ACE::OBJECT(3PM) - Linux man page online | Library functions
Manipulate Ace Data Objects.
Chapter
2017-11-24
Ace::Object(3pm) User Contributed Perl Documentation Ace::Object(3pm)
@kaa.cnrs-mop.fr
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| Phone ->33-67-613324
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| Fax ->33-67-521559
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Paper->The C. elegans sequencing project
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Genome Project Database
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Genome Sequencing
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How to get ACEDB for your Sun
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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 its right pointer, or by using one of the specialized navigation routines
described below.
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.
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";
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 programmatically 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.
db() method
$db = $object->db();
Return the database that the object is associated with.
isClass() method
$bool = $object->isClass();
Returns true if the object is a class (can be fetched from the database).
isTag() method
$bool = $object->isTag();
Returns true if the object is a tag.
tags() method
@tags = $object->tags();
Return all the top-level tags in the object as a list. In the Author example above, the
returned list would be ('Full_name','Laboratory','Address','Paper').
You can fetch tags more deeply nested in the structure by navigating inwards using the
methods listed below.
right() and down() methods
$subtree = $object->right;
$subtree = $object->right($position);
$subtree = $object->down;
$subtree = $object->down($position);
right() and down() provide a low-level way of traversing the tree structure by following
the tree's right and down pointers. Called without any arguments, these two methods will
move one step. Called with a numeric argument >= 0 they will move the indicated number of
steps (zero indicates no movement).
$full_name = $object->right->right;
$full_name = $object->right(2);
$city = $object->right->down->down->right->right->down->down;
$city = $object->right->down(2)->right(2)->down(2);
If $object contains the "Thierry-Mieg J" Author object, then the first series of accesses
shown above retrieves the string "Jean Thierry-Mieg" and the second retrieves "34033
Montpellier." If the right or bottom pointers are NULL, these methods will return undef.
In addition to being somewhat awkard, you will probably never need to use these methods.
A simpler way to retrieve the same information would be to use the at() method described
in the next section.
The right() and down() methods always walk through the tree of the current object. They
do not follow object pointers into the database. Use fetch() (or the deprecated pick() or
follow() methods) instead.
at() method
$subtree = $object->at($tag_path);
@values = $object->at($tag_path);
at() is a simple way to fetch the portion of the tree that you are interested in. It
takes a single argument, a simple tag or a path. A simple tag, such as "Full_name", must
correspond to a tag in the column immediately to the right of the root of the tree. A
path such as "Address.Mail" is a dot-delimited path to the subtree. Some examples are
given below.
($full_name) = $object->at('Full_name');
@address_lines = $object->at('Address.Mail');
The second line above is equivalent to:
@address = $object->at('Address')->at('Mail');
Called without a tag name, at() just dereferences the object, returning whatever is to the
right of it, the same as $object->right
If a path component already has a dot in it, you may escape the dot with a backslash, as
in:
$s=$db->fetch('Sequence','M4');
@homologies = $s->at('Homol.DNA_homol.yk192f7\.3';
This also demonstrates that path components don't necessarily have to be tags, although in
practice they usually are.
at() returns slightly different results depending on the context in which it is called.
In a list context, it returns the column of values to the right of the tag. However, in a
scalar context, it returns the subtree rooted at the tag. To appreciate the difference,
consider these two cases:
$name1 = $object->at('Full_name');
($name2) = $object->at('Full_name');
After these two statements run, $name1 will be the tag object named "Full_name", and
$name2 will be the text object "Jean Thierry-Mieg", The relationship between the two is
that $name1->right leads to $name2. This is a powerful and useful construct, but it can
be a trap for the unwary. If this behavior drives you crazy, use this construct:
$name1 = $object->at('Full_name')->at();
For finer control over navigation, path components can include optional indexes to
indicate navigation to the right of the current path component. Here is the syntax:
$object->at('tag1[index1].tag2[index2].tag3[index3]...');
Indexes are zero-based. An index of [0] indicates no movement relative to the current
component, and is the same as not using an index at all. An index of [1] navigates one
step to the right, [2] moves two steps to the right, and so on. Using the Thierry-Mieg
object as an example again, here are the results of various indexes:
$object = $db->fetch(Author,"Thierry-Mieg J");
$a = $object->at('Address[0]') --> "Address"
$a = $object->at('Address[1]') --> "Mail"
$a = $object->at('Address[2]') --> "CRBM duCNRS"
In an array context, the last index in the path does something very interesting. It
returns the entire column of data K steps to the right of the path, where K is the index.
This is used to implement so-called "tag[2]" syntax, and is very useful in some
circumstances. For example, here is a fragment of code to return the Thierry-Mieg
object's full address without having to refer to each of the intervening "Mail", "E_Mail"
and "Phone" tags explicitly.
@address = $object->at('Address[2]');
--> ('CRBM duCNRS','BP 5051','34033 Montpellier','FRANCE',
'@kaa.cnrs-mop.fr,'33-67-613324','33-67-521559')
Similarly, "tag[3]" will return the column of data three hops to the right of the tag.
"tag[1]" is identical to "tag" (with no index), and will return the column of data to the
immediate right. There is no special behavior associated with using "tag[0]" in an array
context; it will always return the subtree rooted at the indicated tag.
Internal indices such as "Homol[2].BLASTN", do not have special behavior in an array
context. They are always treated as if they were called in a scalar context.
Also see col() and get().
get() method
$subtree = $object->get($tag);
@values = $object->get($tag);
@values = $object->get($tag, $position);
@values = $object->get($tag => $subtag, $position);
The get() method will perform a breadth-first search through the object (columns first,
followed by rows) for the tag indicated by the argument, returning the column of the
portion of the subtree it points to. For example, this code fragment will return the
value of the "Fax" tag.
