Provided by: libace-perl_1.92-4_amd64 bug


       Ace - Object-Oriented Access to ACEDB Databases


           use Ace;
           # open a remote database connection
           $db = Ace->connect(-host => '',
                              -port => 20000100);

           # open a local database connection
           $local = Ace->connect(-path=>'~acedb/my_ace');

           # simple queries
           $sequence  = $db->fetch(Sequence => 'D12345');
           $count     = $db->count(Sequence => 'D*');
           @sequences = $db->fetch(Sequence => 'D*');
           $i         = $db->fetch_many(Sequence=>'*');  # fetch a cursor
           while ($obj = $i->next) {
              print $obj->asTable;

           # complex queries
           $query = <<END;
           find Annotation Ready_for_submission ; follow gene ;
           follow derived_sequence ; >DNA
           @ready_dnas= $db->fetch(-query=>$query);

           $ready = $db->fetch_many(-query=>$query);
           while ($obj = $ready->next) {
               # do something with obj

           # database cut and paste
           $sequence = $db->fetch(Sequence => 'D12345');
           @sequences = $db->fetch(Sequence => 'D*');

           # Get errors
           print Ace->error;
           print $db->error;


       AcePerl provides an interface to the ACEDB object-oriented database.  Both read and write
       access is provided, and ACE objects are returned as similarly-structured Perl objects.
       Multiple databases can be opened simultaneously.

       You will interact with several Perl classes: Ace, Ace::Object, Ace::Iterator, Ace::Model.
       Ace is the database accessor, and can be used to open both remote Ace databases (running
       aceserver or gifaceserver), and local ones.

       Ace::Object is the superclass for all objects returned from the database.  Ace and
       Ace::Object are linked: if you retrieve an Ace::Object from a particular database, it will
       store a reference to the database and use it to fetch any subobjects contained within it.
       You may make changes to the Ace::Object and have those changes written into the database.
       You may also create Ace::Objects from scratch and store them in the database.

       Ace::Iterator is a utility class that acts as a database cursor for long-running ACEDB
       queries.  Ace::Model provides object-oriented access to ACEDB's schema.

       Internally, Ace uses the Ace::Local class for access to local databases and Ace::AceDB for
       access to remote databases.  Ordinarily you will not need to interact directly with either
       of these classes.


   connect() -- multiple argument form
           # remote database
           $db = Ace->connect(-host  =>  '',
                              -port  =>  20000100);

           # local (non-server) database
           $db = Ace->connect(-path  =>  '/usr/local/acedb);

       Use Ace::connect() to establish a connection to a networked or local AceDB database.  To
       establish a connection to an AceDB server, use the -host and/or -port arguments.  For a
       local server, use the -port argument.  The database must be up and running on the
       indicated host and port prior to connecting to an AceDB server.  The full syntax is as

           $db = Ace->connect(-host  =>  $host,
                              -port  =>  $port,
                              -path  =>  $database_path,
                              -program     => $local_connection_program
                              -classmapper =>  $object_class,
                              -timeout     => $timeout,
                              -query_timeout => $query_timeout
                              -cache        => {cache parameters},

       The connect() method uses a named argument calling style, and recognizes the following

       -host, -port
           These arguments point to the host and port of an AceDB server.  AcePerl will use its
           internal compiled code to establish a connection to the server unless explicitly
           overridden with the -program argument.

           This argument indicates the path of an AceDB directory on the local system.  It should
           point to the directory that contains the wspec subdirectory.  User name interpolations
           (~acedb) are OK.

           Name of user to log in as (when using socket server only).  If not provided, will
           attempt an anonymous login.

           Password to log in with (when using socket server).

           An Acedb URL that combines the server type, host, port, user and password in a single
           string.  See the connect() method's "single argument form" description.

           AcePerl can use the Cache::SizeAwareFileCache module to cache objects to disk. This
           can result in dramatically increased performance in environments such as web servers
           in which the same Acedb objects are frequently reused.  To activate this mechanism,
           the Cache::SizeAwareFileCache module must be installed, and you must pass the -cache
           argument during the connect() call.

