NAME

SmartDesc - Index smart.desc file


SYNOPSIS

  use Index::SmartDesc;


DESCRIPTION

  This package is used to index smart.desc file (not public).
  It indexes the file by the accession number (SM00002).
  #SM00004           NL                          NL.HMM  Domain found in Notch and Lin-12
  #SM00005        DEATH                       DEATH.HMM  DEATH domain, found in proteins involved in cell death (apoptosis).
  #SM00006     A4_EXTRA                    A4_EXTRA.HMM  amyloid A4
  #SM00008        HormR                       HormR.HMM  Domain present in hormone receptors
  #SM00013        LRRNT                       LRRNT.HMM  Leucine rich repeat N-terminal domain
  #SM00014      acidPPc                     acidPPc.HMM  Acid phosphatase homologues
  #SM00015           IQ                          IQ.HMM  Short calmodulin-binding motif containing conserved Ile and Gln residues.
  #SM00017        OSTEO                       OSTEO.HMM  Osteopontin
  #SM00018           PD                          PD.HMM  P or trefoil or TFF domain
  #SM00019         SF_P                        SF_P.HMM  Pulmonary surfactant proteins
  #SM00020     Tryp_SPc                    Tryp_SPc.HMM  Trypsin-like serine protease
  # examples here
  use Index::SmartDesc;
  my($res, $msg, $index);
  ($res, $index) = new Index::SmartDesc($file); #Smart file to index
  die $index unless $res;
  ($res, $msg) = $index->setRecDel('dumper', '\n');
  die($msg) unless($res);
  ($res, $r_inx) = $index->buildIndex(['ac', 'name']); #list of entries you want to index. $regexp in this module for allowing rules.
  die($r_inx) unless($res);                            #if no argument given, will build the index with all the rules describe in $regexp.
  #or you can build the index on your own key-value pairs based on regular expression. Only the first match is taken into account.
  #so if you want to index multiple things based on the same line, you need to create another key-value pair.
  ($res, $r_inx) = $index->builIndex({ 'id' => '>(\S+)', 'name' => '^\s+\w+\s+(\S+)' });
  die $r_inx unless $res;
  ($res, $mess) = $index->indexOut($r_inx);               #need a reference to hash table.
  die $mess unless $res;
  my $id = 'SM00135';
  my ($res, $pos) = $index->getIndex($id); #return the position in the file for this $id.
  die $pos unless $res;
  #getEntry returns a reference to an array in case of multiple entries found.
  my ($res, $entry) = $index->getEntry($id); #return the complete entry.
  die $entry unless $res;
  $entry = $entry->[0] if($entry);
  #Either (parsing once the whole entry)
  my($res, $msg) = $index->parseFields(\$entry);
  die $msg unless $res;
  my ($res, $name) = $index->getField('name'); #return the name of this entry.
  $name = $name->[0] if $name;
  my ($res, $name) = $index->getField(['ac', 'name', 'desc']); #return the ac, name and description of this entry.
  if($name){
      my $nm = $name->[0];
      my $ac = $name->[1];
      my $de = $name->[2];
  }
  .... # see below for fields you can retrieve.
  my ($res, $name) = $index->get_name(); #return the name of this smart entry.
  $name = $name->[0] if $name;
  #or simplier
  my ($res, $name) = $index->getField('name', \$entry); #return the name of this smart entry by parsing it on the fly
  $name = $name->[0] if $name;


VERSIONS

$Id: SmartDesc.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 Description:  Create a new object Index::SmartDesc.
 Arguments:    $file a file to index
               $tool Do you want to use Dispatcher::Tool to use index.conf values? (optional)
 Returns:      1, $self on success
               0, msg on failure

_init

       Description: Initialize record delimiter, file and parse configuration file from index configuration file.
       Argument:    
       Returns:     1, '' on success
                    0, msg on error