($fax_no) = $object->get('Fax');
--> "33-67-521559"
The list versus scalar context semantics are the same as in at(), so if you want to
retrieve the scalar value pointed to by the indicated tag, either use a list context as
shown in the example, above, or a dereference, as in:
$fax_no = $object->get('Fax');
--> "Fax"
$fax_no = $object->get('Fax')->at;
--> "33-67-521559"
An optional second argument to get(), $position, allows you to navigate the tree relative
to the retrieved subtree. Like the at() navigational indexes, $position must be a number
greater than or equal to zero. In a scalar context, $position moves rightward through the
tree. In an array context, $position implements "tag[2]" semantics.
For example:
$fax_no = $object->get('Fax',0);
--> "Fax"
$fax_no = $object->get('Fax',1);
--> "33-67-521559"
$fax_no = $object->get('Fax',2);
--> undef # nothing beyond the fax number
@address = $object->get('Address',2);
--> ('CRBM duCNRS','BP 5051','34033 Montpellier','FRANCE',
'@kaa.cnrs-mop.fr,'33-67-613324','33-67-521559')
It is important to note that get() only traverses tags. It will not traverse nodes that
aren't tags, such as strings, integers or objects. This is in keeping with the behavior
of the Ace query language "show" command.
This restriction can lead to confusing results. For example, consider the following
object:
Clone: B0280 Position Map Sequence-III Ends Left 3569
Right 3585
Pmap ctg377 -1040 -1024
Positive Positive_locus nhr-10
Sequence B0280
Location RW
FingerPrint Gel_Number 0
Canonical_for T20H1
K10E5
Bands 1354 18
The following attempt to fetch the left and right positions of the clone will fail,
because the search for the "Left" and "Right" tags cannot traverse "Sequence-III", which
is an object, not a tag:
my $left = $clone->get('Left'); # will NOT work
my $right = $clone->get('Right'); # neither will this one
You must explicitly step over the non-tag node in order to make this query work. This
syntax will work:
my $left = $clone->get('Map',1)->get('Left'); # works
my $left = $clone->get('Map',1)->get('Right'); # works
Or you might prefer to use the tag[2] syntax here:
my($left,$right) = $clone->get('Map',1)->at('Ends[2]');
Although not frequently used, there is a form of get() which allows you to stack subtags:
$locus = $object->get('Positive'=>'Positive_locus');
Only on subtag is allowed. You can follow this by a position if wish to offset from the
subtag.
$locus = $object->get('Positive'=>'Positive_locus',1);
search() method
This is a deprecated synonym for get().
Autogenerated Access Methods
$scalar = $object->Name_of_tag;
$scalar = $object->Name_of_tag($position);
@array = $object->Name_of_tag;
@array = $object->Name_of_tag($position);
@array = $object->Name_of_tag($subtag=>$position);
@array = $object->Name_of_tag(-fill=>$tag);
The module attempts to autogenerate data access methods as needed. For example, if you
refer to a method named "Fax" (which doesn't correspond to any of the built-in methods),
then the code will call the get() method to find a tag named "Fax" and return its
contents.
Unlike get(), this method will always step into objects. This means that:
$map = $clone->Map;
will return the Sequence_Map object pointed to by the Clone's Map tag and not simply a
pointer to a portion of the Clone tree. Therefore autogenerated methods are functionally
equivalent to the following:
$map = $clone->get('Map')->fetch;
The scalar context semantics are also slightly different. In a scalar context, the
autogenerated function will *always* move one step to the right.
The list context semantics are identical to get(). If you want to dereference all members
of a multivalued tag, you have to do so manually:
@papers = $author->Paper;
foreach (@papers) {
my $paper = $_->fetch;
print $paper->asString;
}
You can provide an optional positional index to rapidly navigate through the tree or to
obtain tag[2] behavior. In the following examples, the first two return the object's Fax
number, and the third returns all data two hops to the right of Address.
$object = $db->fetch(Author => 'Thierry-Mieg J');
($fax_no) = $object->Fax;
$fax_no = $object->Fax(1);
@address = $object->Address(2);
You may also position at a subtag, using this syntax:
$representative = $object->Laboratory('Representative');
Both named tags and positions can be combined as follows:
$lab_address = $object->Laboratory(Address=>2);
If you provide a -fill=>$tag argument, then the object fetch will automatically fill the
specified subtree, greatly improving performance. For example:
$lab_address = $object->Laboratory(-filled=>'Address');
** NOTE: In a scalar context, if the node to the right of the tag is ** an object, the
method will perform an implicit dereference of the ** object. For example, in the case
of:
$lab = $author->Laboratory;
**NOTE: The object returned is the dereferenced Laboratory object, not a node in the
Author object. You can control this by giving the autogenerated method a numeric offset,
such as Laboratory(0) or Laboratory(1). For backwards compatibility, Laboratory('@') is
equivalent to Laboratory(1).
The semantics of the autogenerated methods have changed subtly between version 1.57 (the
last stable release) and version 1.62. In earlier versions, calling an autogenerated
method in a scalar context returned the subtree rooted at the tag. In the current
version, an implicit right() and dereference is performed.
fetch() method
$new_object = $object->fetch;
$new_object = $object->fetch($tag);
Follow object into the database, returning a new object. This is the best way to follow
object references. For example:
$laboratory = $object->at('Laboratory')->fetch;
print $laboratory->asString;
Because the previous example is a frequent idiom, the optional $tag argument allows you to
combine the two operations into a single one:
$laboratory = $object->fetch('Laboratory');
follow() method
@papers = $object->follow('Paper');
@filled_papers = $object->follow(-tag=>'Paper',-filled=>1);
@filled_papers = $object->follow(-tag=>'Paper',-filled=>'Author');
The follow() method will follow a tag into the database, dereferencing the column to its
right and returning the objects resulting from this operation. Beware! If you follow a
tag that points to an object, such as the Author "Paper" tag, you will get a list of all
the Paper objects. If you follow a tag that points to a scalar, such as "Full_name", you
will get an empty string. In a scalar context, this method will return the number of
objects that would have been followed.
