Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::GFF::Adaptor::dbi::mysqlcmap -- Database adaptor for an integraded CMap/GBrowse
       mysql schema

SYNOPSIS

       See Bio::DB::GFF

DESCRIPTION

       This adaptor implements a specific mysql database schema that is compatible with
       Bio::DB::GFF.  It inherits from Bio::DB::GFF::Adaptor::dbi, which itself inherits from
       Bio::DB::GFF.

       The schema uses several tables:

       fdata
           This is the feature data table.  Its columns are: -
               fid              feature ID (integer)
               fref           reference sequence name (string)
               fstart         start position relative to reference (integer)
               fstop          stop postion relative to reference (integer)
               ftypeid        feature type ID (integer)
               fscore         feature score (float); may be null
               fstrand        strand; one of "+" or "-"; may be null
               fphase         phase; one of 0, 1 or 2; may be null
               feature_id     group ID used to be 'gid' (integer)
               ftarget_start  for similarity features, the target start position (integer)
               ftarget_stop   for similarity features, the target stop position (integer)

           Note that it would be desirable to normalize the reference sequence name, since there
           are usually many features that share the same reference feature.  However, in the
           current schema, query performance suffers dramatically when this additional join is
           added.

       cmap_feature (replaces fgroup)
           This is the group table. There is one row for each group.  This is the shared table
           between CMap and GBrowse.  There are many CMap related columns but only a few that
           GBrowse uses.

           GBrowse Columns:

               feature_id     the group ID (integer)
               gclass         the class of the group (string)
               feature_name   the name of the group (string)

           The group table serves multiple purposes.  As you might expect, it is used to cluster
           features that logically belong together, such as the multiple exons of the same
           transcript.  It is also used to assign a name and class to a singleton feature.
           Finally, the group table is used to identify the target of a similarity hit.  This is
           consistent with the way in which the group field is used in the GFF version 2 format.

           The cmap_feature.feature_id field joins with the fdata.feature_id field.

           Examples:

             mysql> select * from cmap_feature where feature_name='sjj_2L52.1';
             +--------------+-------------+--------------+
             | feature_id   | gclass      | feature_name |
             +--------------+-------------+--------------+
             | 69736        | PCR_product | sjj_2L52.1   |
             +--------------+-------------+--------------+
             1 row in set (0.70 sec)

             mysql> select fref,fstart,fstop from fdata,cmap_feature
                       where gclass='PCR_product' and feature_name = 'sjj_2L52.1'
                             and fdata.feature_id=cmap_feature.feature_id;
             +---------------+--------+-------+
             | fref          | fstart | fstop |
             +---------------+--------+-------+
             | CHROMOSOME_II |   1586 |  2355 |
             +---------------+--------+-------+
             1 row in set (0.03 sec)

       ftype
           This table contains the feature types, one per row.  Columns are:

               ftypeid      the feature type ID (integer)
               fmethod      the feature type method name (string)
               fsource      the feature type source name (string)

           The ftype.ftypeid field joins with the fdata.ftypeid field.  Example:

             mysql> select fref,fstart,fstop,fmethod,fsource from fdata,cmap_feature,ftype
                    where gclass='PCR_product'
                          and feature_name = 'sjj_2L52.1'
                          and fdata.feature_id=cmap_feature.feature_id
                          and fdata.ftypeid=ftype.ftypeid;
             +---------------+--------+-------+-------------+-----------+
             | fref          | fstart | fstop | fmethod     | fsource   |
             +---------------+--------+-------+-------------+-----------+
             | CHROMOSOME_II |   1586 |  2355 | PCR_product | GenePairs |
             +---------------+--------+-------+-------------+-----------+
             1 row in set (0.08 sec)

       fdna
           This table holds the raw DNA of the reference sequences.  It has three columns:

               fref          reference sequence name (string)
               foffset       offset of this sequence
               fdna          the DNA sequence (longblob)

           To overcome problems loading large blobs, DNA is automatically fragmented into
           multiple segments when loading, and the position of each segment is stored in foffset.
           The fragment size is controlled by the -clump_size argument during initialization.

       fattribute_to_feature
           This table holds "attributes", which are tag/value pairs stuffed into the GFF line.
           The first tag/value pair is treated as the group, and anything else is treated as an
           attribute (weird, huh?).

            CHR_I assembly_tag Finished     2032 2036 . + . Note "Right: cTel33B"
            CHR_I assembly_tag Polymorphism 668  668  . + . Note "A->C in cTel33B"

           The columns of this table are:

               fid                 feature ID (integer)
               fattribute_id       ID of the attribute (integer)
               fattribute_value    text of the attribute (text)

           The fdata.fid column joins with fattribute_to_feature.fid.

       fattribute
           This table holds the normalized names of the attributes.  Fields are:

             fattribute_id      ID of the attribute (integer)
             fattribute_name    Name of the attribute (varchar)

   Data Loading Methods
       In addition to implementing the abstract SQL-generating methods of
       Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of
       Bio::DB::GFF.

   new
        Title   : new
        Usage   : $db = Bio::DB::GFF->new(@args)
        Function: create a new adaptor
        Returns : a Bio::DB::GFF object
        Args    : see below
        Status  : Public

       The new constructor is identical to the "dbi" adaptor's new() method, except that the
       prefix "dbi:mysql" is added to the database DSN identifier automatically if it is not
       there already.

