class contains methods to access data that can appear in a docsum for any
individual item as well as describes methods to traverse the hierarchy of items
present in a document summary.
The unique name for items are accessed via get_name(), the content by
get_content() (if present), and the data type by get_type(). Items can have
ListItems (Item objects with a datatype() 'list'), which in turn can have
StructureItems (Item objects with a datatype of 'structure'). Items are
initially traversed via a DocSum object using next_Item() or obtained all at
once with get_Items(). Similarly, nested Items can be accessed by using
next_ListItem/get_ListItems and next_StructureItem/get_StructureItem. A
flattened list of items can be accessed with get_all_Items().

Methods

Methods description

 Title    : new
 Usage    : 
 Function : 
 Returns  : 
 Args     :

 Title    : get_ids
 Usage    : my ($id) = $item->get_ids;
 Function : returns array or array ref with id
 Returns  : array or array ref
 Args     : none
 Note     : the behavior of this method is to remain consistent with other 
            implementations of get_ids(). To retrieve the single DocSum ID use
            get_id()

 Title    : get_id
 Usage    : my ($id) = $item->get_id;
 Function : returns UID of record
 Returns  : integer
 Args     : none

 Title    : next_ListItem
 Usage    : while (my $ls = $item->next_ListItem) {...}
 Function : iterates through ListItems (nested layer of Item)
 Returns  : single ListItem
 Args     : none

 Title    : get_ListItems
 Usage    : my @ls = $item->get_ListItems
 Function : returns list of, well, List Items
 Returns  : array of List Items
 Args     : none

 Title    : next_StructureItem
 Usage    : while (my $struc = $ls->next_StructureItem) {...}
 Function : iterates through StructureItems (nested layer of ListItem)
 Returns  : single StructureItems
 Args     : none

 Title    : get_StructureItems
 Usage    : my @structs = $ls->get_StructureItems
 Function : returns list of Structure Items
 Returns  : array of StructureItems
 Args     : none

 Title    : next_subItem
 Usage    : while (my $it = $ls->next_subItem) {...}
 Function : iterates through the next layer of Items
 Returns  : single Item
 Args     : none
 Notes    : unlike next_ListItem and next_StructureItem, this generically
            accesses any sub Items (useful for recursive calls, for example)

 Title    : get_subItems
 Usage    : my @items = $ls->get_subItems
 Function : returns list of sub Items
 Returns  : array of Items
 Args     : none
 Notes    : unlike get_ListItems and get_StructureItems, this generically
            accesses any sub Items (useful for recursive calls, for example)

 Title    : get_name
 Usage    : my $nm = $ls->get_name
 Function : retrieves Item/ListItem/StructureItem name for this Item
 Returns  : string
 Args     : none

 Title    : get_type
 Usage    : my $type = $ls->get_type
 Function : retrieves Item/ListItem/StructureItem type 
 Returns  : string
 Args     : none
 Note     : this is not the same as the datatype(), which describes the
            group this Item object belongs to

 Title    : get_content
 Usage    : my $data = $ls->get_content
 Function : retrieves Item/ListItem/StructureItem content (if any)
 Returns  : string
 Args     : none

 Title    : rewind
 Usage    : $item->rewind()
 Function : rewinds iterators
 Returns  : none
 Args     : [optional] No arg - only rewinds current layer
           'all' - rewind all DocSum object layers
                (Items, ListItems, StructureItems)

 Title    : next_Item
 Usage    : while (my $item = $docsum->next_Item) {...}
 Function : iterates through Items (nested layer of Item)
 Returns  : single Item
 Args     : [optional] single arg (string)
            'flatten' - iterates through a flattened list ala
                          get_all_DocSum_Items()

 Title    : get_Items
 Usage    : my @items = $docsum->get_Items
 Function : returns list of, well, Items
 Returns  : array of Items
 Args     : none

 Title    : get_all_Items
 Usage    : my @items = $docsum->get_all_Items
 Function : returns flattened list of all Item objects (Items, ListItems,
            StructureItems)
 Returns  : array of Items
 Args     : none
 Note     : items are added top-down (similar order to using nested calls)
            in original list order.

             1         2        7        8
           Item  -   Item  -  Item  -  Item ...
                     |
                    | 3        6
                 ListItem - ListItem
                   |
                  | 4          5
               Structure - Structure

 Title    : get_all_names
 Usage    : my @names = get_all_names()
 Function : Returns an array of names for all Item(s) in DocSum.
 Returns  : array of unique strings
 Args     : none

 Title    : get_Items_by_name
 Usage    : my @items = get_Items_by_name('CreateDate')
 Function : Returns named Item(s) in DocSum (indicated by passed argument)
 Returns  : array of Item objects
 Args     : string (Item name)

 Title    : get_contents_by_name
 Usage    : my ($data) = get_contents_by_name('CreateDate')
 Function : Returns content for named Item(s) in DocSum (indicated by
            passed argument)
 Returns  : array of values (type varies per Item)
 Args     : string (Item name)

 Title    : get_type_by_name
 Usage    : my $data = get_type_by_name('CreateDate')
 Function : Returns data type for named Item in DocSum (indicated by
            passed argument)
 Returns  : scalar value (string) if present
 Args     : string (Item name)

 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting.  This implementation
            passes an argument for layering Items/subItems
 Note     : Used generically for debugging and print_DocSums methods

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($type) = $self->_rearrange(['DATATYPE'],@args);
    $type ||= 'item';
    $self->datatype($type);
    $self->eutil('esummary');
    $self->rewind('recursive');
    return $self;