The full named-argument form of this call accepts the arguments -tag (mandatory) and
-filled (optional). The former points to the tag to follow. The latter accepts a boolean
argument or the name of a subtag. A numeric true argument will return completely "filled"
objects, increasing network and memory usage, but possibly boosting performance if you
have a high database access latency. Alternatively, you may provide the name of a tag to
follow, in which case just the named portion of the subtree in the followed objects will
be filled (v.g.)
For backward compatibility, if follow() is called without any arguments, it will act like
fetch().
pick() method
Deprecated method. This has the same semantics as fetch(), which should be used instead.
col() method
@column = $object->col;
@column = $object->col($position);
col() flattens a portion of the tree by returning the column one hop to the right of the
current subtree. You can provide an additional positional index to navigate through the
tree using "tag[2]" behavior. This example returns the author's mailing address:
@mailing_address = $object->at('Address.Mail')->col();
This example returns the author's entire address including mail, e-mail and phone:
@address = $object->at('Address')->col(2);
It is equivalent to any of these calls:
$object->at('Address[2]');
$object->get('Address',2);
$object->Address(2);
Use whatever syntax is most comfortable for you.
In a scalar context, col() returns the number of items in the column.
row() method
@row=$object->row();
@row=$object->row($position);
row() will return the row of data to the right of the object. The first member of the
list will be the object itself. In the case of the "Thierry-Mieg J" object, the example
below will return the list ('Address','Mail','CRBM duCNRS').
@row = $object->Address->row();
You can provide an optional position to move rightward one or more places before
retrieving the row. This code fragment will return ('Mail','CRBM duCNRS'):
@row = $object->Address->row(1);
In a scalar context, row() returns the number of items in the row.
asString() method
$object->asString;
asString() returns a pretty-printed ASCII representation of the object tree.
asTable() method
$object->asTable;
asTable() returns the object as a tab-delimited text table.
asAce() method
$object->asAce;
asAce() returns the object as a tab-delimited text table in ".ace" format.
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);
asXML() method
$result = $object->asXML;
asXML() returns a well-formed XML representation of the object. The particular
representation is still under discussion, so this feature is primarily for demonstration.
asGIF() method
($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 -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
-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 -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 -view argument allows you to specify an alternative view for MAP objects
only. If not specified, you'll get the default view.
The option -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 -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
'comment' => a text comment of some sort
coordinates points to an array of points indicating the top-left and bottom-right corners
of the rectangle. class indicates the class of the object this rectangle surrounds. It
may be a database object, or the special word "BUTTON" for one of the display action
buttons. name indicates the name of the object or the button. comment is some piece of
information about the object in question. You can display it in the status bar of the
browser or in a popup window if your browser provides that facility.
asDNA() and asPeptide() methods
$dna = $object->asDNA();
$peptide = $object->asPeptide();
If you are dealing with a sequence object of some sort, these methods will return strings
corresponding to the DNA or peptide sequence in FASTA format.
add_row() method
$result_code = $object->add_row($tag=>$value);
$result_code = $object->add_row($tag=>[list,of,values]);
$result_code = $object->add(-path=>$tag,
-value=>$value);
add_row() updates the tree by adding data to the indicated tag path. The example given
below adds the value "555-1212" to a new Address entry named "Pager". You may call
add_row() a second time to add a new value under this tag, creating multi-valued entries.
$object->add_row('Address.Pager'=>'555-1212');
You may provide a list of values to add an entire row of data. For example:
$sequence->add_row('Assembly_tags'=>['Finished Left',38949,38952,'AC3']);
Actually, the array reference is not entirely necessary, and if you prefer you can use
this more concise notation:
$sequence->add_row('Assembly_tags','Finished Left',38949,38952,'AC3');
No check is done against the database model for the correct data type or tag path. The
update isn't actually performed until you call commit(), at which time a result code
indicates whether the database update was successful.
You may create objects that reference other objects this way:
$lab = new Ace::Object('Laboratory','LM',$db);
$lab->add_row('Full_name','The Laboratory of Medicine');
$lab->add_row('City','Cincinatti');
$lab->add_row('Country','USA');
$author = new Ace::Object('Author','Smith J',$db);
$author->add_row('Full_name','Joseph M. Smith');
$author->add_row('Laboratory',$lab);
$lab->commit();
$author->commit();
The result code indicates whether the addition was syntactically correct. add_row() will
fail if you attempt to add a duplicate entry (that is, one with exactly the same tag and
value). In this case, use replace() instead. Currently there is no checking for an
attempt to add multiple values to a single-valued (UNIQUE) tag. The error will be
detected and reported at commit() time however.
The add() method is an alias for add_row().
See also the Ace->new() method.
add_tree()
$result_code = $object->add_tree($tag=>$ace_object);
$result_code = $object->add_tree(-tag=>$tag,-tree=>$ace_object);
The add_tree() method will insert an entire Ace subtree into the object to the right of
the indicated tag. This can be used to build up complex Ace objects, or to copy portions
of objects from one database to another. The first argument is a tag path, and the second
is the tree that you wish to insert. As with add_row() the database will only be updated
when you call commit().
When inserting a subtree, you must be careful to remember that everything to the *right*
of the node that you are pointing at will be inserted; not the node itself. For example,
given this Sequence object:
Sequence AC3
DB_info Database EMBL
Assembly_tags Finished Left 1 4 AC3
Clone left end 1 4 AC3
Clone right end 5512 5515 K07C5
38949 38952 AC3
Finished Right 38949 38952 AC3
If we use at('Assembly_tags') to fetch the subtree rooted on the "Assembly_tags" tag, it
is the tree to the right of this tag, beginning with "Finished Left", that will be
inserted.
Here is an example of copying the "Assembly_tags" subtree from one database object to
another:
$remote = Ace->connect(-port=>200005) || die "can't connect";
$ac3 = $remote->fetch(Sequence=>'AC3') || die "can't get AC7";
my $assembly = $ac3->at('Assembly_tags');
$local = Ace->connect(-path=>'~acedb') || die "can't connect";
$AC3copy = Ace::Object->new(Sequence=>'AC3copy',$local);
$AC3copy->add_tree('Assembly_tags'=>$tags);
$AC3copy->commit || warn $AC3copy->error;
Notice that this syntax will not work the way you think it should:
$AC3copy->add_tree('Assembly_tags'=>$ac3->at('Assembly_tags'));
This is because call at() in an array context returns the column to the right of the tag,
not the tag itself.
Here's an example of building up a complex structure from scratch using a combination of
add() and add_tree():
$newObj = Ace::Object->new(Sequence=>'A555',$local);
my $assembly = Ace::Object->new(tag=>'Assembly_tags');
$assembly->add('Finished Left'=>[10,20,'ABC']);
$assembly->add('Clone right end'=>[1000,2000,'DEF']);
$assembly->add('Clone right end'=>[8000,9876,'FRED']);
$assembly->add('Finished Right'=>[1000,3000,'ETHEL']);
$newObj->add_tree('Assembly_tags'=>$assembly);
$newObj->commit || warn $newObj->error;
delete() method
$result_code = $object->delete($tag_path,$value);
$result_code = $object->delete(-path=>$tag_path,
-value=>$value);
Delete the indicated tag and value from the object. This example deletes the address line
"FRANCE" from the Author's mailing address:
$object->delete('Address.Mail','FRANCE');
No actual database deletion occurs until you call commit(). The delete() result code
indicates whether the deletion was successful. Currently it is always true, since the
database model is not checked.
replace() method
$result_code = $object->replace($tag_path,$oldvalue,$newvalue);
$result_code = $object->replace(-path=>$tag_path,
-old=>$oldvalue,
-new=>$newvalue);
Replaces the indicated tag and value with the new value. This example changes the address
line "FRANCE" to "LANGUEDOC" in the Author's mailing address:
$object->delete('Address.Mail','FRANCE','LANGUEDOC');
No actual database changes occur until you call commit(). The delete() result code
indicates whether the replace was successful. Currently is true if the old value was
identified.
commit() method
$result_code = $object->commit;
Commits all add(), replace() and delete() operations to the database. It can also be used
to write a completely new object into the database. The result code indicates whether the
object was successfully written. If an error occurred, further details can be found in
the Ace->error() error string.
rollback() method
$object->rollback;
Discard all adds, deletions and replacements, returning the object to the state it was in
prior to the last commit().
rollback() works by deleting the object from Perl memory and fetching the object anew from
AceDB. If someone has changed the object in the database while you were working with it,
you will see this version, or the one you originally fetched.
If you are creating an entirely new object, you must add at least one tag in order to
enter the object into the database.
kill() method
$result_code = $object->kill;
This will remove the object from the database immediately and completely. It does not
wait for a commit(), and does not respond to a rollback(). If successful, you will be
left with an empty object that contains just the class and object names. Use with care!
In the case of failure, which commonly happens when the database is not open for writing,
this method will return undef. A description of the problem can be found by calling the
error() method.
date_style() method
$object->date_style('ace');
This is a convenience method that can be used to set the date format for all objects
returned by the database. It is exactly equivalent to
$object->db->date_style('ace');
Note that the text representation of the date will change for all objects returned from
this database, not just the current one.
isRoot() method
print "Top level object" if $object->isRoot;
This method will return true if the object is a "top level" object, that is the root of an
object tree rather than a subtree.
model() method
$model = $object->model;
This method will return the object's model as an Ace::Model object, or undef if the object
does not have a model. See Ace::Model for details.
timestamp() method
$stamp = $object->timestamp;
The timestamp() method will retrieve the modification time and date from the object. This
works both with top level objects and with subtrees. Timestamp handling must be turned on
in the database, or timestamp() will return undef.
The returned timestamp is actually a UserSession object which can be printed and explored
like any other object. However, there is currently no useful information in UserSession
other than its name.
comment() method
$comment = $object->comment;
This returns the comment attached to an object or object subtree, if any. Comments are
Comment objects and have the interesting property that a single comment can refer to
multiple objects. If there is no comment attached to the current subtree, this method
will return undef.
Currently you cannot create a new comment in AcePerl or edit an old one.
error() method
$error = $object->error;
Returns the error from the previous operation, if any. As in Ace::error(), this string
will only have meaning if the previous operation returned a result code indicating an
error.
factory() method
WARNING - THIS IS DEFUNCT AND NO LONGER WORKS. USE THE Ace->class() METHOD INSTEAD
$package = $object->factory;
When a root Ace object instantiates its tree of tags and values, it creates a hierarchical
structure of Ace::Object objects. The factory() method determines what class to bless
these subsidiary objects into. By default, they are Ace::Object objects, but you can
override this method in a child class in order to create more specialized Ace::Object
classes. The method should return a string corresponding to the package to bless the
object into. It receives the current Ace::Object as its first argument.
debug() method
$object->debug(1);
Change the debugging mode. A zero turns off debugging messages. Integer values produce
debug messages on standard error. Higher integers produce progressively more verbose
messages. This actually is just a front end to Ace->debug(), so the debugging level is
global.
@cshl.org> with extensive help from Jean Thierry-Mieg
<@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1997-1998, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same
terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
NAME
Ace::Object - Manipulate Ace Data ObjectsSYNOPSIS
# open database connection and get an object use Ace; $db = Ace->connect(-host => 'beta.crbm.cnrs-mop.fr', -port => 20000100); $sequence = $db->fetch(Sequence => 'D12345'); # Inspect the object $r = $sequence->at('Visible.Overlap_Right'); @row = $sequence->row; @col = $sequence->col; @tags = $sequence->tags; # Explore object substructure @more_tags = $sequence->at('Visible')->tags; @col = $sequence->at("Visible.$more_tags[1]")->col; # Follow a pointer into database $r = $sequence->at('Visible.Overlap_Right')->fetch; $next = $r->at('Visible.Overlap_left')->fetch; # Classy way to do the same thing $r = $sequence->Overlap_right; $next = $sequence->Overlap_left; # Pretty-print object print $sequence->asString; print $sequence->asTabs; print $sequence->asHTML; # Update object $sequence->replace('Visible.Overlap_Right',$r,'M55555'); $sequence->add('Visible.Homology','GR91198'); $sequence->delete('Source.Clone','MBR122'); $sequence->commit(); # Rollback changes $sequence->rollback() # Get errors print $sequence->error;DESCRIPTION
Ace::Object is the base class for objects returned from ACEDB databases. Currently there is only one type of Ace::Object, but this may change in the future to support more interesting object-specific behaviors. Using the Ace::Object interface, you can explore the internal structure of an Ace::Object, retrieve its content, and convert it 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 Ace. 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->@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 its right pointer, or by using one of the specialized navigation routines
described below.
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.
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";
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 programmatically 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.
db() method
$db = $object->db();
Return the database that the object is associated with.
isClass() method
$bool = $object->isClass();
Returns true if the object is a class (can be fetched from the database).
isTag() method
$bool = $object->isTag();
Returns true if the object is a tag.
tags() method
@tags = $object->tags();
Return all the top-level tags in the object as a list. In the Author example above, the
returned list would be ('Full_name','Laboratory','Address','Paper').
You can fetch tags more deeply nested in the structure by navigating inwards using the
methods listed below.
right() and down() methods
$subtree = $object->right;
$subtree = $object->right($position);
$subtree = $object->down;
$subtree = $object->down($position);
right() and down() provide a low-level way of traversing the tree structure by following
the tree's right and down pointers. Called without any arguments, these two methods will
move one step. Called with a numeric argument >= 0 they will move the indicated number of
steps (zero indicates no movement).
$full_name = $object->right->right;
$full_name = $object->right(2);
$city = $object->right->down->down->right->right->down->down;
$city = $object->right->down(2)->right(2)->down(2);
If $object contains the "Thierry-Mieg J" Author object, then the first series of accesses
shown above retrieves the string "Jean Thierry-Mieg" and the second retrieves "34033
Montpellier." If the right or bottom pointers are NULL, these methods will return undef.
In addition to being somewhat awkard, you will probably never need to use these methods.
A simpler way to retrieve the same information would be to use the at() method described
in the next section.
The right() and down() methods always walk through the tree of the current object. They
do not follow object pointers into the database. Use fetch() (or the deprecated pick() or
follow() methods) instead.
at() method
$subtree = $object->at($tag_path);
@values = $object->at($tag_path);
at() is a simple way to fetch the portion of the tree that you are interested in. It
takes a single argument, a simple tag or a path. A simple tag, such as "Full_name", must
correspond to a tag in the column immediately to the right of the root of the tree. A
path such as "Address.Mail" is a dot-delimited path to the subtree. Some examples are
given below.
($full_name) = $object->at('Full_name');
@address_lines = $object->at('Address.Mail');
The second line above is equivalent to:
@address = $object->at('Address')->at('Mail');
Called without a tag name, at() just dereferences the object, returning whatever is to the
right of it, the same as $object->right
If a path component already has a dot in it, you may escape the dot with a backslash, as
in:
$s=$db->fetch('Sequence','M4');
@homologies = $s->at('Homol.DNA_homol.yk192f7\.3';
This also demonstrates that path components don't necessarily have to be tags, although in
practice they usually are.
at() returns slightly different results depending on the context in which it is called.
In a list context, it returns the column of values to the right of the tag. However, in a
scalar context, it returns the subtree rooted at the tag. To appreciate the difference,
consider these two cases:
$name1 = $object->at('Full_name');
($name2) = $object->at('Full_name');
After these two statements run, $name1 will be the tag object named "Full_name", and
$name2 will be the text object "Jean Thierry-Mieg", The relationship between the two is
that $name1->right leads to $name2. This is a powerful and useful construct, but it can
be a trap for the unwary. If this behavior drives you crazy, use this construct:
$name1 = $object->at('Full_name')->at();
For finer control over navigation, path components can include optional indexes to
indicate navigation to the right of the current path component. Here is the syntax:
$object->at('tag1[index1].tag2[index2].tag3[index3]...');
Indexes are zero-based. An index of [0] indicates no movement relative to the current
component, and is the same as not using an index at all. An index of [1] navigates one
step to the right, [2] moves two steps to the right, and so on. Using the Thierry-Mieg
object as an example again, here are the results of various indexes:
$object = $db->fetch(Author,"Thierry-Mieg J");
$a = $object->at('Address[0]') --> "Address"
$a = $object->at('Address[1]') --> "Mail"
$a = $object->at('Address[2]') --> "CRBM duCNRS"
In an array context, the last index in the path does something very interesting. It
returns the entire column of data K steps to the right of the path, where K is the index.
This is used to implement so-called "tag[2]" syntax, and is very useful in some
circumstances. For example, here is a fragment of code to return the Thierry-Mieg
object's full address without having to refer to each of the intervening "Mail", "E_Mail"
and "Phone" tags explicitly.
@address = $object->at('Address[2]');
--> ('CRBM duCNRS','BP 5051','34033 Montpellier','FRANCE',
'@kaa.cnrs-mop.fr,'33-67-613324','33-67-521559')
Similarly, "tag[3]" will return the column of data three hops to the right of the tag.
"tag[1]" is identical to "tag" (with no index), and will return the column of data to the
immediate right. There is no special behavior associated with using "tag[0]" in an array
context; it will always return the subtree rooted at the indicated tag.
Internal indices such as "Homol[2].BLASTN", do not have special behavior in an array
context. They are always treated as if they were called in a scalar context.
Also see col() and get().
get() method
$subtree = $object->get($tag);
@values = $object->get($tag);
@values = $object->get($tag, $position);
@values = $object->get($tag => $subtag, $position);
The get() method will perform a breadth-first search through the object (columns first,
followed by rows) for the tag indicated by the argument, returning the column of the
portion of the subtree it points to. For example, this code fragment will return the
value of the "Fax" tag.
($fax_no) = $object->get('Fax');
--> "33-67-521559"
The list versus scalar context semantics are the same as in at(), so if you want to
retrieve the scalar value pointed to by the indicated tag, either use a list context as
shown in the example, above, or a dereference, as in:
$fax_no = $object->get('Fax');
--> "Fax"
$fax_no = $object->get('Fax')->at;
--> "33-67-521559"
An optional second argument to get(), $position, allows you to navigate the tree relative
to the retrieved subtree. Like the at() navigational indexes, $position must be a number
greater than or equal to zero. In a scalar context, $position moves rightward through the
tree. In an array context, $position implements "tag[2]" semantics.
For example:
$fax_no = $object->get('Fax',0);
--> "Fax"
$fax_no = $object->get('Fax',1);
--> "33-67-521559"
$fax_no = $object->get('Fax',2);
--> undef # nothing beyond the fax number
@address = $object->get('Address',2);
--> ('CRBM duCNRS','BP 5051','34033 Montpellier','FRANCE',
'@kaa.cnrs-mop.fr,'33-67-613324','33-67-521559')
It is important to note that get() only traverses tags. It will not traverse nodes that
aren't tags, such as strings, integers or objects. This is in keeping with the behavior
of the Ace query language "show" command.
This restriction can lead to confusing results. For example, consider the following
object:
Clone: B0280 Position Map Sequence-III Ends Left 3569
Right 3585
Pmap ctg377 -1040 -1024
Positive Positive_locus nhr-10
Sequence B0280
Location RW
FingerPrint Gel_Number 0
Canonical_for T20H1
K10E5
Bands 1354 18
The following attempt to fetch the left and right positions of the clone will fail,
because the search for the "Left" and "Right" tags cannot traverse "Sequence-III", which
is an object, not a tag:
my $left = $clone->get('Left'); # will NOT work
my $right = $clone->get('Right'); # neither will this one
You must explicitly step over the non-tag node in order to make this query work. This
syntax will work:
my $left = $clone->get('Map',1)->get('Left'); # works
my $left = $clone->get('Map',1)->get('Right'); # works
Or you might prefer to use the tag[2] syntax here:
my($left,$right) = $clone->get('Map',1)->at('Ends[2]');
Although not frequently used, there is a form of get() which allows you to stack subtags:
$locus = $object->get('Positive'=>'Positive_locus');
Only on subtag is allowed. You can follow this by a position if wish to offset from the
subtag.
$locus = $object->get('Positive'=>'Positive_locus',1);
search() method
This is a deprecated synonym for get().
Autogenerated Access Methods
$scalar = $object->Name_of_tag;
$scalar = $object->Name_of_tag($position);
@array = $object->Name_of_tag;
@array = $object->Name_of_tag($position);
@array = $object->Name_of_tag($subtag=>$position);
@array = $object->Name_of_tag(-fill=>$tag);
The module attempts to autogenerate data access methods as needed. For example, if you
refer to a method named "Fax" (which doesn't correspond to any of the built-in methods),
then the code will call the get() method to find a tag named "Fax" and return its
contents.
Unlike get(), this method will always step into objects. This means that:
$map = $clone->Map;
will return the Sequence_Map object pointed to by the Clone's Map tag and not simply a
pointer to a portion of the Clone tree. Therefore autogenerated methods are functionally
equivalent to the following:
$map = $clone->get('Map')->fetch;
The scalar context semantics are also slightly different. In a scalar context, the
autogenerated function will *always* move one step to the right.
The list context semantics are identical to get(). If you want to dereference all members
of a multivalued tag, you have to do so manually:
@papers = $author->Paper;
foreach (@papers) {
my $paper = $_->fetch;
print $paper->asString;
}
You can provide an optional positional index to rapidly navigate through the tree or to
obtain tag[2] behavior. In the following examples, the first two return the object's Fax
number, and the third returns all data two hops to the right of Address.
$object = $db->fetch(Author => 'Thierry-Mieg J');
($fax_no) = $object->Fax;
$fax_no = $object->Fax(1);
@address = $object->Address(2);
You may also position at a subtag, using this syntax:
$representative = $object->Laboratory('Representative');
Both named tags and positions can be combined as follows:
$lab_address = $object->Laboratory(Address=>2);
If you provide a -fill=>$tag argument, then the object fetch will automatically fill the
specified subtree, greatly improving performance. For example:
$lab_address = $object->Laboratory(-filled=>'Address');
** NOTE: In a scalar context, if the node to the right of the tag is ** an object, the
method will perform an implicit dereference of the ** object. For example, in the case
of:
$lab = $author->Laboratory;
**NOTE: The object returned is the dereferenced Laboratory object, not a node in the
Author object. You can control this by giving the autogenerated method a numeric offset,
such as Laboratory(0) or Laboratory(1). For backwards compatibility, Laboratory('@') is
equivalent to Laboratory(1).
The semantics of the autogenerated methods have changed subtly between version 1.57 (the
last stable release) and version 1.62. In earlier versions, calling an autogenerated
method in a scalar context returned the subtree rooted at the tag. In the current
version, an implicit right() and dereference is performed.
fetch() method
$new_object = $object->fetch;
$new_object = $object->fetch($tag);
Follow object into the database, returning a new object. This is the best way to follow
object references. For example:
$laboratory = $object->at('Laboratory')->fetch;
print $laboratory->asString;
Because the previous example is a frequent idiom, the optional $tag argument allows you to
combine the two operations into a single one:
$laboratory = $object->fetch('Laboratory');
follow() method
@papers = $object->follow('Paper');
@filled_papers = $object->follow(-tag=>'Paper',-filled=>1);
@filled_papers = $object->follow(-tag=>'Paper',-filled=>'Author');
The follow() method will follow a tag into the database, dereferencing the column to its
right and returning the objects resulting from this operation. Beware! If you follow a
tag that points to an object, such as the Author "Paper" tag, you will get a list of all
the Paper objects. If you follow a tag that points to a scalar, such as "Full_name", you
will get an empty string. In a scalar context, this method will return the number of
objects that would have been followed.