         Argument       Description
         --------       -----------

         -dsn           the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040"

         -user          username for authentication

         -pass          the password for authentication

   get_dna
        Title   : get_dna
        Usage   : $string = $db->get_dna($name,$start,$stop,$class)
        Function: get DNA string
        Returns : a string
        Args    : name, class, start and stop of desired segment
        Status  : Public

       This method performs the low-level fetch of a DNA substring given its name, class and the
       desired range.  This should probably be moved to the parent class.

   schema
        Title   : schema
        Usage   : $schema = $db->schema
        Function: return the CREATE script for the schema
        Returns : a list of CREATE statemetns
        Args    : none
        Status  : protected

       This method returns a list containing the various CREATE statements needed to initialize
       the database tables.

   make_classes_query
        Title   : make_classes_query
        Usage   : ($query,@args) = $db->make_classes_query
        Function: return query fragment for generating list of reference classes
        Returns : a query and args
        Args    : none
        Status  : public

   setup_load
        Title   : setup_load
        Usage   : $db->setup_load
        Function: called before load_gff_line()
        Returns : void
        Args    : none
        Status  : protected

       This method performs schema-specific initialization prior to loading a set of GFF records.
       It prepares a set of DBI statement handlers to be used in loading the data.

   load_gff_line
        Title   : load_gff_line
        Usage   : $db->load_gff_line($fields)
        Function: called to load one parsed line of GFF
        Returns : true if successfully inserted
        Args    : hashref containing GFF fields
        Status  : protected

       This method is called once per line of the GFF and passed a series of parsed data items
       that are stored into the hashref $fields.  The keys are:

        ref          reference sequence
        source       annotation source
        method       annotation method
        start        annotation start
        stop         annotation stop
        score        annotation score (may be undef)
        strand       annotation strand (may be undef)
        phase        annotation phase (may be undef)
        group_class  class of annotation's group (may be undef)
        group_name   ID of annotation's group (may be undef)
        target_start start of target of a similarity hit
        target_stop  stop of target of a similarity hit
        attributes   array reference of attributes, each of which is a [tag=>value] array ref

   get_feature_id
        Title   : get_feature_id
        Usage   : $integer = $db->get_feature_id($ref,$start,$stop,$typeid,$groupid)
        Function: get the ID of a feature
        Returns : an integer ID or undef
        Args    : none
        Status  : private

       This internal method is called by load_gff_line to look up the integer ID of an existing
       feature.  It is ony needed when replacing a feature with new information.

   get_table_id
        Title   : get_table_id
        Usage   : $integer = $db->get_table_id($table,@ids)
        Function: get the ID of a group or type
        Returns : an integer ID or undef
        Args    : none
        Status  : private

       This internal method is called by load_gff_line to look up the integer ID of an existing
       feature type or group.  The arguments are the name of the table, and two string
       identifiers.  For feature types, the identifiers are the method and source.  For groups,
       the identifiers are group name and class.

       This method requires that a statement handler named lookup_$table, have been created
       previously by setup_load().  It is here to overcome deficiencies in mysql's INSERT syntax.

   make_features_by_name_where_part
        Title   : make_features_by_name_where_part
        Usage   : $db->make_features_by_name_where_part
        Function: create the SQL fragment needed to select a feature by its group name & class
        Returns : a SQL fragment and bind arguments
        Args    : see below
        Status  : Protected

   make_features_join_part
        Title   : make_features_join_part
        Usage   : $string = $db->make_features_join_part()
        Function: make join part of the features query
        Returns : a string
        Args    : none
        Status  : protected

       This method creates the part of the features query that immediately follows the WHERE
       keyword.

   search_notes
        Title   : search_notes
        Usage   : @search_results = $db->search_notes("full text search string",$limit)
        Function: Search the notes for a text string, using mysql full-text search
        Returns : array of results
        Args    : full text search string, and an optional row limit
        Status  : public

       This is a mysql-specific method.  Given a search string, it performs a full-text search of
       the notes table and returns an array of results.  Each row of the returned array is a
       arrayref containing the following fields:

         column 1     A Bio::DB::GFF::Featname object, suitable for passing to segment()
         column 2     The text of the note
         column 3     A relevance score.

   make_features_order_by_part
        Title   : make_features_order_by_part
        Usage   : ($query,@args) = $db->make_features_order_by_part()
        Function: make the ORDER BY part of the features() query
        Returns : a SQL fragment and bind arguments, if any
        Args    : none
        Status  : protected

       This method creates the part of the features query that immediately follows the ORDER BY
       part of the query issued by features() and related methods.

   create_cmap_viewer_link
        Title   : create_cmap_viewer_link
        Usage   : $link_str = $db->create_cmap_viewer_link(data_source=>$ds,group_id=>$gid)
        Function:
        Returns :
        Args    :
        Status  :

BUGS

       none ;-)

SEE ALSO

       Bio::DB::GFF, bioperl

AUTHOR

       Ben Faga <faga@cshl.org>.

       Modified from mysql.pm by:

       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2002 Cold Spring Harbor Laboratory.

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.