           The value of -cache is a hash reference containing the arguments to be passed to
           Cache::SizeAwareFileCache.  For example:

              -cache => {
                         cache_root         => '/usr/tmp/acedb',
                         cache_depth        => 4,
                         default_expires_in => '1 hour'

           If not otherwise specified, the following cache parameters are assumed:

                  Parameter               Default Value
                  ---------               -------------
                  namespace               Server URL (e.g. sace://localhost:2005)
                  cache_root              /tmp/FileCache (dependent on system temp directory)
                  default_expires_in      1 day
                  auto_purge_interval     12 hours

           By default, the cache is not size limited (the "max_size" property is set to
           $NO_MAX_SIZE).  To adjust the size you may consider calling the Ace object's cache()
           method to retrieve the physical cache and then calling the cache object's
           limit_size($max_size) method from time to time.  See Cache::SizeAwareFileCache for
           more details.

           By default AcePerl will use its internal compiled code calls to establish a connection
           to Ace servers, and will launch a tace subprocess to communicate with local Ace
           databases.  The -program argument allows you to customize this behavior by forcing
           AcePerl to use a local program to communicate with the database.  This argument should
           point to an executable on your system.  You may use either a complete path or a bare
           command name, in which case the PATH environment variable will be consulted.  For
           example, you could force AcePerl to use the aceclient program to connect to the remote
           host by connecting this way:

             $db = Ace->connect(-host => '',
                                -port => 20000100,

           The optional -classmapper argument (alias -class) points to the class you would like
           to return from database queries.  It is provided for your use if you subclass
           Ace::Object.  For example, if you have created a subclass of Ace::Object called
           Ace::Object::Graphics, you can have the database return this subclass by default by
           connecting this way:

             $db = Ace->connect(-host => '',
                                -port => 20000100,

           The value of -class can be a hash reference consisting of AceDB class names as keys
           and Perl class names as values.  If a class name does not exist in the hash, a key
           named _DEFAULT_ will be looked for.  If that does not exist, then Ace will default to

           The value of -class can also be an object or a classname that implements a class_for()
           method.  This method will receive three arguments containing the AceDB class name,
           object ID and database handle.  It should return a string indicating the perl class to

           If no response from the server is received within $timeout seconds, the call will
           return an undefined value.  Internally timeout sets an alarm and temporarily
           intercepts the ALRM signal.  You should be aware of this if you use ALRM for your own

           NOTE: this feature is temporarily disabled (as of version 1.40) because it is
           generating unpredictable results when used with Apache/mod_perl.

           If any query takes longer than $query_timeout seconds, will return an undefined value.
           This value can only be set at connect time, and cannot be changed once set.

       If arguments are omitted, they will default to the following values:

           -host          localhost
           -port          200005;
           -path          no default
           -program       tace
           -class         Ace::Object
           -timeout       25
           -query_timeout 120

       If you prefer to use a more Smalltalk-like message-passing syntax, you can open a
       connection this way too:

         $db = connect Ace -host=>'',-port=>20000100;

       The return value is an Ace handle to use to access the database, or undef if the
       connection fails.  If the connection fails, an error message can be retrieved by calling

       You may check the status of a connection at any time with ping().  It will return a true
       value if the database is still connected.  Note that Ace will timeout clients that have
       been inactive for any length of time.  Long-running clients should attempt to reestablish
       their connection if ping() returns false.

           $db->ping() || die "not connected";

       You may perform low-level calls using the Ace client C API by calling db().  This fetches
       an Ace::AceDB object.  See THE LOW LEVEL C API for details on using this object.

           $low_level = $db->db();

   connect() -- single argument form
         $db = Ace->connect('sace://')

       Ace->connect() also accepts a single argument form using a URL-type syntax.  The general
       syntax is:


       The :port and /path parts are protocol-dependent as described above.


           Connect to a socket server at the indicated hostname and port.  Example:


           If not provided, the port defaults to 2005.

           Connect to an RPC server at the indicated hostname and RPC service number.  Example:


           If not provided, the port defaults to 200005

           Open up the local database at /path/to/database using tace.  Example:


           Same as the previous.

   close() Method
       You can explicitly close a database by calling its close() method:


       This is not ordinarily necessary because the database will be automatically close when it
       -- and all objects retrieved from it -- go out of scope.

   reopen() Method
       The ACeDB socket server can time out.  The reopen() method will ping the server and if it
       is not answering will reopen the connection.  If the database is live (or could be
       resurrected), this method returns true.