}

sub get_ids {

    my $self = shift;
    return ($self->{'_id'});

}

sub get_id {

    my $self = shift;
    return $self->{'_id'};

}

sub next_ListItem {

    my $self = shift;
    unless ($self->{'_lists_it'}) {
        my @lists = $self->get_ListItems;
        # reset the structure iterator (required!)
        delete $self->{'_structures_it'} if $self->{'_structures_it'};
        $self->{'_lists_it'} = sub {return shift @lists}
    }        
    return $self->{'_lists_it'}->();

}

sub get_ListItems {

    my $self = shift;
    my @items = $self->get_type eq 'List' ? $self->get_subItems : ();
    return @items;

}

sub next_StructureItem {

    my $self = shift;
    unless ($self->{'_structures_it'}) {
        my @structs = $self->get_StructureItems;
        $self->{'_structures_it'} = sub {return shift @structs}
    }
    return $self->{'_structures_it'}->();

}

sub get_StructureItems {

    my $self = shift;
    my @items = $self->get_type eq 'Structure' ? $self->get_subItems : ();
    return @items;

}

sub next_subItem {

    my $self = shift;
    unless ($self->{'_subitem_it'}) {
        my @structs = $self->get_subItems;
        $self->{'_subitem_it'} = sub {return shift @structs}
    }
    return $self->{'_subitem_it'}->();

}

sub get_subItems {

    my $self = shift;
    ref $self->{'_items'}  ? return @{ $self->{'_items'} } : return ();

}

sub get_name {

    my $self = shift;
    return $self->{'_itemname'};

}

sub get_type {

    my $self = shift;
    return $self->{'_itemtype'};

}

sub get_content {

    my $self = shift;
    return $self->{'_itemcontent'};

}

sub rewind {

    my ($self, $request) = @_;
    if ($request && $request eq 'all') {
        map {$_->rewind()} $self->get_ListItems;
    }
    delete $self->{"_lists_it"} if $self->{"_lists_it"};
    delete $self->{"_structures_it"} if $self->{"_structures_it"};

}

sub next_Item {

    my ($self, $request) = @_;
    unless ($self->{"_items_it"}) {
        #my @items = $self->get_Items;
        my @items = ($request && $request eq 'flatten') ?
                    $self->get_all_Items :
                    $self->get_Items ;
        $self->{"_items_it"} = sub {return shift @items}
    }
    $self->{'_items_it'}->();

}

sub get_Items {

    my $self = shift;
    return ref $self->{'_items'} ? @{ $self->{'_items'} } : return ();

}

sub get_all_Items {

    my $self = shift;
    unless ($self->{'_ordered_items'}) {
        for my $item ($self->get_Items) {
            push @{$self->{'_ordered_items'}}, $item;
            for my $ls ($item->get_ListItems) {
                push @{$self->{'_ordered_items'}}, $ls;
                for my $st ($ls->get_StructureItems) {
                    push @{$self->{'_ordered_items'}}, $st;                
                } 
            }
        }
    }
    return @{$self->{'_ordered_items'}};

}

sub get_all_names {

    my ($self) = @_;
    my %tmp;
    my @data = grep {!$tmp{$_}++}
        map {$_->get_name} $self->get_all_Items;
    return @data;

}

sub get_Items_by_name {

    my ($self, $key) = @_;
    return unless $key;
    my @data = grep {$_->get_name eq $key}
        $self->get_all_Items;
    return @data;

}

sub get_contents_by_name {

    my ($self, $key) = @_;
    return unless $key;
    my @data = map {$_->get_content} 
        grep {$_->get_name eq $key}
        $self->get_all_Items;
    return @data;

}

sub get_type_by_name {

    my ($self, $key) = @_;
    return unless $key;
    my ($it) = grep {$_->get_name eq $key} $self->get_all_Items;
    return $it->get_type;
}

# private data method

}

sub _add_data {

    my ($self, $data) = @_;
    if ($data->{Item}) {
        my $objtype = lc $data->{Type}.'_item';
        $self->{'_id'} = $data->{Id} if exists $data->{Id};
        for my $sd (@{ $data->{Item} } ) {
            $sd->{Id} = $data->{Id} if exists $data->{Id};
            my $subdoc = Bio::Tools::EUtilities::Summary::Item->new(
                                -datatype => $objtype,
                                -verbose => $self->verbose);
            $subdoc->_add_data($sd);
            push @{ $self->{'_items'} }, $subdoc;
        }
    }
    for my $nm (qw(Type content Name)) {
        $self->{'_item'.lc $nm} = $data->{$nm} if defined $data->{$nm};
    }
    $self->{'_id'} = $data->{Id} if exists $data->{Id};

}

sub to_string {

    my $self = shift;
    my $level = shift || 0;
    # this is the field length for the initial data (spaces are padded in front)
    my $pad = 20 - $level;
    my $content = $self->get_content || '';
    my $string .= sprintf("%-*s%-*s%s\n",
        $level, '',
        $pad, $self->get_name(),
        $self->_text_wrap(':',
             ' ' x ($pad).':',
             $content));
    for my $sub ($self->get_subItems) {
        $string .= $sub->to_string(4 + $level);
    }
    return $string;
}

1;

}

General documentation

User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
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Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to
help us keep track the bugs and their resolution.
Bug reports can be submitted via the web.

  https://redmine.open-bio.org/projects/bioperl/

Email cjfields at bioperl dot org

The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _