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

NAME

       Bio::PullParserI - A base module for fast 'pull' parsing

SYNOPSIS

           # do not use this class, it is intended for parser module
           # writers only

DESCRIPTION

       If you are writing a module to parse some new format, you may wish to use a 'pull'
       approach whereby you only do work (reading file data, parsing it, turning the parsed data
       in an object) when absolutely necessary.

       PullParserI provides a system for doing exactly that. As a PullParser you need a chunk. A
       chunk is just a Bio::Root::IO that contains all the raw data you would want to parse. You
       can use the chunk() method to create a chunk from a filename, existing filehandle or even
       a string. If you make a chunk from a large file, but actually only want your chunk to be
       some portion of the whole file, supply start and end amounts in bytes to chunk() at the
       same time.  The methods _chunk_seek() and _chunk_tell() provide seeks and tells that are
       relative to the start and end of your chunk, not the whole file.

       The other thing you will need to decide when making a chunk is how to handle piped input.
       A PullParser typically needs seekable data to parse, so if your data is piped in and
       unseekable, you must decide between creating a temp file or reading the input into memory,
       which will be done before the chunk becomes usable and you can begin any parsing.
       Alternatively you can choose to force a sequential read, in which case you can make use of
       _dependencies() to define the linear order of methods that would result in the file being
       read sequentially. The return value of _sequential() is also useful here, if you would
       need to cache some data or otherwise behave differently during a sequential read.

       The main method in the system is get_field(). This method relies on the existance of a
       private hash reference accessible to it with the method _fields(). That hash ref should
       have as keys all the sorts of data you will want to parse (eg. 'score'), and prior to
       parsing the values would be undefined. A user of your module can then call either
       $module->get_field('score') or $module->score and get_field will either return the answer
       from $self->_fields->{score} if it is defined, or call a method _discover_score() first if
       not. So for the system to work you need to define a _discover_*() method for every field
       in the fields hash, and ensure that the method stores an answer in the fields hash.

       How you implement your _discover_* methods is up to you, though you should never call a
       _discover_* method directly yourself; always use get_field(), since get_field() will deal
       with calling dependent methods for you if a forced sequenctial read is in progress due to
       piped input. You will almost certainly want to make use of the various chunk-related
       methods of this class (that are denoted private by the leading '_'; this means you can use
       them as the author of a parser class, but users of your parser should not).

       Primary amongst them is _*_chunk_by_end() to which you provide text that represents the
       end of your desired chunk and it does a readline with your argument as $/. The chunk knows
       about its line-endings, so if you want your end definition to include a new line, just
       always use "\n" and PullParserI will do any necessary conversion for you.

       If your input data is hierarchical (eg. report->many results->many hits->many hsps), and
       you want an object at the leaf of the hierarchy to have access to information that is
       shared amongst all of them (is parsed in the root), you don't have to copy the data to
       each leaf object; simply by defining parent(), when you call get_field() and the requested
       field isn't in your leaf's fields hash, the leaf's parent will be asked for the field
       instead, and so on till root.

       See Bio::SearchIO::hmmer_pull for an example of implementing a parser using PullParserI.

FEEDBACK

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

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

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

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

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

CONTRIBUTORS

       Inspired by a posting by Aaron J. Mackey

APPENDIX

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

   _fields
        Title   : _fields
        Usage   : $obj->_fields( { field1 => undef } );
                  my $fields_ref = $obj->_fields;
        Function: Get/set the hash reference containing all the fields for this parser
        Returns : hash ref
        Args    : none to get, OR hash ref to set

   has_field
        Title   : has_field
        Usage   : if ($obj->has_field('field_name') {...}
        Function: Ask if a particular object has a given field (doesn't ask ancestors)
        Returns : boolean
        Args    : string (the field name to test)

   get_field
        Title   : get_field
        Usage   : my $field_value = $obj->get_field('field_name');
        Function: Get the value of a given field. If this $obj doesn't have the field,
                  it's parent() will be asked, and so on until there are no more
                  parents.
        Returns : scalar, warns if a value for the field couldn't be found and returns
                  undef.
        Args    : string (the field to get)

   parent
        Title   : parent
        Usage   : $obj->parent($parent_obj);
                  my $parent_obj = $obj->parent;
        Function: Get/set the parent object of this one.
        Returns : Bio::PullParserI
        Args    : none to get, OR Bio::PullParserI to set

   chunk
        Title   : chunk
        Usage   : $obj->chunk($filename);
                  my $chunk = $obj->chunk;
        Function: Get/set the chunk of this parser.
        Returns : Bio:Root::IO
        Args    : none to get, OR
                  First argument of a GLOB reference, filename string, string data to
                  treat as the chunk, or Bio::Root::IO.
                  Optionally, also provide:
                  -start => int : the byte position within the thing described by the
                                  first argument to consider as the start of this
                                  chunk (default 0)
                  -end   => int : the byte position to consider as the end (default
                                  true end)
                  -piped_behaviour => 'memory'|'temp_file'|'sequential_read'

                  The last option comes into effect when the first argument is
                  something that cannot be seeked (eg. piped input filehandle).
                   'memory'          means read all the piped input into a string
                                     first, then set the chunk to that string.
                   'temp_file'       means read all the piped input and output it to
                                     a temp file, then set the chunk to that temp file.
                   'sequential_read' means that the piped input should be read
                                     sequentially and your parsing code must cope with
                                     not being able to seek.
                  'memory' is the fastest but uses the most memory. 'temp_file' and
                  'sequential_read' can be slow, with 'temp_file' being the most memory
                  efficient but requiring disc space. The default is 'sequential_read'.
                  Note that in versions of perl earlier than 5.8 only temp_file works
                  and will be used regardless of what value is supplied here.

   _sequential
        Title   : _sequential
        Usage   : if ($obj->_sequential) {...}
        Function: Ask if we have to do operations such that the input is read
                  sequentially.
        Returns : boolean
        Args    : none to get, OR boolean to set (typically, you should never set this
                  yourself)

   _dependencies
        Title   : _dependencies
        Usage   : $obj->_dependencies( { field1 => field2 } );
                  my $dependancy = $obj->_dependencies('field_name');
        Function: Set the fields that are dependent on each other, or get the field
                  than another is dependent upon.
        Returns : string (a field name)
        Args    : string (a field name) to get, OR hash ref to initially set, with
                  field names as keys and values, key field being dependent upon value
                  field.

   _chunk_true_start
        Title   : _chunk_true_start
        Usage   : my $true_start = $obj->_chunk_true_start;
        Function: Get/set the true start position of the chunk within the filehandle
                  it is part of.
        Returns : int
        Args    : none to get, OR int to set (typically, you won't set this yourself)

   _chunk_true_end
        Title   : _chunk_true_end
        Usage   : my $true_end = $obj->_chunk_true_end;
        Function: Get/set for the true end position of the chunk within the filehandle
                  it is part of.
        Returns : int
        Args    : none to get, OR int to set (typically, you won't set this yourself)

   _line_ending
        Title   : _line_ending
        Usage   : my $line_ending = $obj->_line_ending;
        Function: Get/set for the line ending for the chunk.
        Returns : string
        Args    : none to get, OR string to set (typically, you won't set this
                  yourself)

   _chunk_seek
        Title   : _chunk_seek
        Usage   : $obj->_chunk_seek($pos);
        Function: seek() the chunk to the provided position in bytes, relative to the
                  defined start of the chunk within its filehandle.

                  In _sequential() mode, this function does nothing.

        Returns : n/a
        Args    : int

   _chunk_tell
        Title   : _chunk_seek
        Usage   : my $pos = $obj->_chunk_tell;
        Function: Get the current tell() position within the chunk, relative to the
                  defined start of the chunk within its filehandle.

                  In _sequential() mode, this function does nothing.

        Returns : int
        Args    : none

   _get_chunk_by_nol
        Title   : _chunk_seek
        Usage   : my $string = $obj->_get_chunk_by_nol;
        Function: Get a chunk of chunk() from the current position onward for the given
                  number of lines.
        Returns : string
        Args    : int (number of lines you want)

   _get_chunk_by_end
        Title   : _get_chunk_by_end
        Usage   : my $string = $obj->_get_chunk_by_end;
        Function: Get a chunk of chunk() from the current position onward till the end
                  of the line, as defined by the supplied argument.
        Returns : string
        Args    : string (line ending - if you want the line ending to include a new
                  line, always use \n)

   _find_chunk_by_end
        Title   : _find_chunk_by_end
        Usage   : my $string = $obj->_find_chunk_by_end;
        Function: Get the start and end of what would be a chunk of chunk() from the
                  current position onward till the end of the line, as defined by the
                  supplied argument.

                  In _sequential() mode, this function does nothing.

        Returns : _chunk_tell values for start and end in 2 element list
        Args    : string (line ending - if you want the line ending to include a new
                  line, always use \n)

   AUTOLOAD
        Title   : AUTOLOAD
        Usage   : n/a
        Function: Assumes that any unknown method called should be treated as
                  get_field($method_name).
        Returns : n/a
        Args    : n/a