       Once you have established a connection and have an Ace databaes handle, several methods
       can be used to query the ACE database to retrieve objects.  You can then explore the
       objects, retrieve specific fields from them, or update them using the Ace::Object methods.
       Please see Ace::Object.

   fetch() method
           $count   = $db->fetch($class,$name_pattern);
           $object  = $db->fetch($class,$name);
           @objects = $db->fetch($class,$name_pattern,[$count,$offset]);
           @objects = $db->fetch(-name=>$name_pattern,
           @objects = $db->fetch(-query=>$query);

       Ace::fetch() retrieves objects from the database based on their class and name.  You may
       retrieve a single object by requesting its name, or a group of objects by fetching a name
       pattern.  A pattern contains one or more wildcard characters, where "*" stands for zero or
       more characters, and "?" stands for any single character.

       This method behaves differently depending on whether it is called in a scalar or a list
       context, and whether it is asked to search for a name pattern or a simple name.

       When called with a class and a simple name, it returns the object referenced by that time,
       or undef, if no such object exists.  In an array context, it will return an empty list.

       When called with a class and a name pattern in a list context, fetch() returns the list of
       objects that match the name.  When called with a pattern in a scalar context, fetch()
       returns the number of objects that match without actually retrieving them from the
       database.  Thus, it is similar to count().

       In the examples below, the first line of code will fetch the Sequence object whose
       database ID is D12345.  The second line will retrieve all objects matching the pattern
       D1234*.  The third line will return the count of objects that match the same pattern.

          $object =  $db->fetch(Sequence => 'D12345');
          @objects = $db->fetch(Sequence => 'D1234*');
          $cnt =     $db->fetch(Sequence =>'D1234*');

       A variety of communications and database errors may occur while processing the request.
       When this happens, undef or an empty list will be returned, and a string describing the
       error can be retrieved by calling Ace->error.

       When retrieving database objects, it is possible to retrieve a "filled" or an "unfilled"
       object.  A filled object contains the entire contents of the object, including all tags
       and subtags.  In the case of certain Sequence objects, this may be a significant amount of
       data.  Unfilled objects consist just of the object name.  They are filled in from the
       database a little bit at a time as tags are requested.  By default, fetch() returns the
       unfilled object.  This is usually a performance win, but if you know in advance that you
       will be needing the full contents of the retrieved object (for example, to display them in
       a tree browser) it can be more efficient to fetch them in filled mode. You do this by
       calling fetch() with the argument of -fill set to a true value.

       The -filltag argument, if provided, asks the database to fill in the subtree anchored at
       the indicated tag.  This will improve performance for frequently-accessed subtrees.  For

          @objects = $db->fetch(-name    => 'D123*',
                                -class   => 'Sequence',
                                -filltag => 'Visible');

       This will fetch all Sequences named D123* and fill in their Visible trees in a single

       Other arguments in the named parameter calling form are -count, to retrieve a certain
       maximum number of objects, and -offset, to retrieve objects beginning at the indicated
       offset into the list.  If you want to limit the number of objects returned, but wish to
       learn how many objects might have been retrieved, pass a reference to a scalar variable in
       the -total argument.  This will return the object count.  This example shows how to fetch
       100 Sequence objects, starting at Sequence number 500:

         @some_sequences = $db->fetch('Sequence','*',100,500);

       The next example uses the named argument form to fetch 100 Sequence objects starting at
       Sequence number 500, and leave the total number of Sequences in $total:

         @some_sequences = $db->fetch(-class  => 'Sequence',
                                      -count  => 100,
                                      -offset => 500,
                                      -total  => \$total);

       Notice that if you leave out the -name argument the "*" wildcard is assumed.

       You may also pass an arbitrary Ace query string with the -query argument.  This will
       supersede any name and class you provide.  Example:

         @ready_dnas= $db->fetch(-query=>
             'find Annotation Ready_for_submission ; follow gene ;
              follow derived_sequence ; >DNA');

       If your request is likely to retrieve very many objects, fetch() many consume a lot of
       memory, even if -fill is false.  Consider using fetch_many() instead (see below).  Also
       see the get() method, which is equivalent to the simple two-argument form of fetch().

       get() method
              $object = $db->get($class,$name [,$fill]);

           The get() method will return one and only one AceDB object identified by its class and
           name.  The optional $fill argument can be used to control how much data is retrieved
           from the database. If $fill is absent or undefined, then the method will return a
           lightweight "stub" object that is filled with information as requested in a lazy
           fashion. If $fill is the number "1" then the retrieved object contains all the
           relevant information contained within the database.  Any other true value of $fill
           will be treated as a tag name: the returned object will be prefilled with the subtree
           to the right of that tag.


              # return lightweight stub for Author object "Sulston JE."
              $author = $db->get(Author=>'Sulston JE');

              # return heavyweight object
              $author = $db->get(Author=>'Sulston JE',1);

              # return object containing the Address subtree
              $author = $db->get(Author=>'Sulston JE','Address');

           The get() method is equivalent to this form of the fetch() method:

              $object = $db->fetch($class=>$name);

   aql() method
           $count   = $db->aql($aql_query);
           @objects = $db->aql($aql_query);

       Ace::aql() will perform an AQL query on the database.  In a scalar context it returns the
       number of rows returned.  In an array context it returns a list of rows.  Each row is an
       anonymous array containing the columns returned by the query as an Ace::Object.

       If an AQL error is encountered, will return undef or an empty list and set Ace->error to
       the error message.

       Note that this routine is not optimized -- there is no iterator defined.  All results are
       returned synchronously, leading to large memory consumption for certain queries.

   put() method
          $cnt = $db->put($obj1,$obj2,$obj3);

       This method will put the list of objects into the database, overwriting like-named objects
       if they are already there.  This can be used to copy an object from one database to
       another, provided that the models are compatible.

       The method returns the count of objects successfully written into the database.  In case
       of an error, processing will stop at the last object successfully written and an error
       message will be placed in Ace->error();

   parse() method
         $object = $db->parse('data to parse');

       This will parse the Ace tags contained within the "data to parse" string, convert it into
       an object in the databse, and return the resulting Ace::Object.  In case of a parse error,
       the undefined value will be returned and a (hopefully informative) description of the
       error will be returned by Ace->error().

       For example:

         $author = $db->parse(<<END);
         Author : "Glimitz JR"
         Full_name "Jonathan R. Glimitz"
         Mail  "128 Boylston Street"
         Mail  "Boston, MA"
         Mail  "USA"
         Laboratory GM

       This method can also be used to parse several objects, but only the last object
       successfully parsed will be returned.

   parse_longtext() method
         $object = $db->parse($title,$text);

       This will parse the long text (which may contain carriage returns and other funny
       characters) and place it into the database with the given title.  In case of a parse
       error, the undefined value will be returned and a (hopefully informative) description of
       the error will be returned by Ace->error(); otherwise, a LongText object will be returned.

       For example:

         $author = $db->parse_longtext('A Novel Inhibitory Domain',<<END);
         We have discovered a novel inhibitory domain that inhibits
         many classes of proteases, including metallothioproteins.
         This inhibitory domain appears in three different gene families studied
         to date...

   parse_file() method
         @objects = $db->parse_file('/path/to/file');
         @objects = $db->parse_file('/path/to/file',1);

       This will call parse() to parse each of the objects found in the indicated .ace file,
       returning the list of objects successfully loaded into the database.

       By default, parsing will stop at the first object that causes a parse error.  If you wish
       to forge on after an error, pass a true value as the second argument to this method.

       Any parse error messages are accumulated in Ace->error().

   new() method
         $object = $db->new($class => $name);

       This method creates a new object in the database of type $class and name $name.  If
       successful, it returns the newly-created object.  Otherwise it returns undef and sets

       $name may contain sprintf()-style patterns.  If one of the patterns is %d (or a variant),
       Acedb uses a class-specific unique numbering to return a unique name.  For example:

         $paper = $db->new(Paper => 'wgb%06d');

       The object is created in the database atomically.  There is no chance to rollback as there
       is in Ace::Object's object editing methods.