The full named-argument form of this call accepts the arguments -tag (mandatory) and
-filled (optional). The former points to the tag to follow. The latter accepts a boolean
argument or the name of a subtag. A numeric true argument will return completely "filled"
objects, increasing network and memory usage, but possibly boosting performance if you
have a high database access latency. Alternatively, you may provide the name of a tag to
follow, in which case just the named portion of the subtree in the followed objects will
be filled (v.g.)
For backward compatibility, if follow() is called without any arguments, it will act like
fetch().
pick() method
Deprecated method. This has the same semantics as fetch(), which should be used instead.
col() method
@column = $object->col;
@column = $object->col($position);
col() flattens a portion of the tree by returning the column one hop to the right of the
current subtree. You can provide an additional positional index to navigate through the
tree using "tag[2]" behavior. This example returns the author's mailing address:
@mailing_address = $object->at('Address.Mail')->col();
This example returns the author's entire address including mail, e-mail and phone:
@address = $object->at('Address')->col(2);
It is equivalent to any of these calls:
$object->at('Address[2]');
$object->get('Address',2);
$object->Address(2);
Use whatever syntax is most comfortable for you.
In a scalar context, col() returns the number of items in the column.
row() method
@row=$object->row();
@row=$object->row($position);
row() will return the row of data to the right of the object. The first member of the
list will be the object itself. In the case of the "Thierry-Mieg J" object, the example
below will return the list ('Address','Mail','CRBM duCNRS').
@row = $object->Address->row();
You can provide an optional position to move rightward one or more places before
retrieving the row. This code fragment will return ('Mail','CRBM duCNRS'):
@row = $object->Address->row(1);
In a scalar context, row() returns the number of items in the row.
asString() method
$object->asString;
asString() returns a pretty-printed ASCII representation of the object tree.
asTable() method
$object->asTable;
asTable() returns the object as a tab-delimited text table.
asAce() method
$object->asAce;
asAce() returns the object as a tab-delimited text table in ".ace" format.
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);
asXML() method
$result = $object->asXML;
asXML() returns a well-formed XML representation of the object. The particular
representation is still under discussion, so this feature is primarily for demonstration.
asGIF() method
($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 -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
-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 -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 -view argument allows you to specify an alternative view for MAP objects
only. If not specified, you'll get the default view.
The option -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 -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
'comment' => a text comment of some sort
coordinates points to an array of points indicating the top-left and bottom-right corners
of the rectangle. class indicates the class of the object this rectangle surrounds. It
may be a database object, or the special word "BUTTON" for one of the display action
buttons. name indicates the name of the object or the button. comment is some piece of
information about the object in question. You can display it in the status bar of the
browser or in a popup window if your browser provides that facility.
asDNA() and asPeptide() methods
$dna = $object->asDNA();
$peptide = $object->asPeptide();
If you are dealing with a sequence object of some sort, these methods will return strings
corresponding to the DNA or peptide sequence in FASTA format.
add_row() method
$result_code = $object->add_row($tag=>$value);
$result_code = $object->add_row($tag=>[list,of,values]);
$result_code = $object->add(-path=>$tag,
-value=>$value);
add_row() updates the tree by adding data to the indicated tag path. The example given
below adds the value "555-1212" to a new Address entry named "Pager". You may call
add_row() a second time to add a new value under this tag, creating multi-valued entries.
$object->add_row('Address.Pager'=>'555-1212');
You may provide a list of values to add an entire row of data. For example:
$sequence->add_row('Assembly_tags'=>['Finished Left',38949,38952,'AC3']);
Actually, the array reference is not entirely necessary, and if you prefer you can use
this more concise notation:
$sequence->add_row('Assembly_tags','Finished Left',38949,38952,'AC3');
No check is done against the database model for the correct data type or tag path. The
update isn't actually performed until you call commit(), at which time a result code
indicates whether the database update was successful.
You may create objects that reference other objects this way:
$lab = new Ace::Object('Laboratory','LM',$db);
$lab->add_row('Full_name','The Laboratory of Medicine');
$lab->add_row('City','Cincinatti');
$lab->add_row('Country','USA');
$author = new Ace::Object('Author','Smith J',$db);
$author->add_row('Full_name','Joseph M. Smith');
$author->add_row('Laboratory',$lab);
$lab->commit();
$author->commit();
The result code indicates whether the addition was syntactically correct. add_row() will
fail if you attempt to add a duplicate entry (that is, one with exactly the same tag and
value). In this case, use replace() instead. Currently there is no checking for an
attempt to add multiple values to a single-valued (UNIQUE) tag. The error will be
detected and reported at commit() time however.
The add() method is an alias for add_row().
See also the Ace->new() method.
add_tree()
$result_code = $object->add_tree($tag=>$ace_object);
$result_code = $object->add_tree(-tag=>$tag,-tree=>$ace_object);
The add_tree() method will insert an entire Ace subtree into the object to the right of
the indicated tag. This can be used to build up complex Ace objects, or to copy portions
of objects from one database to another. The first argument is a tag path, and the second
is the tree that you wish to insert. As with add_row() the database will only be updated
when you call commit().
When inserting a subtree, you must be careful to remember that everything to the *right*
of the node that you are pointing at will be inserted; not the node itself. For example,
given this Sequence object:
Sequence AC3
DB_info Database EMBL
Assembly_tags Finished Left 1 4 AC3
Clone left end 1 4 AC3
Clone right end 5512 5515 K07C5
38949 38952 AC3
Finished Right 38949 38952 AC3
If we use at('Assembly_tags') to fetch the subtree rooted on the "Assembly_tags" tag, it
is the tree to the right of this tag, beginning with "Finished Left", that will be
inserted.
