AcePerl
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Ace/Object.pm view on Meta::CPAN
my @r;
# This is for tag[1] semantics
if ($pos == 1) {
for (my $o=$self->right; defined($o); $o=$o->down) {
push (@r,$o);
}
} else {
# This is for tag[2] semantics
for (my $o=$self->right; defined($o); $o=$o->down) {
next unless defined(my $right = $o->right($pos-2));
push (@r,$right->col);
}
}
return @r;
}
#### Search for a tag, and return the column ####
#### Uses a breadth-first search (cols then rows) ####
sub search {
my $self = shift;
my $tag = shift unless $_[0]=~/^-/;
my ($subtag,$pos,$filled) = rearrange(['SUBTAG','POS',['FILL','FILLED']],@_);
my $lctag = lc $tag;
# With caching, the old way of following ends up cloning the object
# -- which we don't want. So more-or-less emulate the earlier
# behavior with an explicit get and fetch
# return $self->follow(-tag=>$tag,-filled=>$filled) if $filled;
if ($filled) {
my @node = $self->search($tag) or return; # watch out for recursion!
my @obj = map {$_->fetch} @node;
foreach (@obj) {$_->right if defined $_}; # trigger a fill
return wantarray ? @obj : $obj[0];
}
TRY: {
# look in our tag cache first
if (exists $self->{'.PATHS'}) {
# we've already cached the desired tree
last TRY if exists $self->{'.PATHS'}{$lctag};
# not cached, so try parents of tag
my $m = $self->model;
my @parents = $m->path($lctag) if $m;
my $tree;
foreach (@parents) {
($tree = $self->{'.PATHS'}{lc $_}) && last;
}
if ($tree) {
$self->{'.PATHS'}{$lctag} = $tree->search($tag);
$self->_dirty(1);
last TRY;
}
}
# If the object hasn't been filled already, then we can use
# acedb's query mechanism to fetch the subobject. This is a
# big win for large objects. ...However, we have to disable
# this feature if timestamps are active.
unless ($self->filled) {
my $subobject = $self->newFromText(
$self->db->show($self->class,$self->name,$tag),
$self->db
);
if ($subobject) {
$subobject->{'.nocache'}++;
$self->_attach_subtree($lctag => $subobject);
} else {
$self->{'.PATHS'}{$lctag} = undef;
}
$self->_dirty(1);
last TRY;
}
my @col = $self->col;
foreach (@col) {
next unless $_->isTag;
if (lc $_ eq $lctag) {
$self->{'.PATHS'}{$lctag} = $_;
$self->_dirty(1);
last TRY;
}
}
# if we get here, we didn't find it in the column,
# so we call ourselves recursively to find it
foreach (@col) {
next unless $_->isTag;
if (my $r = $_->search($tag)) {
$self->{'.PATHS'}{$lctag} = $r;
$self->_dirty(1);
last TRY;
}
}
# If we got here, we just didn't find it. So tag the cache
# as empty so that we don't try again
$self->{'.PATHS'}{$lctag} = undef;
$self->_dirty(1);
}
my $t = $self->{'.PATHS'}{$lctag};
return unless $t;
if (defined $subtag) {
if ($subtag =~ /^\d+$/) {
$pos = $subtag;
} else { # position on subtag and search again
return $t->fetch->search($subtag,$pos)
if $t->isObject || (defined($t->right) and $t->right->isObject);
return $t->search($subtag,$pos);
}
}
return defined $pos ? $t->right($pos) : $t unless wantarray;
# We do something verrrry interesting in an array context.
# If no position is defined, we return the column to the right.
# If a position is defined, we return everything $POS tags
Ace/Object.pm view on Meta::CPAN
into various types of text representation. You can also fetch a
representation of any object as a GIF image.
If you have write access to the databases, add new data to an object,
replace existing data, or kill it entirely. You can also create a new
object de novo and write it into the database.
For information on connecting to ACEDB databases and querying them,
see L<Ace>.
=head1 ACEDB::OBJECT METHODS
The structure of an Ace::Object is very similar to that of an Acedb
object. It is a tree structure like this one (an Author object):
Thierry-Mieg J->Full_name ->Jean Thierry-Mieg
|
Laboratory->FF
|
Address->Mail->CRBM duCNRS
| | |
| | BP 5051
| | |
| | 34033 Montpellier
| | |
| | FRANCE
| |
| E_mail->mieg@kaa.cnrs-mop.fr
| |
| Phone ->33-67-613324
| |
| Fax ->33-67-521559
|
Paper->The C. elegans sequencing project
|
Genome Project Database
|
Genome Sequencing
|
How to get ACEDB for your Sun
|
ACEDB is Hungry
Each object in the tree has two pointers, a "right" pointer to the
node on its right, and a "down" pointer to the node beneath it. Right
pointers are used to store hierarchical relationships, such as
Address->Mail->E_mail, while down pointers are used to store lists,
such as the multiple papers written by the Author.
Each node in the tree has a type and a name. Types include integers,
strings, text, floating point numbers, as well as specialized
biological types, such as "dna" and "peptide." Another fundamental
type is "tag," which is a text identifier used to label portions of
the tree. Examples of tags include "Paper" and "Laboratory" in the
example above.
In addition to these built-in types, there are constructed types known
as classes. These types are specified by the data model. In the
above example, "Thierry-Mieg J" is an object of the "Author" class,
and "Genome Project Database" is an object of the "Paper" class. An
interesting feature of objects is that you can follow them into the
database, retrieving further information. For example, after
retrieving the "Genome Project Database" Paper from the Author object,
you could fetch more information about it, either by following B<its>
right pointer, or by using one of the specialized navigation routines
described below.
=head2 new() method
$object = new Ace::Object($class,$name,$database);
$object = new Ace::Object(-class=>$class,
-name=>$name,
-db=>database);
You can create a new Ace::Object from scratch by calling the new()
routine with the object's class, its identifier and a handle to the
database to create it in. The object won't actually be created in the
database until you add() one or more tags to it and commit() it (see
below). If you do not provide a database handle, the object will be
created in memory only.
Arguments can be passed positionally, or as named parameters, as shown
above.
This routine is usually used internally. See also add_row(),
add_tree(), delete() and replace() for ways to manipulate this object.
=head2 name() method
$name = $object->name();
Return the name of the Ace::Object. This happens automatically
whenever you use the object in a context that requires a string or a
number. For example:
$object = $db->fetch(Author,"Thierry-Mieg J");
print "$object did not write 'Pride and Prejudice.'\n";
=head2 class() method
$class = $object->class();
Return the class of the object. The return value may be one of
"float," "int," "date," "tag," "txt," "dna," "peptide," and "scalar."
(The last is used internally by Perl to represent objects created
programatically prior to committing them to the database.) The class
may also be a user-constructed type such as Sequence, Clone or
Author. These user-constructed types usually have an initial capital
letter.
=head2 db() method
$db = $object->db();
Return the database that the object is associated with.
=head2 isClass() method
$bool = $object->isClass();
Returns true if the object is a class (can be fetched from the
Ace/Object.pm view on Meta::CPAN
$object->asString;
asString() returns a pretty-printed ASCII representation of the object
tree.
=head2 asTable() method
$object->asTable;
asTable() returns the object as a tab-delimited text table.
=head2 asAce() method
$object->asAce;
asAce() returns the object as a tab-delimited text table in ".ace"
format.
=head2 asHTML() method
$object->asHTML;
$object->asHTML(\&tree_traversal_code);
asHTML() returns an HTML 3 table representing the object, suitable for
incorporation into a Web browser page. The callback routine, if
provided, will have a chance to modify the object representation
before it is incorporated into the table, for example by turning it
into an HREF link. The callback takes a single argument containing
the object, and must return a string-valued result. It may also
return a list as its result, in which case the first member of the
list is the string representation of the object, and the second
member is a boolean indicating whether to prune the table at this
level. For example, you can prune large repetitive lists.
Here's a complete example:
sub process_cell {
my $obj = shift;
return "$obj" unless $obj->isObject || $obj->isTag;
my @col = $obj->col;
my $cnt = scalar(@col);
return ("$obj -- $cnt members",1); # prune
if $cnt > 10 # if subtree to big
# tags are bold
return "<B>$obj</B>" if $obj->isTag;
# objects are blue
return qq{<FONT COLOR="blue">$obj</FONT>} if $obj->isObject;
}
$object->asHTML(\&process_cell);
=head2 asXML() method
$result = $object->asXML;
asXML() returns a well-formed XML representation of the object. The
particular representation is still under discussion, so this feature
is primarily for demonstration.
=head2 asGIF() method
($gif,$boxes) = $object->asGIF();
($gif,$boxes) = $object->asGIF(-clicks=>[[$x1,$y1],[$x2,$y2]...]
-dimensions=> [$width,$height],
-coords => [$top,$bottom],
-display => $display_type,
-view => $view_type,
-getcoords => $true_or_false
);
asGIF() returns the object as a GIF image. The contents of the GIF
will be whatever xace would ordinarily display in graphics mode, and
will vary for different object classes.
You can optionally provide asGIF with a B<-clicks> argument to
simulate the action of a user clicking on the image. The click
coordinates should be formatted as an array reference that contains a
series of two-element subarrays, each corresponding to the X and Y
coordinates of a single mouse click. There is currently no way to
pass information about middle or right mouse clicks, dragging
operations, or keystrokes. You may also specify a B<-dimensions> to
control the width and height of the returned GIF. Since there is no
way of obtaining the preferred size of the image in advance, this is
not usually useful.
The optional B<-display> argument allows you to specify an alternate
display for the object. For example, Clones can be displayed either
with the PMAP display or with the TREE display. If not specified, the
default display is used.
The optional B<-view> argument allows you to specify an alternative
view for MAP objects only. If not specified, you'll get the default
view.
The option B<-coords> argument allows you to provide the top and
bottom of the display for MAP objects only. These coordinates are in
the map's native coordinate system (cM, bp). By default, AceDB will
show most (but not necessarily all) of the map according to xace's
display rules. If you call this method with the B<-getcoords>
argument and a true value, it will return a two-element array
containing the coordinates of the top and bottom of the map.
asGIF() returns a two-element array. The first element is the GIF
data. The second element is an array reference that indicates special
areas of the image called "boxes." Boxes are rectangular areas that
surround buttons, and certain displayed objects. Using the contents
of the boxes array, you can turn the GIF image into a client-side
image map. Unfortunately, not everything that is clickable is
represented as a box. You still have to pass clicks on unknown image
areas back to the server for processing.
Each box in the array is a hash reference containing the following
keys:
'coordinates' => [$left,$top,$right,$bottom]
'class' => object class or "BUTTON"
'name' => object name, if any
Ace/Object.pm view on Meta::CPAN
# This is unsatisfactory because it duplicates much of the code
# of asTable.
sub _asAce {
my($self,$out,$level,$tags) = @_;
# ugly optimization for speed
if ($self->{'.raw'}){
my ($a,$start,$end) = @{$self}{qw(.col .start_row .end_row)};
my (@last);
foreach (@{$self->{'.raw'}}[$start..$end]){
my $j=1;
$$out .= join("\t",@$tags) . "\t" if ($level==0) && (@$tags);
my (@to_modify) = @{$_}[$a..$#{$_}];
foreach (@to_modify) {
my ($class,$name) =Ace->split($_);
if (defined($name)) {
$name = $self->_ace_format($class,$name);
if (_isObject($class) || $name=~/[^\w.-]/) {
$name=~s/"/\\"/g; #escape quotes with slashes
$name = qq/\"$name\"/;
}
} else {
$name = $last[$j] if $name eq '';
}
$_ = $last[$j++] = $name;
$$out .= "$_\t";
}
$$out .= "\n";
$level = 0;
}
chop($$out);
return;
}
$$out .= join("\t",@$tags) . "\t" if ($level==0) && (@$tags);
$$out .= $self->escape . "\t";
if (defined $self->right) {
push(@$tags,$self->escape);
$self->right->_asAce($out,$level+1,$tags);
pop(@$tags);
}
if ($self->down) {
$$out .= "\n";
$self->down->_asAce($out,0,$tags);
}
}
sub _to_ace_date {
my $self = shift;
my $string = shift;
return $string unless lc($self->date_style) eq 'ace';
%MO = (Jan=>1,Feb=>2,Mar=>3,
Apr=>4,May=>5,Jun=>6,
Jul=>7,Aug=>8,Sep=>9,
Oct=>10,Nov=>11,Dec=>12) unless %MO;
my ($day,$mo,$yr) = split(" ",$string);
return "$yr-$MO{$mo}-$day";
}
### Return an XML syntax representation ###
### Consider this feature experimental ###
sub asXML {
my $self = shift;
return unless defined($self->right);
my ($do_content,$do_class,$do_value,$do_timestamps) = rearrange([qw(CONTENT CLASS VALUE TIMESTAMPS)],@_);
$do_content = 0 unless defined $do_content;
$do_class = 1 unless defined $do_class;
$do_value = 1 unless defined $do_value;
$do_timestamps = 1 unless (defined $do_timestamps && !$do_timestamps) || !$self->db->timestamps;
my %options = (content => $do_content,
class => $do_class,
value => $do_value,
timestamps => $do_timestamps);
my $name = $self->escapeXML($self->name);
my $class = $self->class;
my $string = '';
$self->_asXML(\$string,0,0,'',0,\%options);
return $string;
}
sub _asXML {
my($self,$out,$position,$level,$current_tag,$tag_level,$opts) = @_;
do {
my $name = $self->escapeXML($self->name);
my $class = $self->class;
my ($tagname,$attributes,$content) = ('','',''); # prevent uninitialized variable warnings
my $tab = " " x ($level-$position); # four spaces
$current_tag ||= $class;
$content = $name if $opts->{content};
if ($self->isTag) {
$current_tag = $tagname = $name;
$tag_level = 0;
} else {
$tagname = $tag_level > 0 ? sprintf "%s-%d",$current_tag,$tag_level + 1 : $current_tag;
$class = "#$class" unless $self->isObject;
$attributes .= qq( class="$class") if $opts->{class};
$attributes .= qq( value="$name") if $opts->{value};
}
if (my $c = $self->comment) {
$c = $self->escapeXML($c);
$attributes .= qq( comment="$c");
}
if ($opts->{timestamps} && (my $timestamp = $self->timestamp)) {
$timestamp = $self->escapeXML($timestamp);
$attributes .= qq( timestamp="$timestamp");
}
$tagname = $self->_xmlNumber($tagname) if $tagname =~ /^\d/;
unless (defined $self->right) { # lone tag
$$out .= $self->isTag || !$opts->{content} ? qq($tab<$tagname$attributes />\n)
: qq($tab<$tagname$attributes>$content</$tagname>\n);
} elsif ($self->isTag) { # most tags are implicit in the XML tag names
if (!XML_COLLAPSE_TAGS or $self->right->isTag) {
$$out .= qq($tab<$tagname$attributes>\n);
$level = $self->right->_asXML($out,$position,$level+1,$current_tag,$tag_level + !XML_COLLAPSE_TAGS,$opts);
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