       See also the Ace::Object->add() and replace() methods.

   list() method
           @objects = $db->list(class,pattern,[count,offset]);
           @objects = $db->list(-class=>$class,

       This is a deprecated method.  Use fetch() instead.

   count() method
           $count = $db->count($class,$pattern);
           $count = $db->count(-query=>$query);

       This function queries the database for a list of objects matching the specified class and
       pattern, and returns the object count.  For large sets of objects this is much more time
       and memory effective than fetching the entire list.

       The class and name pattern are the same as the list() method above.

       You may also provide a -query argument to instead specify an arbitrary ACE query such as
       "find Author COUNT Paper > 80".  See find() below.

   find() method
           @objects = $db->find($query_string);
           @objects = $db->find(-query => $query_string,
                                -offset=> $offset,
                                -count => $count
                                -fill  => $fill);

       This allows you to pass arbitrary Ace query strings to the server and retrieve all objects
       that are returned as a result.  For example, this code fragment retrieves all papers
       written by Jean and Danielle Thierry-Mieg.

           @papers = $db->find('author IS "Thierry-Mieg *" ; >Paper');

       You can find the full query syntax reference guide plus multiple examples at

       In the named parameter calling form, -count, -offset, and -fill have the same meanings as
       in fetch().

   fetch_many() method
           $obj = $db->fetch_many($class,$pattern);

           $obj = $db->fetch_many(-class=>$class,
                                  -name =>$pattern,
                                  -fill =>$filled,

           $obj = $db->fetch_many(-query=>$query);

       If you expect to retrieve many objects, you can fetch an iterator across the data set.
       This is friendly both in terms of network bandwidth and memory consumption.  It is simple
       to use:

           $i = $db->fetch_many(Sequence,'*');  # all sequences!!!!
           while ($obj = $i->next) {
              print $obj->asTable;

       The iterator will return undef when it has finished iterating, and cannot be used again.
       You can have multiple iterators open at once and they will operate independently of each

       Like fetch(), fetch_many() takes an optional -fill (or -filled) argument which retrieves
       the entire object rather than just its name.  This is efficient on a network with high
       latency if you expect to be touching many parts of the object (rather than just retrieving
       the value of a few tags).

       fetch_many() retrieves objects from the database in groups of a certain maximum size, 40
       by default.  This can be tuned using the optional -chunksize argument.  Chunksize is only
       a hint to the database.  It may return fewer objects per transaction, particularly if the
       objects are large.

       You may provide raw Ace query string with the -query argument.  If present the -name and
       -class arguments will be ignored.

   find_many() method
       This is an alias for fetch_many().  It is now deprecated.

   keyset() method
           @objects = $db->keyset($keyset_name);

       This method returns all objects in a named keyset.  Wildcard characters are accepted, in
       which case all keysets that match the pattern will be retrieved and merged into a single
       list of unique objects.

   grep() method
           @objects = $db->grep($grep_string);
           $count   = $db->grep($grep_string);
           @objects = $db->grep(-pattern => $grep_string,
                                -offset=> $offset,
                                -count => $count,
                                -fill  => $fill,
                                -filltag => $filltag,
                                -total => \$total,
                                -long  => 1,

       This performs a "grep" on the database, returning all object names or text that contain
       the indicated grep pattern.  In a scalar context this call will return the number of
       matching objects.  In an array context, the list of matching objects are retrieved.  There
       is also a named-parameter form of the call, which allows you to specify the number of
       objects to retrieve, the offset from the beginning of the list to retrieve from, whether
       the retrieved objects should be filled initially.  You can use -total to discover the
       total number of objects that match, while only retrieving a portion of the list.

       By default, grep uses a fast search that only examines class names and lexiques.  By
       providing a true value to the -long parameter, you can search inside LongText and other
       places that are not usually touched on, at the expense of much more CPU time.

       Due to "not listable" objects that may match during grep, the list of objects one can
       retrieve may not always match the count.

   model() method
         $model = $db->model('Author');

       This will return an Ace::Model object corresponding to the indicated class.

   new() method
          $obj = $db->new($class,$name);
          $obj = $db->new(-class=>$class,

       Create a new object in the database with the indicated class and name and return a pointer
       to it.  Will return undef if the object already exists in the database.  The object isn't
       actually written into the database until you call Ace::Object::commit().

   raw_query() method
           $r = $db->raw_query('Model');

       Send a command to the database and return its unprocessed output.  This method is
       necessary to gain access to features that are not yet implemented in this module, such as
       model browsing and complex queries.

   classes() method
          @classes = $db->classes();
          @all_classes = $db->classes(1);

       This method returns a list of all the object classes known to the server.  In a list
       context it returns an array of class names.  In a scalar context, it the number of classes
       defined in the database.

       Ordinarily classes() will return only those classes that are exposed to the user interface
       for browsing, the so-called "visible" classes.  Pass a true argument to the call to
       retrieve non-visible classes as well.

   class_count() method
          %classes = $db->class_count()

       This returns a hash in which the keys are the class names and the values are the total
       number of objects in that class.  All classes are returned, including invisible ones.  Use
       this method if you need to count all classes simultaneously.  If you only want to count
       one or two classes, it may be more efficient to call count($class_name) instead.

       This method transiently uses a lot of memory.  It should not be used with Ace 4.5 servers,
       as they contain a memory leak in the counting routine.

   status() method
           %status = $db->status;
           $status = $db->status;

       Returns various bits of status information from the server.  In an array context, returns
       a hash of hashes.  In a scalar context, returns a reference to a hash of hashes.  Keys and
       subkeys are as follows

                  program     name of acedb binary
                  version     version of acedb binary
                  build       build date of acedb binary in format Jan 25 2003 16:21:24

                  title       name of the database
                  version     version of the database
                  dbformat    database format version number
                  directory   directory in which the database is stored
                  session     session number
                  user        user under which server is running
                  write       whether the server has write access
                  address     global address - not known if this is useful

                  classes     number of classes defined
                  keys        number of keys defined
                  memory      amount of memory used by acedb objects (bytes)

       For example, to get the program version:

          my $version = $db->status->{code}{version};

   title() method
           my $title = $db->title

       Returns the version of the current database, equivalent to $db->status->{database}{title};

   version() method
           my $version = $db->version;

       Returns the version of the current database, equivalent to

   date_style() method
         $style = $db->date_style();
         $style = $db->date_style('ace');
         $style = $db->date_style('java');

       For historical reasons, AceDB can display dates using either of two different formats.
       The first format, which I call "ace" style, puts the year first, as in "1997-10-01".  The
       second format, which I call "java" style, puts the day first, as in "01 Oct 1997 00:00:00"
       (this is also the style recommended for Internet dates).  The default is to use the latter

       date_style() can be used to set or retrieve the current style.  Called with no arguments,
       it returns the current style, which will be one of "ace" or "java."  Called with an
       argument, it will set the style to one or the other.

   timestamps() method
         $timestamps_on = $db->timestamps();

       Whenever a data object is updated, AceDB records the time and date of the update, and the
       user ID it was running under.  Ordinarily, the retrieval of timestamp information is
       suppressed to conserve memory and bandwidth.  To turn on timestamps, call the timestamps()
       method with a true value.  You can retrieve the current value of the setting by calling
       the method with no arguments.

       Note that activating timestamps disables some of the speed optimizations in AcePerl.  Thus
       they should only be activated if you really need the information.

       Sets or queries the auto_save variable.  If true, the "save" command will be issued
       automatically before the connection to the database is severed.  The default is true.


          $flag = $db->auto_save;

   error() method

       This returns the last error message.  Like UNIX errno, this variable is not reset between
       calls, so its contents are only valid after a method call has returned a result value
       indicating a failure.

       For your convenience, you can call error() in any of several ways:

           print Ace->error();
           print $db->error();  # $db is an Ace database handle
           print $obj->error(); # $object is an Ace::Object

       There's also a global named $Ace::Error that you are free to use.

   datetime() and date()
         $datetime = Ace->datetime($time);
         $today    = Ace->datetime();
         $date     = Ace->date($time);
         $today    = Ace->date([$time]);

       These convenience functions convert the UNIX timestamp given by $time (seconds since the
       epoch) into a datetime string in the format that ACEDB requires.  date() will truncate the
       time portion.