Here is an example of copying the "Assembly_tags" subtree from one database object to
another:
$remote = Ace->connect(-port=>200005) || die "can't connect";
$ac3 = $remote->fetch(Sequence=>'AC3') || die "can't get AC7";
my $assembly = $ac3->at('Assembly_tags');
$local = Ace->connect(-path=>'~acedb') || die "can't connect";
$AC3copy = Ace::Object->new(Sequence=>'AC3copy',$local);
$AC3copy->add_tree('Assembly_tags'=>$tags);
$AC3copy->commit || warn $AC3copy->error;
Notice that this syntax will not work the way you think it should:
$AC3copy->add_tree('Assembly_tags'=>$ac3->at('Assembly_tags'));
This is because call at() in an array context returns the column to the right of the tag,
not the tag itself.
Here's an example of building up a complex structure from scratch using a combination of
add() and add_tree():
$newObj = Ace::Object->new(Sequence=>'A555',$local);
my $assembly = Ace::Object->new(tag=>'Assembly_tags');
$assembly->add('Finished Left'=>[10,20,'ABC']);
$assembly->add('Clone right end'=>[1000,2000,'DEF']);
$assembly->add('Clone right end'=>[8000,9876,'FRED']);
$assembly->add('Finished Right'=>[1000,3000,'ETHEL']);
$newObj->add_tree('Assembly_tags'=>$assembly);
$newObj->commit || warn $newObj->error;
delete() method
$result_code = $object->delete($tag_path,$value);
$result_code = $object->delete(-path=>$tag_path,
-value=>$value);
Delete the indicated tag and value from the object. This example deletes the address line
"FRANCE" from the Author's mailing address:
$object->delete('Address.Mail','FRANCE');
No actual database deletion occurs until you call commit(). The delete() result code
indicates whether the deletion was successful. Currently it is always true, since the
database model is not checked.
replace() method
$result_code = $object->replace($tag_path,$oldvalue,$newvalue);
$result_code = $object->replace(-path=>$tag_path,
-old=>$oldvalue,
-new=>$newvalue);
Replaces the indicated tag and value with the new value. This example changes the address
line "FRANCE" to "LANGUEDOC" in the Author's mailing address:
$object->delete('Address.Mail','FRANCE','LANGUEDOC');
No actual database changes occur until you call commit(). The delete() result code
indicates whether the replace was successful. Currently is true if the old value was
identified.
commit() method
$result_code = $object->commit;
Commits all add(), replace() and delete() operations to the database. It can also be used
to write a completely new object into the database. The result code indicates whether the
object was successfully written. If an error occurred, further details can be found in
the Ace->error() error string.
rollback() method
$object->rollback;
Discard all adds, deletions and replacements, returning the object to the state it was in
prior to the last commit().
rollback() works by deleting the object from Perl memory and fetching the object anew from
AceDB. If someone has changed the object in the database while you were working with it,
you will see this version, or the one you originally fetched.
If you are creating an entirely new object, you must add at least one tag in order to
enter the object into the database.
kill() method
$result_code = $object->kill;
This will remove the object from the database immediately and completely. It does not
wait for a commit(), and does not respond to a rollback(). If successful, you will be
left with an empty object that contains just the class and object names. Use with care!
In the case of failure, which commonly happens when the database is not open for writing,
this method will return undef. A description of the problem can be found by calling the
error() method.
date_style() method
$object->date_style('ace');
This is a convenience method that can be used to set the date format for all objects
returned by the database. It is exactly equivalent to
$object->db->date_style('ace');
Note that the text representation of the date will change for all objects returned from
this database, not just the current one.
isRoot() method
print "Top level object" if $object->isRoot;
This method will return true if the object is a "top level" object, that is the root of an
object tree rather than a subtree.
model() method
$model = $object->model;
This method will return the object's model as an Ace::Model object, or undef if the object
does not have a model. See Ace::Model for details.
timestamp() method
$stamp = $object->timestamp;
The timestamp() method will retrieve the modification time and date from the object. This
works both with top level objects and with subtrees. Timestamp handling must be turned on
in the database, or timestamp() will return undef.
The returned timestamp is actually a UserSession object which can be printed and explored
like any other object. However, there is currently no useful information in UserSession
other than its name.
comment() method
$comment = $object->comment;
This returns the comment attached to an object or object subtree, if any. Comments are
Comment objects and have the interesting property that a single comment can refer to
multiple objects. If there is no comment attached to the current subtree, this method
will return undef.
Currently you cannot create a new comment in AcePerl or edit an old one.
error() method
$error = $object->error;
Returns the error from the previous operation, if any. As in Ace::error(), this string
will only have meaning if the previous operation returned a result code indicating an
error.
factory() method
WARNING - THIS IS DEFUNCT AND NO LONGER WORKS. USE THE Ace->class() METHOD INSTEAD
$package = $object->factory;
When a root Ace object instantiates its tree of tags and values, it creates a hierarchical
structure of Ace::Object objects. The factory() method determines what class to bless
these subsidiary objects into. By default, they are Ace::Object objects, but you can
override this method in a child class in order to create more specialized Ace::Object
classes. The method should return a string corresponding to the package to bless the
object into. It receives the current Ace::Object as its first argument.
debug() method
$object->debug(1);
Change the debugging mode. A zero turns off debugging messages. Integer values produce
debug messages on standard error. Higher integers produce progressively more verbose
messages. This actually is just a front end to Ace->debug(), so the debugging level is
global.
SEE ALSO
Ace, Ace::Model, Ace::Object, Ace::Local, Ace::Sequence,Ace::Sequence::MultiAUTHOR
Lincoln Stein <@cshl.org> with extensive help from Jean Thierry-Mieg
<@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1997-1998, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same
terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.| This manual | Reference | Other manuals |
|---|---|---|
| Ace::Object(3pm) | referred by | |
| refer to | fax(1) |