       If not provided, $time defaults to localtime().


         $debug_level = Ace->debug([$new_level])

       This class method gets or sets the debug level.  Higher integers increase verbosity.  0 or
       undef turns off debug messages.

        $db = Ace->name2db($name [,$database])

       This class method associates a database URL with an Ace database object. This is used
       internally by the Ace::Object class in order to discover what database they "belong" to.

       Get or set the Cache::SizeAwareFileCache object, if one has been created.

         $obj = $db->memory_cache_fetch($class,$name)

       Given an object class and name return a copy of the object from the in-memory cache.  The
       object will only be cached if a copy of the object already exists in memory space.  This
       is ordinarily called internally.

       Store an object into the memory cache.  This is ordinarily called internally.

       Delete an object from the memory cache. This is ordinarily called internally.

       Completely clears the memory cache.

         $obj = $db->file_cache_fetch($class,$name)

       Given an object class and name return a copy of the object from the file cache.  This is
       ordinarily called internally.

       Store an object into the file cache.  This is ordinarily called internally.

       Delete an object from the file cache.  This is ordinarily called internally.


       Internally makes C-language calls to libace to send query strings to the server and
       to retrieve the results.  The class that exports the low-level calls is named Ace::AceDB.

       The following methods are available in Ace::AceDB:

           Connect to the host $host at port $port. Queries will time out after $query_timeout
           seconds.  If timeout is not specified, it defaults to 120 (two minutes).

           If successful, this call returns an Ace::AceDB connection object.  Otherwise, it
           returns undef.  Example:

             $acedb = Ace::AceDB->new('localhost',200005,5)
                      || die "Couldn't connect";

           The Ace::AceDB object can also be accessed from the high-level Ace interface by
           calling the ACE::db() method:

             $db = Ace->new(-host=>'localhost',-port=>200005);
             $acedb = $db->db();

           Send the query string $request to the server and return a true value if successful.
           You must then call read() repeatedly in order to fetch the query result.

           Read the result from the last query sent to the server and return it as a string.  ACE
           may return the result in pieces, breaking between whole objects.  You may need to read
           repeatedly in order to fetch the entire result.  Canonical example:

             $acedb->query("find Sequence D*");
             die "Got an error ",$acedb->error() if $acedb->status == STATUS_ERROR;
             while ($acedb->status == STATUS_PENDING) {
                $result .= $acedb->read;

           Return the status code from the last operation.  Status codes are exported by default
           when you use  The status codes you may see are:

             STATUS_WAITING    The server is waiting for a query.
             STATUS_PENDING    A query has been sent and Ace is waiting for
                               you to read() the result.
             STATUS_ERROR      A communications or syntax error has occurred

           Returns a more detailed error code supplied by the Ace server.  Check this value when
           STATUS_ERROR has been returned.  These constants are also exported by default.
           Possible values:


           Please see the ace client library documentation for a full description of these error
           codes and their significance.

           This method may return true after you have performed one or more read() operations,
           and indicates that there is more data to read.  You will not ordinarily have to call
           this method.


       1. The ACE model should be consulted prior to updating the database.

       2. There is no automatic recovery from connection errors.

       3. Debugging has only one level of verbosity, despite the best of intentions.

       4. Performance is poor when fetching big objects, because of many object references that
       must be created.  This could be improved.

       5. When called in an array context at("tag[0]") should return the current tag's entire
       column.  It returns the current subtree instead.

       6. There is no way to add comments to objects.

       7. When timestamps are active, many optimizations are disabled.

       8. Item number eight is still missing.


       Ace::Object, Ace::Local, Ace::Model, Ace::Sequence,Ace::Sequence::Multi.


       Lincoln Stein <> with extensive help from Jean Thierry-Mieg

       Copyright (c) 1997-1998 Cold Spring Harbor Laboratory

       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.


       Hey! The above document had some coding errors, which are explained below:

       Around line 1194:
           '=item' outside of any '=over'

       Around line 1224:
           You forgot a '=back' before '=head2'